RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9313
(356 letters)
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 443 bits (1142), Expect = e-157
Identities = 190/365 (52%), Positives = 240/365 (65%), Gaps = 51/365 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E +NLIVNY+PQTMTQEE++ LF+S+GE+ESCKL+RDK T QSLGYGFVNY R EDAE+
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSR 143
A+ LNGL+LQNK+IKVSYARPSS++IK ANLYVSGLPK MTQ +LE++F P+G IITSR
Sbjct: 61 AVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSR 120
Query: 144 ILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITV 203
IL D + +SKG+GF+RF++ EA+ A++ LNGT P G +EPITV
Sbjct: 121 ILSD---------------NVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITV 165
Query: 204 KFANSPAGRAK-----ALAANLNAQAAAMRHFAAAMRHFGNPLHH-SARFK--------- 248
KFAN+P+ L A N Q + P+HH +ARF+
Sbjct: 166 KFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAV 225
Query: 249 ------------------FAPLTADLLNNSMLPP---KSLHGSGWCIFVYNLAPETEDNV 287
+P D + + G+G+CIFVYNL+P+T++ V
Sbjct: 226 LAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETV 285
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
LWQLFGPFGAVQNVK++RD T +CKG+GFV MTNYDEA AI SLNGY LG+R+LQVSF
Sbjct: 286 LWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF 345
Query: 348 KTHKP 352
KT+K
Sbjct: 346 KTNKA 350
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 179 bits (455), Expect = 2e-53
Identities = 88/195 (45%), Positives = 124/195 (63%), Gaps = 16/195 (8%)
Query: 21 DVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTED 80
D N +NLIVNY+PQ MT EL LF ++G + +C+++RD T S GY FV++ D
Sbjct: 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEAD 161
Query: 81 AERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTII 140
++RAI LNG+ ++NK +KVSYARP E+IK NLYV+ LP+ +T + L+ +F YG I+
Sbjct: 162 SQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIV 221
Query: 141 TSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEP 200
IL DK+ +GTP +G+ FVRFN+ EA+ A+ LN IPEG S+P
Sbjct: 222 QKNILRDKL---------TGTP------RGVAFVRFNKREEAQEAISALNNVIPEGGSQP 266
Query: 201 ITVKFANSPAGRAKA 215
+TV+ A G+AKA
Sbjct: 267 LTVRLAEE-HGKAKA 280
Score = 42.3 bits (99), Expect = 2e-04
Identities = 23/78 (29%), Positives = 42/78 (53%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
SG + V L + D L+ LF G + +++RD +T G+ FV + ++ A
Sbjct: 106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRA 165
Query: 330 IQSLNGYALGDRLLQVSF 347
I++LNG + ++ L+VS+
Sbjct: 166 IKNLNGITVRNKRLKVSY 183
Score = 36.9 bits (85), Expect = 0.014
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL D+ L +FG +G + ++RD T +G FV +EA AI +L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255
Query: 334 N 334
N
Sbjct: 256 N 256
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 162 bits (412), Expect = 2e-50
Identities = 56/78 (71%), Positives = 65/78 (83%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
GWCIFVYNL P+ ++++LWQLF PFGAV NVKV+RD T KCKG+GFV MTNY+EA AI
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60
Query: 331 QSLNGYALGDRLLQVSFK 348
SLNGY LG R+LQVSFK
Sbjct: 61 ASLNGYRLGGRVLQVSFK 78
Score = 64.6 bits (158), Expect = 2e-13
Identities = 29/75 (38%), Positives = 41/75 (54%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+ V +P + L LFS G V + K+IRD TT + GYGFV E+A AI
Sbjct: 3 CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62
Query: 88 LNGLKLQNKSIKVSY 102
LNG +L + ++VS+
Sbjct: 63 LNGYRLGGRVLQVSF 77
Score = 38.5 bits (90), Expect = 3e-04
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V LP + L LF P+G + ++ +R + KG GF
Sbjct: 3 CIFVYNLPPDADESLLWQLFSPFGAVTNVKV---------IRDLTT------NKCKGYGF 47
Query: 174 VRFNQHIEAEHAMQELNGT 192
V + EA A+ LNG
Sbjct: 48 VTMTNYEEAYSAIASLNGY 66
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 152 bits (385), Expect = 2e-46
Identities = 58/77 (75%), Positives = 68/77 (88%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQ+E++ LFSS+GE+ESCKLIRDK T QSLGYGFVNY EDAE+AI
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 87 ELNGLKLQNKSIKVSYA 103
LNGL+LQNK+IKVSYA
Sbjct: 62 TLNGLRLQNKTIKVSYA 78
Score = 51.7 bits (124), Expect = 8e-09
Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 17/95 (17%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQ+++ +LF G I + +++ DK V+G S G
Sbjct: 1 KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDK---------VTG------QSLGY 45
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GFV + +AE A+ LNG + ++ I V +A
Sbjct: 46 GFVNYVDPEDAEKAINTLNGLRLQ--NKTIKVSYA 78
Score = 49.0 bits (117), Expect = 8e-08
Identities = 22/65 (33%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
T+D + LF G +++ K++RD T + G+GFV + ++A AI +LNG L ++
Sbjct: 14 TQDE-IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72
Query: 343 LQVSF 347
++VS+
Sbjct: 73 IKVSY 77
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 148 bits (374), Expect = 9e-45
Identities = 64/83 (77%), Positives = 74/83 (89%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
G+GWCIFVYNL+P+++++VLWQLFGPFGAV NVKV+RD T KCKGFGFV MTNYDEA
Sbjct: 1 GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Query: 329 AIQSLNGYALGDRLLQVSFKTHK 351
AI SLNGY LGDR+LQVSFKT+K
Sbjct: 61 AIASLNGYRLGDRVLQVSFKTNK 83
Score = 46.6 bits (110), Expect = 6e-07
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ N P + + L LF G V + K+IRD T + G+GFV ++A AI L
Sbjct: 7 FVYNLSPDS-DESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 89 NGLKLQNKSIKVSY 102
NG +L ++ ++VS+
Sbjct: 66 NGYRLGDRVLQVSF 79
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 147 bits (372), Expect = 2e-44
Identities = 63/83 (75%), Positives = 73/83 (87%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
G+GWCIFVYNLAP+ ++++LWQ+FGPFGAV NVKV+RD T KCKGFGFV MTNYDEA
Sbjct: 1 GTGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Query: 329 AIQSLNGYALGDRLLQVSFKTHK 351
AI SLNGY LGDR+LQVSFKT+K
Sbjct: 61 AIASLNGYRLGDRVLQVSFKTNK 83
Score = 45.9 bits (108), Expect = 1e-06
Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
L +F G V + K+IRD T + G+GFV ++A AI LNG +L ++ ++VS+
Sbjct: 20 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79
Score = 27.8 bits (61), Expect = 2.3
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V L + L +F P+G + ++ +R F + KG GFV
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKV---------IRDFNTNK------CKGFGFV 50
Query: 175 RFNQHIEAEHAMQELNG 191
+ EA A+ LNG
Sbjct: 51 TMTNYDEAAMAIASLNG 67
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 142 bits (359), Expect = 1e-42
Identities = 64/81 (79%), Positives = 70/81 (86%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
GWCIFVYNL+PE +++VLWQLFGPFGAV NVKV+RD T KCKGFGFV MTNYDEA AI
Sbjct: 1 GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60
Query: 331 QSLNGYALGDRLLQVSFKTHK 351
SLNGY LGDR+LQVSFKT K
Sbjct: 61 ASLNGYRLGDRVLQVSFKTSK 81
Score = 47.8 bits (113), Expect = 2e-07
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ N P+ + L LF G V + K+IRD TT + G+GFV ++A AI L
Sbjct: 5 FVYNLSPEA-DESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 89 NGLKLQNKSIKVSY 102
NG +L ++ ++VS+
Sbjct: 64 NGYRLGDRVLQVSF 77
Score = 30.1 bits (67), Expect = 0.45
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V L + L LF P+G + ++ +R F + KG GFV
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKV---------IRDFTTNK------CKGFGFV 48
Query: 175 RFNQHIEAEHAMQELNG 191
+ EA A+ LNG
Sbjct: 49 TMTNYDEAAMAIASLNG 65
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes. Since
the Hu proteins share high homology with the Drosophila
embryonic lethal abnormal vision (ELAV) protein, the Hu
family is sometimes referred to as the ELAV family.
Drosophila ELAV is exclusively expressed in neurons and
is required for the correct differentiation and survival
of neurons in flies. The neuronal members of the Hu
family include Hu-antigen B (HuB or ELAV-2 or Hel-N1),
Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D
(HuD or ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 79
Score = 141 bits (358), Expect = 3e-42
Identities = 56/94 (59%), Positives = 68/94 (72%), Gaps = 15/94 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANLYVSGLPK MTQ++LE LF PYG IITSRILCD + +S+G+G
Sbjct: 1 ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCD---------------NVTGLSRGVG 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F+RF++ IEAE A++ LNGTIP GA+EPITVKFA
Sbjct: 46 FIRFDKRIEAERAIKALNGTIPPGATEPITVKFA 79
Score = 68.1 bits (167), Expect = 1e-14
Identities = 31/79 (39%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL V+ +P+TMTQ+EL+ LFS G + + +++ D T S G GF+ + + +AERAI
Sbjct: 1 ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60
Query: 87 ELNGLKLQ--NKSIKVSYA 103
LNG + I V +A
Sbjct: 61 ALNGTIPPGATEPITVKFA 79
Score = 45.4 bits (108), Expect = 1e-06
Identities = 19/63 (30%), Positives = 30/63 (47%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L LF P+G + +++ D T +G GF+ EA AI++L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 334 NGY 336
NG
Sbjct: 63 NGT 65
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 136 bits (343), Expect = 4e-40
Identities = 57/81 (70%), Positives = 67/81 (82%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
GWCIF+YNL + ++ +LWQ+FGPFGAV NVKV+RD T KCKGFGFV MTNY+EA AI
Sbjct: 1 GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60
Query: 331 QSLNGYALGDRLLQVSFKTHK 351
SLNGY LGD++LQVSFKT K
Sbjct: 61 ASLNGYRLGDKILQVSFKTSK 81
Score = 47.8 bits (113), Expect = 2e-07
Identities = 24/60 (40%), Positives = 35/60 (58%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
L +F G V + K+IRD T + G+GFV E+A AI LNG +L +K ++VS+
Sbjct: 18 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSF 77
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 127 bits (319), Expect = 1e-36
Identities = 58/82 (70%), Positives = 69/82 (84%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ +NLIVNY+PQ MTQEEL+ LF S+GE+ESCKL+RDK T QSLGYGFVNY +DAE+
Sbjct: 2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
AI LNGL+LQ K+IKVSYARP
Sbjct: 62 AINTLNGLRLQTKTIKVSYARP 83
Score = 43.6 bits (102), Expect = 7e-06
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 275 FVYNLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ N P+ L LFG G +++ K+VRD T + G+GFV + +A AI +L
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66
Query: 334 NGYALGDRLLQVSF 347
NG L + ++VS+
Sbjct: 67 NGLRLQTKTIKVSY 80
Score = 43.6 bits (102), Expect = 7e-06
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQE+L++LF G I + +++ DK+ + S G
Sbjct: 4 KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQ---------------SLGY 48
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 49 GFVNYIDPKDAEKAINTLNG 68
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 126 bits (317), Expect = 2e-36
Identities = 59/81 (72%), Positives = 69/81 (85%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQEE + LF S+GE+ESCKL+RDK T QSLGYGFVNY +DAE+AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 87 ELNGLKLQNKSIKVSYARPSS 107
LNGL+LQ K+IKVSYARPSS
Sbjct: 63 TLNGLRLQTKTIKVSYARPSS 83
Score = 42.4 bits (99), Expect = 2e-05
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 291 LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
LFG G +++ K+VRD T + G+GFV + +A AI +LNG L + ++VS+
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78
Score = 41.6 bits (97), Expect = 3e-05
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQE+ +LF G I + +++ DK+ + S G
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQ---------------SLGY 46
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 47 GFVNYIDPKDAEKAINTLNG 66
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 124 bits (313), Expect = 1e-35
Identities = 47/77 (61%), Positives = 63/77 (81%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQEEL+ LF ++G +ESCK++RD+ T QSLGYGFV+Y DA++AI
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 87 ELNGLKLQNKSIKVSYA 103
LNG +++NK +KVSYA
Sbjct: 61 TLNGFEIRNKRLKVSYA 77
Score = 57.0 bits (138), Expect = 1e-10
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 278 NLAPETEDNV-LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY 336
N P+ L LF G +++ K+VRD T + G+GFV + ++A AI +LNG+
Sbjct: 6 NYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65
Query: 337 ALGDRLLQVSF 347
+ ++ L+VS+
Sbjct: 66 EIRNKRLKVSY 76
Score = 50.4 bits (121), Expect = 2e-08
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL V+ LP+ MTQE+L +LF G I + +I+ D+ I S G GF
Sbjct: 2 NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDR---------------ITGQSLGYGF 46
Query: 174 VRFNQHIEAEHAMQELNG 191
V + +A+ A+ LNG
Sbjct: 47 VDYVDENDAQKAINTLNG 64
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 124 bits (312), Expect = 1e-35
Identities = 59/84 (70%), Positives = 69/84 (82%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ +NLIVNY+PQ MTQEE + LF S+GE+ESCKL+RDK T QSLGYGFVNY DA++
Sbjct: 1 DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60
Query: 84 AIIELNGLKLQNKSIKVSYARPSS 107
AI LNGLKLQ K+IKVSYARPSS
Sbjct: 61 AINTLNGLKLQTKTIKVSYARPSS 84
Score = 44.0 bits (103), Expect = 5e-06
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 291 LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
LFG G +++ K+VRD T + G+GFV + ++A AI +LNG L + ++VS+
Sbjct: 23 LFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSY 79
Score = 40.9 bits (95), Expect = 5e-05
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQE+ ++LF G I + +++ DK+ + S G
Sbjct: 3 KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQ---------------SLGY 47
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +A+ A+ LNG
Sbjct: 48 GFVNYVDPNDADKAINTLNG 67
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 124 bits (312), Expect = 2e-35
Identities = 49/81 (60%), Positives = 64/81 (79%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLI+NY+PQT+T EE + LF +VG V++CK++RDK T S G+GFV+Y EDA+RAI
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60
Query: 87 ELNGLKLQNKSIKVSYARPSS 107
LNGL+LQNK IKV+YARP
Sbjct: 61 TLNGLQLQNKRIKVAYARPGG 81
Score = 55.5 bits (134), Expect = 3e-10
Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 278 NLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY 336
N P+T D LF G V+N K+VRD +T GFGFV + ++A AI++LNG
Sbjct: 6 NYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGL 65
Query: 337 ALGDRLLQVSF 347
L ++ ++V++
Sbjct: 66 QLQNKRIKVAY 76
Score = 46.2 bits (110), Expect = 6e-07
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL ++ LP+ +T E+ +LF G + +I VR +G S G GF
Sbjct: 2 NLIINYLPQTLTDEEFRSLFLAVGPVKNCKI---------VRDKRTG------YSYGFGF 46
Query: 174 VRFNQHIEAEHAMQELNG 191
V + +A+ A++ LNG
Sbjct: 47 VDYQSAEDAQRAIRTLNG 64
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 123 bits (309), Expect = 4e-35
Identities = 59/80 (73%), Positives = 68/80 (85%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQ+EL+ LFSS+GEVES KLIRDK SLGYGFVNY +DAERAI
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 87 ELNGLKLQNKSIKVSYARPS 106
LNGL+LQ+K+IKVSYARPS
Sbjct: 62 TLNGLRLQSKTIKVSYARPS 81
Score = 43.9 bits (103), Expect = 4e-06
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R NL V+ LP++MTQ++L +LF G + +++++ DK+A S G
Sbjct: 1 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH---------------SLGY 45
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 46 GFVNYVNAKDAERAINTLNG 65
Score = 40.8 bits (95), Expect = 5e-05
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 275 FVYNLAPE--TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ N P+ T+D L LF G V++ K++RD G+GFV N +A AI +
Sbjct: 4 LIVNYLPQNMTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62
Query: 333 LNGYALGDRLLQVSF 347
LNG L + ++VS+
Sbjct: 63 LNGLRLQSKTIKVSY 77
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 124 bits (314), Expect = 1e-31
Identities = 87/333 (26%), Positives = 135/333 (40%), Gaps = 63/333 (18%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N+ V + +++ + L FS G + SCK+ D+ +S GYGFV++ + E A+ AI
Sbjct: 88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAAI 146
Query: 86 IELNGLKLQNKSIKVSYARPSSE-----AIKRANLYVSGLPKHMTQEDLENLFRPYGTII 140
++NG+ L +K + V E K NLYV L + ++ L LF +G I
Sbjct: 147 QKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEIT 206
Query: 141 TSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEP 200
++ ++ D S R F FV F +H +A A++E+NG A E
Sbjct: 207 SAAVMKDG--SGRSRGF--------------AFVNFEKHEDAAKAVEEMNGKKIGLAKEG 250
Query: 201 --ITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLN 258
+ V A A R L M+ G L
Sbjct: 251 KKLYVGRAQKRAEREAELRRKFEE-----LQQERKMKAQGVNL----------------- 288
Query: 259 NSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+V NL D L +LF G + + KV+ D + +GFGFV
Sbjct: 289 ----------------YVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKG-VSRGFGFV 331
Query: 319 CMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHK 351
C +N +EA A+ ++G LG + L V+ K
Sbjct: 332 CFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK 364
Score = 112 bits (281), Expect = 3e-27
Identities = 79/306 (25%), Positives = 129/306 (42%), Gaps = 72/306 (23%)
Query: 37 TMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
+T+ +L LF G V S ++ RD T +SLGYG+VN+ DAERA+ +N +L K
Sbjct: 11 DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGK 70
Query: 97 SIKV--SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENV 154
I++ S PS N++V L K + + L + F +G I++ ++ D EN
Sbjct: 71 PIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD----ENG 126
Query: 155 RSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
+ S+G GFV F + A+ A+Q++NG +
Sbjct: 127 K------------SRGYGFVHFEKEESAKAAIQKVNGML--------------------- 153
Query: 215 ALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCI 274
LN + + F PL KF L
Sbjct: 154 -----LNDKEVYVGRFIKKHEREAAPLK-----KFTNL---------------------- 181
Query: 275 FVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
+V NL P ++ L +LF FG + + V++D + +GF FV +++A A++ +N
Sbjct: 182 YVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSG-RSRGFAFVNFEKHEDAAKAVEEMN 240
Query: 335 GYALGD 340
G +G
Sbjct: 241 GKKIGL 246
Score = 99.1 bits (247), Expect = 8e-23
Identities = 61/233 (26%), Positives = 105/233 (45%), Gaps = 41/233 (17%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
++ +NL V + ++ +++L+ LF+ GE+ S +++D + +S G+ FVN+ + EDA +
Sbjct: 176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAK 234
Query: 84 AIIELNGLKL----QNKSIKVSYARPSSE--AIKRA----------------NLYVSGLP 121
A+ E+NG K+ + K + V A+ +E A R NLYV L
Sbjct: 235 AVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLD 294
Query: 122 KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIE 181
+T E L LF G I +++++ D+ +S+G GFV F+ E
Sbjct: 295 DTVTDEKLRELFSECGEITSAKVMLDE----------------KGVSRGFGFVCFSNPEE 338
Query: 182 AEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAM 234
A A+ E++G + G +P+ V A R L MR
Sbjct: 339 ANRAVTEMHGRMLGG--KPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGS 389
Score = 48.3 bits (115), Expect = 4e-06
Identities = 28/79 (35%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P G G IFV NL ++ L+ F FG + + KV D + K +G+GFV
Sbjct: 81 PSLRRSGVG-NIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEK 138
Query: 323 YDEAVFAIQSLNGYALGDR 341
+ A AIQ +NG L D+
Sbjct: 139 EESAKAAIQKVNGMLLNDK 157
Score = 47.5 bits (113), Expect = 6e-06
Identities = 24/72 (33%), Positives = 44/72 (61%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +L P+ + L+ LF PFG V +V+V RD T + G+G+V N +A A++++
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 334 NGYALGDRLLQV 345
N LG + +++
Sbjct: 63 NFKRLGGKPIRI 74
Score = 37.5 bits (87), Expect = 0.010
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
A+LYV L +T+ L +LF+P+G +++ R+ D + + S G G
Sbjct: 1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRD---------------SVTRRSLGYG 45
Query: 173 FVRFNQHIEAEHAMQELN 190
+V F +AE A++ +N
Sbjct: 46 YVNFQNPADAERALETMN 63
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 110 bits (275), Expect = 5e-30
Identities = 55/104 (52%), Positives = 73/104 (70%), Gaps = 15/104 (14%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
+I+ ANLYVSGLPK MTQ++LE LF YG IITSRIL D++ +S
Sbjct: 2 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG---------------VS 46
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+G+GF+RF++ IEAE A++ LNG P GA+EPITVKFAN+P+ +
Sbjct: 47 RGVGFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQK 90
Score = 57.9 bits (139), Expect = 7e-11
Identities = 32/86 (37%), Positives = 53/86 (61%), Gaps = 2/86 (2%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL V+ +P+TMTQ+EL+ LFS G + + +++ D+ T S G GF+ + + +AE A
Sbjct: 4 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63
Query: 85 IIELNGLKL--QNKSIKVSYARPSSE 108
I LNG K + I V +A S+
Sbjct: 64 IKGLNGQKPPGATEPITVKFANNPSQ 89
Score = 30.5 bits (68), Expect = 0.30
Identities = 19/62 (30%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 334 NG 335
NG
Sbjct: 68 NG 69
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 107 bits (268), Expect = 3e-29
Identities = 54/94 (57%), Positives = 66/94 (70%), Gaps = 15/94 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANLYVSGLPK MTQ++LE LF YG IITSRIL D++ +S+G+G
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTG---------------VSRGVG 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F+RF++ IEAE A++ LNG PEGASEPITVKFA
Sbjct: 46 FIRFDKRIEAEEAIKGLNGQKPEGASEPITVKFA 79
Score = 62.6 bits (152), Expect = 1e-12
Identities = 29/66 (43%), Positives = 45/66 (68%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL V+ +P+TMTQ+EL+ LFS G + + +++RD+ T S G GF+ + + +AE AI
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 87 ELNGLK 92
LNG K
Sbjct: 61 GLNGQK 66
Score = 38.8 bits (90), Expect = 3e-04
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L QLF +G + +++RD T +G GF+ EA AI+ L
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 334 NG 335
NG
Sbjct: 63 NG 64
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 105 bits (263), Expect = 2e-28
Identities = 54/95 (56%), Positives = 68/95 (71%), Gaps = 15/95 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANLYVSGLPK M+Q+++E LF YG IITSRIL D+ V+G IS+G+G
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQ---------VTG------ISRGVG 46
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
F+RF++ IEAE A++ LNG P GA+EPITVKFAN
Sbjct: 47 FIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFAN 81
Score = 55.8 bits (134), Expect = 3e-10
Identities = 26/67 (38%), Positives = 45/67 (67%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++NL V+ +P+TM+Q+E++ LFS G + + +++ D+ T S G GF+ + + +AE AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
Query: 86 IELNGLK 92
LNG K
Sbjct: 61 KGLNGQK 67
Score = 30.0 bits (67), Expect = 0.40
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L + QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 334 NG 335
NG
Sbjct: 64 NG 65
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 103 bits (258), Expect = 9e-28
Identities = 54/96 (56%), Positives = 68/96 (70%), Gaps = 15/96 (15%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
+ ANLYVSGLPK MTQ++LE LF YG IITSRIL D+ V+G +S+G
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ---------VTG------VSRG 45
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+GF+RF++ IEAE A++ LNG P GA+EPITVKFA
Sbjct: 46 VGFIRFDKRIEAEEAIKGLNGQKPSGAAEPITVKFA 81
Score = 59.0 bits (142), Expect = 2e-11
Identities = 28/68 (41%), Positives = 46/68 (67%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL V+ +P+TMTQ+EL+ LFS G + + +++ D+ T S G GF+ + + +AE A
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60
Query: 85 IIELNGLK 92
I LNG K
Sbjct: 61 IKGLNGQK 68
Score = 31.2 bits (70), Expect = 0.15
Identities = 19/62 (30%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 334 NG 335
NG
Sbjct: 65 NG 66
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 98.2 bits (244), Expect = 1e-25
Identities = 44/97 (45%), Positives = 62/97 (63%), Gaps = 15/97 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANLY+SGLP+ MTQ+D+E++F +G II SR+L D+ +S+G+
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATG---------------LSRGVA 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F+RF++ EAE A+ NG P G+SEPITVKFA +P
Sbjct: 46 FIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANP 82
Score = 51.2 bits (122), Expect = 1e-08
Identities = 22/66 (33%), Positives = 42/66 (63%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P+TMTQ++++ +FS G + + +++ D+ T S G F+ + + +AE AI
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60
Query: 87 ELNGLK 92
NG K
Sbjct: 61 SFNGHK 66
Score = 32.7 bits (74), Expect = 0.049
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 290 QLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY 336
+F FG + N +V+ D T +G F+ EA AI S NG+
Sbjct: 19 DMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGH 65
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 85.3 bits (212), Expect = 4e-21
Identities = 32/73 (43%), Positives = 48/73 (65%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV NL P+T + L +LF FG V++V++VRD +T K KGF FV + ++A A+++
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 333 LNGYALGDRLLQV 345
LNG L R L+V
Sbjct: 61 LNGKELDGRPLKV 73
Score = 83.0 bits (206), Expect = 3e-20
Identities = 34/73 (46%), Positives = 48/73 (65%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V +P T+EEL+ LFS G+VES +L+RDK T +S G+ FV + EDAE+A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 88 LNGLKLQNKSIKV 100
LNG +L + +KV
Sbjct: 61 LNGKELDGRPLKV 73
Score = 68.8 bits (169), Expect = 5e-15
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+V LP T+E+L LF +G + + R++ DK SKG F
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE---------------TGKSKGFAF 45
Query: 174 VRFNQHIEAEHAMQELNGTIPEG 196
V F +AE A++ LNG +G
Sbjct: 46 VEFESEEDAEKALEALNGKELDG 68
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 81.6 bits (202), Expect = 1e-19
Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 16/93 (17%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLY+S LP HM ++DLE + +PYG +I++RIL D S+G+GF
Sbjct: 2 NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ----------------SRGVGF 45
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
R + E + + NG +G EP+ VKFA
Sbjct: 46 ARMESREKCEDIISKFNGKYLKGEGEPLLVKFA 78
Score = 43.5 bits (103), Expect = 6e-06
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P M +++L+ + G+V S +++RD QS G GF E E I
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG-QSRGVGFARMESREKCEDIIS 59
Query: 87 ELNG 90
+ NG
Sbjct: 60 KFNG 63
Score = 34.6 bits (80), Expect = 0.007
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + P+G V + +++RD + + +G GF M + ++ I
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG-QSRGVGFARMESREKCEDIISKF 61
Query: 334 NGYALGDRL--LQVSF 347
NG L L V F
Sbjct: 62 NGKYLKGEGEPLLVKF 77
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 80.7 bits (199), Expect = 3e-19
Identities = 34/94 (36%), Positives = 57/94 (60%), Gaps = 15/94 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
NLYV+ LP+ +T+++L +F YG I+ +L DK +G P +G+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDK---------STGLP------RGVA 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
FVR+++ EA+ A+ LNGTIP G++ P++V++A
Sbjct: 46 FVRYDKREEAQAAISSLNGTIPPGSTMPLSVRYA 79
Score = 56.8 bits (137), Expect = 1e-10
Identities = 26/64 (40%), Positives = 41/64 (64%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL V +P+ +T++EL+ +F + G + C L+RDK+T G FV Y + E+A+ AI
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 87 ELNG 90
LNG
Sbjct: 61 SLNG 64
Score = 40.3 bits (94), Expect = 8e-05
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + ++ L ++F +G + ++RD T +G FV +EA AI SL
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 334 NG 335
NG
Sbjct: 63 NG 64
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 86.9 bits (215), Expect = 9e-19
Identities = 80/374 (21%), Positives = 140/374 (37%), Gaps = 86/374 (22%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ + +L FS VG+V + I+D+ + +S G +V +Y ++ + L G L
Sbjct: 97 LALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFY-DVESVIKALALTGQML 155
Query: 94 QNKSIKVSYARPSSEAIK-RA---------------NLYVSGLPKHMTQEDLENLFRPYG 137
+ I V SS+A K RA LYV L ++T+++L +F P+G
Sbjct: 156 LGRPIIVQ----SSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFG 211
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGA 197
I ++ D PE + SKG GF++F+ EA+ A++ +NG E A
Sbjct: 212 DIEDVQLHRD--------------PETGR-SKGFGFIQFHDAEEAKEALEVMNGF--ELA 254
Query: 198 SEPITVKFANSPAGRAKAL------------AANLNAQAAAMRHFAAA------------ 233
PI V +A A NLN +
Sbjct: 255 GRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPG 314
Query: 234 ----MRHFGNPLHHSARFKFAP------LTADLLNNSMLPPKSLHGSGWCIFVYNL-APE 282
+ P A + NS +P + + + C+ + N+ P
Sbjct: 315 TGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPA 374
Query: 283 TEDNVLWQL---------FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
TE+ + +G V ++ V + G ++ ++ D A+ A Q+L
Sbjct: 375 TEEEPNFDNEILDDVKEECSKYGGVVHI-YVDTKNS---AGKIYLKFSSVDAALAAFQAL 430
Query: 334 NGYALGDRLLQVSF 347
NG G +++ +F
Sbjct: 431 NGRYFGGKMITAAF 444
Score = 61.5 bits (149), Expect = 2e-10
Identities = 53/243 (21%), Positives = 90/243 (37%), Gaps = 63/243 (25%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
++V L + DL F G + + + D+ S SKG+
Sbjct: 89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR---------NSRR------SKGV 133
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFA 231
+V F A+ L G + G PI V+ + + RA A +
Sbjct: 134 AYVEFYDVESVIKALA-LTGQMLLG--RPIIVQSSQAEKNRAAKAATHQ----------- 179
Query: 232 AAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQL 291
P K ++V NL + L Q+
Sbjct: 180 --------PGDIPNFLK-------------------------LYVGNLHFNITEQELRQI 206
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF-KTH 350
F PFG +++V++ RDP+T + KGFGF+ + +EA A++ +NG+ L R ++V + +
Sbjct: 207 FEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS 266
Query: 351 KPL 353
L
Sbjct: 267 TYL 269
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 77.3 bits (191), Expect = 5e-18
Identities = 32/78 (41%), Positives = 49/78 (62%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ L V+ + T++EL+ LFS G VE L++D T +S G+GFV + EDA+ AI
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 87 ELNGLKLQNKSIKVSYAR 104
+LNG +L+ + IKV A+
Sbjct: 62 DLNGKELEGRVIKVEKAK 79
Score = 66.1 bits (162), Expect = 7e-14
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ T + L LF FG V+ V +++DP+T + +GFGFV + ++A AI+ L
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 334 NGYALGDRLLQV 345
NG L R+++V
Sbjct: 64 NGKELEGRVIKV 75
Score = 58.8 bits (143), Expect = 2e-11
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 17/93 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+VSGL T+++LE LF +G + ++ D E S+G GF
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGE---------------SRGFGF 47
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F +A+ A+++LNG EG I V+ A
Sbjct: 48 VTFESVEDADAAIRDLNGKELEG--RVIKVEKA 78
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 77.0 bits (190), Expect = 6e-18
Identities = 32/68 (47%), Positives = 43/68 (63%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV +L+PE + L F PFG + + +VV+D QT K KG+GFV ++A AIQS+
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 334 NGYALGDR 341
NG LG R
Sbjct: 62 NGQWLGGR 69
Score = 61.2 bits (149), Expect = 3e-12
Identities = 24/75 (32%), Positives = 45/75 (60%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
++ V + + E L+ F+ GE+ ++++D T +S GYGFV++ + EDAE AI
Sbjct: 1 HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60
Query: 88 LNGLKLQNKSIKVSY 102
+NG L ++I+ ++
Sbjct: 61 MNGQWLGGRAIRTNW 75
Score = 46.6 bits (111), Expect = 5e-07
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L + E L F P+G I +R++ D M + SKG GF
Sbjct: 1 HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKD-MQT--------------GKSKGYGF 45
Query: 174 VRFNQHIEAEHAMQELNG 191
V F + +AE+A+Q +NG
Sbjct: 46 VSFVKKEDAENAIQSMNG 63
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 81.9 bits (201), Expect = 1e-17
Identities = 52/187 (27%), Positives = 88/187 (47%), Gaps = 26/187 (13%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSL 68
+++S +S +S E+N+ L V +P +T+E+L+ LF G V+ +L+RD+ T +S
Sbjct: 100 RSSESPKSRQKS--KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAI------------------ 110
G+ FV + E AE+AI ELNG +L+ + ++V A+P+S+
Sbjct: 158 GFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRG 217
Query: 111 ------KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
K NLYV LP +E+L +LF+ G I+ + + K G
Sbjct: 218 KALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEAS 277
Query: 165 PQISKGI 171
+
Sbjct: 278 KDALESN 284
Score = 70.0 bits (170), Expect = 2e-13
Identities = 31/82 (37%), Positives = 44/82 (53%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV NL + + L +LF FG V+ V++VRD +T K +GF FV + + A AI+
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176
Query: 333 LNGYALGDRLLQVSFKTHKPLP 354
LNG L R L+V P
Sbjct: 177 LNGKELEGRPLRVQKAQPASQP 198
Score = 66.9 bits (162), Expect = 2e-12
Identities = 53/274 (19%), Positives = 86/274 (31%), Gaps = 49/274 (17%)
Query: 74 NYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLF 133
E + + + S + L+V LP +T+EDL LF
Sbjct: 77 EREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELF 136
Query: 134 RPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTI 193
+ +G + R++ D+ S+G FV F AE A++ELNG
Sbjct: 137 KKFGPVKRVRLVRDR---------------ETGKSRGFAFVEFESEESAEKAIEELNGKE 181
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLT 253
EG P+ V+ A + L+ NL+A A
Sbjct: 182 LEG--RPLRVQKAQPASQPRSELSNNLDASFA---------------------------- 211
Query: 254 ADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCK 313
L ++V NL +T + L LF G + + K
Sbjct: 212 ----KKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPK 267
Query: 314 GFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
FV +A+ + N + R + +F
Sbjct: 268 SRSFVGNEASKDALESNSRGNKKKILGRGPRKAF 301
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 76.1 bits (188), Expect = 2e-17
Identities = 32/78 (41%), Positives = 48/78 (61%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL V +P +T+E+L+ LF GEV S ++I D+ T +S G+GFV E+A AI +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 88 LNGLKLQNKSIKVSYARP 105
LNG +++ V+ ARP
Sbjct: 61 LNGTDFGGRTLTVNEARP 78
Score = 73.4 bits (181), Expect = 1e-16
Identities = 30/74 (40%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + L LFG FG V + +V+ D +T + +GFGFV M +EA AI+ L
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61
Query: 334 NGYALGDRLLQVSF 347
NG G R L V+
Sbjct: 62 NGTDFGGRTLTVNE 75
Score = 62.6 bits (153), Expect = 1e-12
Identities = 32/94 (34%), Positives = 50/94 (53%), Gaps = 17/94 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLYV LP ++T+EDL++LF +G + ++R++ D+ +G S+G GF
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRE---------TGR------SRGFGF 45
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
V EA A+++LNGT G +TV A
Sbjct: 46 VEMETAEEANAAIEKLNGTDFGG--RTLTVNEAR 77
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 75.3 bits (186), Expect = 2e-17
Identities = 26/77 (33%), Positives = 44/77 (57%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T E+L+ FS VG ++ C +++DK + + G+G+V + EDA+RA+ E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 89 NGLKLQNKSIKVSYARP 105
K + I V +A+
Sbjct: 62 KKTKFGGRKIHVEFAKK 78
Score = 64.9 bits (159), Expect = 2e-13
Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL +T D L + F G ++ VV+D + KC+GFG+V ++A A++
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 334 NGYALGDRLLQVSFKTHK 351
G R + V F K
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 46.1 bits (110), Expect = 7e-07
Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 17/92 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T E LE F G I ++ DK G+ + +G G+V
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDK-----------GSKK----CRGFGYV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F +A+ A++E T G I V+FA
Sbjct: 47 TFALEEDAKRALEEKKKTKFGG--RKIHVEFA 76
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 73.8 bits (182), Expect = 7e-17
Identities = 29/70 (41%), Positives = 46/70 (65%), Gaps = 1/70 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+T + L LF FG ++++++VRD +T + KGF FV + ++A A+++L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 334 NGYALGDRLL 343
NG LG R L
Sbjct: 60 NGKELGGREL 69
Score = 71.5 bits (176), Expect = 5e-16
Identities = 28/71 (39%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T+E+L+ LFS G +ES +++RD+T +S G+ FV + EDAE+A+ L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDET-GRSKGFAFVEFEDEEDAEKALEAL 59
Query: 89 NGLKLQNKSIK 99
NG +L + ++
Sbjct: 60 NGKELGGRELR 70
Score = 66.1 bits (162), Expect = 4e-14
Identities = 28/82 (34%), Positives = 39/82 (47%), Gaps = 16/82 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T+EDL++LF +G I + RI+ D+ SKG FV
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR----------------SKGFAFV 44
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +AE A++ LNG G
Sbjct: 45 EFEDEEDAEKALEALNGKELGG 66
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 73.9 bits (182), Expect = 7e-17
Identities = 32/73 (43%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T+E+L+ LFS GE+ES +++RDK +S G+ FV + EDAE+A+ L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEAL 59
Query: 89 NGLKLQNKSIKVS 101
NG +L + +KVS
Sbjct: 60 NGKELDGRKLKVS 72
Score = 72.3 bits (178), Expect = 3e-16
Identities = 31/73 (42%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+T + L +LF FG +++V++VRD K KGF FV + ++A A+++L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 334 NGYALGDRLLQVS 346
NG L R L+VS
Sbjct: 60 NGKELDGRKLKVS 72
Score = 66.2 bits (162), Expect = 5e-14
Identities = 30/90 (33%), Positives = 40/90 (44%), Gaps = 18/90 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T+EDL LF +G I + RI+ DK SKG FV
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK----------------DGKSKGFAFV 44
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVK 204
F +AE A++ LNG +G + V
Sbjct: 45 EFESPEDAEKALEALNGKELDG--RKLKVS 72
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 73.8 bits (182), Expect = 9e-17
Identities = 26/64 (40%), Positives = 43/64 (67%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T+++L+ +F GE+E +L RD T +S GYGF+ + EDA++A+ +LNG +L +
Sbjct: 10 ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRP 69
Query: 98 IKVS 101
IKV
Sbjct: 70 IKVG 73
Score = 63.0 bits (154), Expect = 6e-13
Identities = 25/64 (39%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
TED+ L +F PFG ++ V++ RDP+T + KG+GF+ + ++A A++ LNG+ L R
Sbjct: 11 TEDD-LRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRP 69
Query: 343 LQVS 346
++V
Sbjct: 70 IKVG 73
Score = 48.4 bits (116), Expect = 9e-08
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 17/89 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L ++T++DL +F P+G I ++ D SKG GF+
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGR---------------SKGYGFI 45
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITV 203
+F +A+ A+++LNG E A PI V
Sbjct: 46 QFADAEDAKKALEQLNGF--ELAGRPIKV 72
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 73.1 bits (180), Expect = 1e-16
Identities = 31/73 (42%), Positives = 45/73 (61%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+Y+L E D L+QLF PFG V + KV D T + K FGFV N + A AI+++
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 334 NGYALGDRLLQVS 346
NG+ +G + L+V
Sbjct: 61 NGFQVGGKRLKVQ 73
Score = 70.4 bits (173), Expect = 1e-15
Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + ++P T ++L LF+ G V S K+ DK T QS +GFV+Y E A+ AI +
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 89 NGLKLQNKSIKVS 101
NG ++ K +KV
Sbjct: 61 NGFQVGGKRLKVQ 73
Score = 60.3 bits (147), Expect = 5e-12
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ LP T +DL LF P+G +I++++ DK SK GFV
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDK---------------NTGQSKCFGFV 45
Query: 175 RFNQHIEAEHAMQELNG 191
++ A+ A++ +NG
Sbjct: 46 SYDNPESAQAAIKAMNG 62
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 72.2 bits (178), Expect = 3e-16
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + E+ L + F G V+ V++VRD +T KGFG+V D A++ L
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-L 60
Query: 334 NGYALGDRLLQVS 346
NG L R ++V
Sbjct: 61 NGIKLKGRKIRVK 73
Score = 53.3 bits (129), Expect = 2e-09
Identities = 22/63 (34%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
+EEL+ F G+VE+ +++RD+ T G+G+V ++T+D+ ++LNG+KL+ + I
Sbjct: 12 EEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVL-FKTKDSVALALKLNGIKLKGRKI 70
Query: 99 KVS 101
+V
Sbjct: 71 RVK 73
Score = 30.6 bits (70), Expect = 0.19
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 16/76 (21%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V LP + +E+L F G + RI+ D+ I KG G+V
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKT---------------GIGKGFGYVL 47
Query: 176 FNQHIEAEHAMQELNG 191
F ++ +LNG
Sbjct: 48 FKT-KDSVALALKLNG 62
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 69.6 bits (171), Expect = 3e-15
Identities = 23/65 (35%), Positives = 42/65 (64%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G +E +++ D+ T +S G+GFV + EDA+ A LNG+++ + I
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71
Query: 99 KVSYA 103
+V Y+
Sbjct: 72 RVDYS 76
Score = 64.6 bits (158), Expect = 2e-13
Identities = 24/75 (32%), Positives = 45/75 (60%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G ++ V+VV D +T + +GFGFV + ++A A +
Sbjct: 1 CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60
Query: 333 LNGYALGDRLLQVSF 347
LNG + R ++V +
Sbjct: 61 LNGMEIDGRRIRVDY 75
Score = 34.9 bits (81), Expect = 0.006
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V GL + T+ DL +F YG I +++ D+ S+G GFV
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGR---------------SRGFGFV 46
Query: 175 RFNQHIEAEHAMQELNG 191
F +A+ A + LNG
Sbjct: 47 YFESVEDAKEAKERLNG 63
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 68.7 bits (169), Expect = 5e-15
Identities = 24/72 (33%), Positives = 43/72 (59%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V NL+ + +++ L +LF PFG + V + +D +T + +GF FV ++A AI+ LNG
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Query: 336 YALGDRLLQVSF 347
+ + +L V +
Sbjct: 64 FGYDNLILSVEW 75
Score = 62.9 bits (154), Expect = 8e-13
Identities = 27/74 (36%), Positives = 42/74 (56%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V + + +++L+ LF G + L +DK T QS G+ FV ++ EDAERAI +LNG
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Query: 91 LKLQNKSIKVSYAR 104
N + V +A+
Sbjct: 64 FGYDNLILSVEWAK 77
Score = 43.3 bits (103), Expect = 7e-06
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 15/75 (20%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
V+ L + ++DL LFRP+G I SR+ +++ E S+G FV F
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPI--SRV------------YLAKDKET-GQSRGFAFVTF 48
Query: 177 NQHIEAEHAMQELNG 191
+ +AE A+++LNG
Sbjct: 49 HTREDAERAIEKLNG 63
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 67.2 bits (165), Expect = 2e-14
Identities = 33/91 (36%), Positives = 45/91 (49%), Gaps = 16/91 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LPK T+ED+ LF YG I I+ DK SKG FV
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDK---------------DTGQSKGCAFV 46
Query: 175 RFNQHIEAEHAMQELNGTIP-EGASEPITVK 204
+F+ EA+ A++ L+G + GAS P+ VK
Sbjct: 47 KFSSREEAQKAIEALHGKVTMPGASRPLQVK 77
Score = 65.3 bits (160), Expect = 1e-13
Identities = 26/62 (41%), Positives = 39/62 (62%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P+T T+E+++ LF G +E +IRDK T QS G FV + E+A++AI L
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61
Query: 89 NG 90
+G
Sbjct: 62 HG 63
Score = 49.1 bits (118), Expect = 6e-08
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG-YAL--G 339
TE++V LF +G ++ V ++RD T + KG FV ++ +EA AI++L+G +
Sbjct: 12 TEEDV-RALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGA 70
Query: 340 DRLLQV 345
R LQV
Sbjct: 71 SRPLQV 76
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 66.9 bits (164), Expect = 4e-14
Identities = 28/78 (35%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGA-VQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
G +F+ NL PE ++ +L+ F FG +Q K++RDP T KGF F+ +++ + A
Sbjct: 1 GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60
Query: 330 IQSLNGYALGDRLLQVSF 347
I+++NG L +R + VS+
Sbjct: 61 IEAMNGQYLCNRPITVSY 78
Score = 54.2 bits (131), Expect = 1e-09
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 43 LQHLFSSVGE-VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVS 101
L FS+ G +++ K++RD T S G+ F++Y E ++ AI +NG L N+ I VS
Sbjct: 18 LYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVS 77
Query: 102 YAR 104
YA
Sbjct: 78 YAF 80
Score = 36.5 bits (85), Expect = 0.002
Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 16/94 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANL++ L + ++ L + F +G I+ + + +R +G SKG
Sbjct: 2 ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKI--------MRDPDTGN------SKGFA 47
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F+ ++ ++ A++ +NG PITV +A
Sbjct: 48 FISYDSFEASDAAIEAMNGQYLCN--RPITVSYA 79
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 66.4 bits (163), Expect = 4e-14
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + +D L +LFG +G + + KV++D K KGFGFV N++ A A++ L
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62
Query: 334 NGYALGDRLLQV 345
NG + + L V
Sbjct: 63 NGKEVNGKKLYV 74
Score = 65.3 bits (160), Expect = 1e-13
Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ V + + M E+L+ LF G++ S K+++D +S G+GFVN+ E A++A+ E
Sbjct: 3 NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEE 61
Query: 88 LNGLKLQNKSIKVSYA 103
LNG ++ K + V A
Sbjct: 62 LNGKEVNGKKLYVGRA 77
Score = 52.6 bits (127), Expect = 4e-09
Identities = 28/83 (33%), Positives = 40/83 (48%), Gaps = 16/83 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
N+YV L + M E L+ LF YG I ++++ M + +S KG GF
Sbjct: 3 NVYVKNLGEDMDDEKLKELFGKYGKITSAKV----MKDDEGKS------------KGFGF 46
Query: 174 VRFNQHIEAEHAMQELNGTIPEG 196
V F H A+ A++ELNG G
Sbjct: 47 VNFENHEAAQKAVEELNGKEVNG 69
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammals, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 65.2 bits (160), Expect = 1e-13
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + +T+ L +FS G V S ++ RD T +SLGY +VN+ DAERA+ L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 89 NGLKLQNKSIKV 100
N ++ K I++
Sbjct: 62 NFDVIKGKPIRI 73
Score = 50.2 bits (121), Expect = 3e-08
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 15/76 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L +T+ L +F P G +++ R+ C R ++ S G +V
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRV-C--------RDLITRR------SLGYAYV 46
Query: 175 RFNQHIEAEHAMQELN 190
F +AE A+ LN
Sbjct: 47 NFQNPADAERALDTLN 62
Score = 46.8 bits (112), Expect = 4e-07
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V +L P+ + +L+++F P G V +++V RD T + G+ +V N +A A+ +
Sbjct: 1 SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60
Query: 333 LN 334
LN
Sbjct: 61 LN 62
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 65.0 bits (159), Expect = 1e-13
Identities = 26/75 (34%), Positives = 42/75 (56%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T E+ + L S G VE C L+ ++T +S GYGFV Y A +A +L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 89 NGLKLQNKSIKVSYA 103
+G ++ + ++V +A
Sbjct: 62 DGKQIGGRKLQVDWA 76
Score = 54.2 bits (131), Expect = 9e-10
Identities = 27/77 (35%), Positives = 38/77 (49%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL E D +L PFGAV+ +V T + KG+GFV + A+ A
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60
Query: 333 LNGYALGDRLLQVSFKT 349
L+G +G R LQV +
Sbjct: 61 LDGKQIGGRKLQVDWAD 77
Score = 43.8 bits (104), Expect = 4e-06
Identities = 24/82 (29%), Positives = 30/82 (36%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V LP T E L P+G + R V S +G SKG GFV
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAV--ERCFL-------VYSESTGE------SKGYGFV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
+ A A +L+G G
Sbjct: 47 EYASKASALKAKNQLDGKQIGG 68
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 64.6 bits (158), Expect = 2e-13
Identities = 26/69 (37%), Positives = 39/69 (56%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+N+ + +P T E+L+ L G++ S K I DK T + GYGFV++ E A +AI
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 87 ELNGLKLQN 95
LNG +Q
Sbjct: 61 GLNGRGVQA 69
Score = 63.8 bits (156), Expect = 4e-13
Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
N+Y+ GLP + T EDLE L +P+G II+++ + DK ++ KG GF
Sbjct: 2 NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNK---------------CKGYGF 46
Query: 174 VRFNQHIEAEHAMQELNG 191
V F+ A A++ LNG
Sbjct: 47 VDFDSPEAALKAIEGLNG 64
Score = 53.4 bits (129), Expect = 1e-09
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 279 LAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYAL 338
L P T D L +L PFG + + K + D +T KCKG+GFV + + A+ AI+ LNG
Sbjct: 8 LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRG- 66
Query: 339 GDRLLQVSF 347
+Q F
Sbjct: 67 ----VQAQF 71
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 64.5 bits (157), Expect = 2e-13
Identities = 25/77 (32%), Positives = 42/77 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + ++TQE+L FS V ++ ++ D T +S GYGFV + EDA+ A+ +L
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 89 NGLKLQNKSIKVSYARP 105
KL + +++ A
Sbjct: 62 KNKKLHGRILRLDIAER 78
Score = 55.2 bits (133), Expect = 5e-10
Identities = 22/76 (28%), Positives = 36/76 (47%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA L F +++ VV DP+T + +G+GFV ++A A+ L
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 334 NGYALGDRLLQVSFKT 349
L R+L++
Sbjct: 62 KNKKLHGRILRLDIAE 77
Score = 39.8 bits (93), Expect = 1e-04
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L +TQEDL + F I K A V PE + S+G GFV
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPI--------KHA------VVVTDPETGE-SRGYGFV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A+ +L G
Sbjct: 47 TFAMLEDAQEALAKLKNKKLHG 68
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 63.8 bits (156), Expect = 3e-13
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + L + F PFGA++ V+V +D KG+ FV ++ A AI ++
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56
Query: 334 NGYALGDRLLQVS 346
NG ++ + ++ S
Sbjct: 57 NGTSINGQTVKCS 69
Score = 58.0 bits (141), Expect = 4e-11
Identities = 28/86 (32%), Positives = 39/86 (45%), Gaps = 21/86 (24%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+YV LP +T+E+L+ F P+G I E VR F + KG
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAI------------EEVRVF----KD-----KGYA 39
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGAS 198
FVRF+ H A A+ +NGT G +
Sbjct: 40 FVRFDTHEAAATAIVAVNGTSINGQT 65
Score = 54.5 bits (132), Expect = 7e-10
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P +T+EELQ FS G +E ++ +DK GY FV + E A AI+ +NG +
Sbjct: 8 LPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAVNGTSI 61
Query: 94 QNKSIKVSYAR 104
+++K S+ +
Sbjct: 62 NGQTVKCSWGK 72
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed in
all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. The family also
includes yeast ortholog mRNA 3'-end-processing protein
RNA15 and similar proteins. RNA15 is a core subunit of
cleavage factor IA (CFIA), an essential transcriptional
3'-end processing factor from Saccharomyces cerevisiae.
RNA recognition by CFIA is mediated by an N-terminal
RRM, which is contained in the RNA15 subunit of the
complex. The RRM of RNA15 has a strong preference for
GU-rich RNAs, mediated by a binding pocket that is
entirely conserved in both yeast and vertebrate RNA15
orthologs.
Length = 75
Score = 62.3 bits (152), Expect = 1e-12
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+ + + L ++F G V + ++V D T K KG+GF + + A AI++L
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 334 NGYALGDRLLQVSF 347
NGY R L+V F
Sbjct: 61 NGYEFNGRALRVDF 74
Score = 60.3 bits (147), Expect = 6e-12
Identities = 27/74 (36%), Positives = 42/74 (56%)
Query: 30 IVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
V +P T+E+L +FS VG V S +L+ D+ T + GYGF + E A AI LN
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 90 GLKLQNKSIKVSYA 103
G + ++++V +A
Sbjct: 62 GYEFNGRALRVDFA 75
Score = 32.6 bits (75), Expect = 0.037
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V +P T+E L +F G +++ R++ D+ +G P KG GF
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDR---------DTGKP------KGYGFCE 46
Query: 176 FNQHIEAEHAMQELNG 191
F A A++ LNG
Sbjct: 47 FEDIETAASAIRNLNG 62
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 62.2 bits (152), Expect = 2e-12
Identities = 27/73 (36%), Positives = 46/73 (63%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV +L E D VL + F + + Q KVVRD +T K KG+GFV ++ ++ + A++ +
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68
Query: 334 NGYALGDRLLQVS 346
NG +G+R +++
Sbjct: 69 NGKYVGNRPIKLR 81
Score = 49.1 bits (118), Expect = 7e-08
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T E L FS + K++RDK T +S GYGFV++ D +A+ E+NG + N+ I
Sbjct: 19 TDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPI 78
Query: 99 KVS 101
K+
Sbjct: 79 KLR 81
Score = 36.8 bits (86), Expect = 0.002
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V L +T E L F Y + ++++ DK + SKG GFV
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGK---------------SKGYGFV 53
Query: 175 RFNQHIEAEHAMQELNG 191
F+ + AM+E+NG
Sbjct: 54 SFSDPNDYLKAMKEMNG 70
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 61.6 bits (150), Expect = 3e-12
Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN-- 95
+T+++L+ F+ GE++ +++DK T +S G +V + + A RA+ E+NG L
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
Query: 96 KSIKV 100
K +KV
Sbjct: 74 KPLKV 78
Score = 53.9 bits (130), Expect = 1e-09
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 15/85 (17%)
Query: 122 KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIE 181
K +T++DL F P+G I ++ DK E SKG+ +V+F +
Sbjct: 12 KSVTEDDLREAFAPFGEIQDIWVVKDKQTKE---------------SKGVAYVKFAKASS 56
Query: 182 AEHAMQELNGTIPEGASEPITVKFA 206
A AM+E+NG G ++P+ V A
Sbjct: 57 AARAMEEMNGKCLGGDTKPLKVLIA 81
Score = 48.9 bits (117), Expect = 7e-08
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDR 341
TED+ L + F PFG +Q++ VV+D QT + KG +V A A++ +NG LG
Sbjct: 15 TEDD-LREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 61.2 bits (149), Expect = 3e-12
Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 37 TMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
T+T++ L LFS +G ++SCKLIR+ Y FV YY A A+ +NG + +
Sbjct: 9 TVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTMNGRLILGQ 65
Query: 97 SIKVSYA 103
IKV++A
Sbjct: 66 EIKVNWA 72
Score = 45.0 bits (107), Expect = 2e-06
Identities = 17/72 (23%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +++L +LF G +++ K++R+ + FV ++ A A+Q++
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57
Query: 334 NGYALGDRLLQV 345
NG + + ++V
Sbjct: 58 NGRLILGQEIKV 69
Score = 27.7 bits (62), Expect = 2.1
Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 20/92 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L + +T++ L LF G I + C + + FV
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKS----CKLIREHGNDPY--------------AFV 42
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ H A A+Q +NG + G + I V +A
Sbjct: 43 EYYDHRSAAAALQTMNGRLILG--QEIKVNWA 72
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 61.1 bits (149), Expect = 3e-12
Identities = 32/94 (34%), Positives = 44/94 (46%), Gaps = 18/94 (19%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
NLYV L + E L F P+GTI +++++ D E R SKG G
Sbjct: 2 VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD----EKGR------------SKGFG 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
FV F+ EA A+ E+NG I +P+ V A
Sbjct: 46 FVCFSSPEEATKAVTEMNGRII--GGKPLYVALA 77
Score = 60.7 bits (148), Expect = 5e-12
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +D L + F PFG + + KV+ D + + KGFGFVC ++ +EA A+ +
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTEM 62
Query: 334 NGYALGDRLLQVSF 347
NG +G + L V+
Sbjct: 63 NGRIIGGKPLYVAL 76
Score = 57.6 bits (140), Expect = 6e-11
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
NL V + ++ E L+ FS G + S K++ D+ +S G+GFV + E+A +A+
Sbjct: 1 GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAV 59
Query: 86 IELNGLKLQNKSIKVSYA 103
E+NG + K + V+ A
Sbjct: 60 TEMNGRIIGGKPLYVALA 77
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 61.5 bits (150), Expect = 3e-12
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 270 SGWCIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
S + I++ L E TE ++L +F +G + ++ +VRD +T K KGF F+ + +
Sbjct: 9 SAY-IYIGGLPYELTEGDIL-CVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66
Query: 329 AIQSLNGYALGDRLLQV 345
A+ +LNG L R ++V
Sbjct: 67 AVDNLNGIKLLGRTIRV 83
Score = 47.2 bits (113), Expect = 4e-07
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII---ELNGL 91
P +T+ ++ +FS GE+ L+RDK T +S G+ F+ Y ED I+ LNG+
Sbjct: 18 PYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY---EDQRSTILAVDNLNGI 74
Query: 92 KLQNKSIKVSYAR 104
KL ++I+V + R
Sbjct: 75 KLLGRTIRVDHVR 87
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 61.0 bits (148), Expect = 4e-12
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV +L+PE D L+ F F + + +V+ D ++ + +G+GFV + +A AI +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 334 NGYALGDRLLQVSF 347
NG LG R ++ ++
Sbjct: 62 NGKWLGSRPIRCNW 75
Score = 46.7 bits (111), Expect = 4e-07
Identities = 23/75 (30%), Positives = 41/75 (54%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ V + +T L FS+ +++ D + +S GYGFV++ +DAE AI E
Sbjct: 1 NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60
Query: 88 LNGLKLQNKSIKVSY 102
+NG L ++ I+ ++
Sbjct: 61 MNGKWLGSRPIRCNW 75
Score = 37.9 bits (88), Expect = 6e-04
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
N++V L +T L F + + +R++ D SG S+G GF
Sbjct: 1 NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMK---------SGR------SRGYGF 45
Query: 174 VRFNQHIEAEHAMQELNG 191
V F +AE+A+ E+NG
Sbjct: 46 VSFRSQQDAENAINEMNG 63
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 61.1 bits (149), Expect = 4e-12
Identities = 23/62 (37%), Positives = 40/62 (64%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T E+L+ +FS G+++SC++IRDK T SL Y F+ + ED E A +++ + + ++ I
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75
Query: 99 KV 100
V
Sbjct: 76 HV 77
Score = 42.3 bits (100), Expect = 2e-05
Identities = 20/74 (27%), Positives = 36/74 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L P T D L +F FG +++ +V+RD +T + F+ ++ A +
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65
Query: 334 NGYALGDRLLQVSF 347
+ + DR + V F
Sbjct: 66 DNVLIDDRRIHVDF 79
Score = 30.7 bits (70), Expect = 0.19
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L T EDLE +F +G I + + +R +G S F+
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEV---------IRDKKTGD------SLQYAFI 50
Query: 175 RFNQHIEAEHAMQELNGTI 193
F + E A +++ +
Sbjct: 51 EFETKEDCEEAYFKMDNVL 69
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 61.0 bits (148), Expect = 4e-12
Identities = 25/72 (34%), Positives = 45/72 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L+ +T + L Q+F +G + V VV+D +T + +GFGFV N D+A A+ ++
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 334 NGYALGDRLLQV 345
NG ++ R ++V
Sbjct: 63 NGKSVDGRQIRV 74
Score = 51.4 bits (123), Expect = 9e-09
Identities = 20/68 (29%), Positives = 41/68 (60%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++ L+ +FS G++ +++D+ T +S G+GFV + +DA+ A++ +NG + + I
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQI 72
Query: 99 KVSYARPS 106
+V A S
Sbjct: 73 RVDQAGKS 80
Score = 45.2 bits (107), Expect = 2e-06
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 15/84 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
L++ GL ++ LE +F YG I ++ D+ E RS +G G
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQRS------------RGFG 45
Query: 173 FVRFNQHIEAEHAMQELNGTIPEG 196
FV F +A+ AM +NG +G
Sbjct: 46 FVTFENPDDAKDAMMAMNGKSVDG 69
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 60.6 bits (148), Expect = 5e-12
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
N+ + + +++ + L FS+ G + SCK+ D+ S GYGFV++ E A RAI
Sbjct: 3 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIE 61
Query: 87 ELNGLKLQNKSIKV 100
++NG+ L +K + V
Sbjct: 62 KVNGMLLNDKKVFV 75
Score = 49.5 bits (119), Expect = 5e-08
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IF+ NL ++ L+ F FG + + KV D KG+GFV + AV AI+ +
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENG-GSKGYGFVHFETEEAAVRAIEKV 63
Query: 334 NGYALGDRLLQV 345
NG L D+ + V
Sbjct: 64 NGMLLNDKKVFV 75
Score = 47.5 bits (114), Expect = 2e-07
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
N+++ L K + + L + F +G I++ ++ D EN SKG G
Sbjct: 3 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD----EN------------GGSKGYG 46
Query: 173 FVRFNQHIEAEHAMQELNGTI 193
FV F A A++++NG +
Sbjct: 47 FVHFETEEAAVRAIEKVNGML 67
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 60.8 bits (147), Expect = 5e-12
Identities = 34/75 (45%), Positives = 44/75 (58%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
G +F+Y+L E D L Q F PFG V + KV D QT K FGFV N D A AI
Sbjct: 4 GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63
Query: 331 QSLNGYALGDRLLQV 345
Q++NG+ +G + L+V
Sbjct: 64 QAMNGFQIGTKRLKV 78
Score = 52.3 bits (125), Expect = 4e-09
Identities = 27/76 (35%), Positives = 41/76 (53%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ NL + ++PQ T +L F G V S K+ DK T S +GFV+Y + A+ A
Sbjct: 3 EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62
Query: 85 IIELNGLKLQNKSIKV 100
I +NG ++ K +KV
Sbjct: 63 IQAMNGFQIGTKRLKV 78
Score = 48.1 bits (114), Expect = 2e-07
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 15/79 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
NL++ LP+ T DL F P+G +I++++ DK + +SK G
Sbjct: 5 CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTN---------------LSKCFG 49
Query: 173 FVRFNQHIEAEHAMQELNG 191
FV ++ A+ A+Q +NG
Sbjct: 50 FVSYDNPDSAQAAIQAMNG 68
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 59.9 bits (145), Expect = 9e-12
Identities = 32/75 (42%), Positives = 44/75 (58%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
G +F+Y+L E D L Q+F PFG V + KV D T + K FGFV N A AI
Sbjct: 4 GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63
Query: 331 QSLNGYALGDRLLQV 345
Q++NG+ +G + L+V
Sbjct: 64 QAMNGFQIGMKRLKV 78
Score = 53.3 bits (128), Expect = 2e-09
Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
NL + ++PQ EL +F G V S K+ D+ T QS +GFV++ A+ AI
Sbjct: 5 CNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQ 64
Query: 87 ELNGLKLQNKSIKV 100
+NG ++ K +KV
Sbjct: 65 AMNGFQIGMKRLKV 78
Score = 47.2 bits (112), Expect = 3e-07
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL++ LP+ +L +F P+G +I++++ D+ ++ SK GF
Sbjct: 6 NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQ---------------SKCFGF 50
Query: 174 VRFNQHIEAEHAMQELNG 191
V F+ A+ A+Q +NG
Sbjct: 51 VSFDNPASAQAAIQAMNG 68
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 60.5 bits (146), Expect = 9e-12
Identities = 35/81 (43%), Positives = 46/81 (56%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
G +F+Y+L E D L Q+F PFG V + KV D QT K FGFV N A AI
Sbjct: 7 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66
Query: 331 QSLNGYALGDRLLQVSFKTHK 351
Q++NG+ +G + L+V K K
Sbjct: 67 QAMNGFQIGMKRLKVQLKRSK 87
Score = 52.0 bits (124), Expect = 9e-09
Identities = 27/85 (31%), Positives = 46/85 (54%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ +NL + ++PQ ++L +F G V S K+ DK T S +GFV+Y A+ A
Sbjct: 6 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65
Query: 85 IIELNGLKLQNKSIKVSYARPSSEA 109
I +NG ++ K +KV R +++
Sbjct: 66 IQAMNGFQIGMKRLKVQLKRSKNDS 90
Score = 47.4 bits (112), Expect = 4e-07
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 15/79 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANL++ LP+ +DL +F P+G ++++++ DK + +SK G
Sbjct: 8 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN---------------LSKCFG 52
Query: 173 FVRFNQHIEAEHAMQELNG 191
FV ++ + A+ A+Q +NG
Sbjct: 53 FVSYDNPVSAQAAIQAMNG 71
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM3 in
hnRNP R, hnRNP Q, and APOBEC-1 complementation factor
(ACF). hnRNP R is a ubiquitously expressed nuclear
RNA-binding protein that specifically bind mRNAs with a
preference for poly(U) stretches and has been implicated
in mRNA processing and mRNA transport, and also acts as
a regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as a
component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA transport.
ACF is an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members contain three conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 72
Score = 58.8 bits (143), Expect = 2e-11
Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 11/78 (14%)
Query: 31 VNYV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
V YV P + T+E+L+ LFS GEVE K I+D Y FV++ +DA +A+ E
Sbjct: 3 VLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEE 54
Query: 88 LNGLKLQNKSIKVSYARP 105
+NG +L+ I+VS A+P
Sbjct: 55 MNGKELEGSPIEVSLAKP 72
Score = 56.1 bits (136), Expect = 2e-10
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL T + L +LF +G V+ VK ++D + FV D+AV A++ +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 334 NGYALGDRLLQVSF 347
NG L ++VS
Sbjct: 56 NGKELEGSPIEVSL 69
Score = 40.3 bits (95), Expect = 7e-05
Identities = 30/92 (32%), Positives = 38/92 (41%), Gaps = 25/92 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV LP T+E L LF YG + E V+ K FV
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEV------------ERVK-----------KIKDYAFV 40
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F + +A AM+E+NG EG+ PI V A
Sbjct: 41 HFEERDDAVKAMEEMNGKELEGS--PIEVSLA 70
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 59.1 bits (143), Expect = 2e-11
Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 274 IFVYNLAPETEDNVLWQLF-GPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
IFV +L+PE ++ L LF F + ++ K++ DP T +G+GFV ++ ++ A+
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 333 LNGYALGDRLLQVSFKT 349
+ G G R +++S T
Sbjct: 64 MQGVYCGGRPMRISTAT 80
Score = 49.1 bits (117), Expect = 7e-08
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 37 TMTQEELQHLFSSV-GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
+ + +L LF S +S K++ D T S GYGFV + D +RA+IE+ G+
Sbjct: 12 EVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGG 71
Query: 96 KSIKVSYA 103
+ +++S A
Sbjct: 72 RPMRISTA 79
Score = 37.1 bits (86), Expect = 0.001
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 18/93 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFR-PYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V L + + DL +LF+ + + +++I+ D + +S+G GF
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTG---------------VSRGYGF 48
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
VRF+ + + A+ E+ G G P+ + A
Sbjct: 49 VRFSDENDQQRALIEMQGVYCGG--RPMRISTA 79
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 58.4 bits (142), Expect = 3e-11
Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 274 IFVYNLAPETEDNVLWQLF-GPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
IFV +LAP+ D +L + F + +V+ KVV DP T + KG+GFV + DE A+
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 333 LNGYALGDRLLQVSFKT 349
+NG R ++VS T
Sbjct: 64 MNGVYCSSRPMRVSPAT 80
Score = 53.1 bits (128), Expect = 3e-09
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSV-GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+ V + +T LQ F + V K++ D T +S GYGFV + ++ +RA+ E
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 88 LNGLKLQNKSIKVSYA 103
+NG+ ++ ++VS A
Sbjct: 64 MNGVYCSSRPMRVSPA 79
Score = 43.8 bits (104), Expect = 5e-06
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 16/78 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRP-YGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V L +T L+ FR Y ++ ++++ D V+G SKG GF
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDP---------VTG------RSKGYGF 48
Query: 174 VRFNQHIEAEHAMQELNG 191
VRF E + A+ E+NG
Sbjct: 49 VRFGDEDERDRALTEMNG 66
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 58.2 bits (141), Expect = 4e-11
Identities = 35/95 (36%), Positives = 49/95 (51%), Gaps = 19/95 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K T++D+ LF P+GTI IL + SKG FV
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN----------------SKGCAFV 47
Query: 175 RFNQHIEAEHAMQELNG--TIPEGASEPITVKFAN 207
+F+ H EA+ A+ L+G T+P GAS + VKFA+
Sbjct: 48 KFSSHAEAQAAINALHGSQTMP-GASSSLVVKFAD 81
Score = 41.7 bits (98), Expect = 3e-05
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
+TED+V +LF PFG ++ ++R P KG FV +++ EA AI +L+G
Sbjct: 13 QTEDDVR-RLFEPFGTIEECTILRGPDG-NSKGCAFVKFSSHAEAQAAINALHG 64
Score = 37.0 bits (86), Expect = 0.001
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + T+++++ LF G +E C ++R S G FV + +A+ AI L
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAINAL 62
Query: 89 NG 90
+G
Sbjct: 63 HG 64
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2). MSSP-1 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence CT(A/T)(A/T)T, and stimulates
DNA replication in the system using SV40 DNA. MSSP-1 is
identical with Scr2, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-1 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with c-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 85
Score = 57.8 bits (139), Expect = 5e-11
Identities = 36/100 (36%), Positives = 52/100 (52%), Gaps = 22/100 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLY+S LP M +++LEN+ +P+G +I++RIL D SGT S+G+GF
Sbjct: 2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS----------SGT------SRGVGF 45
Query: 174 VRFNQHIEAEHAMQELNGTI---PEGAS---EPITVKFAN 207
R + E + NG P G S EP+ KFA+
Sbjct: 46 ARMESTEKCEAVISHFNGKFIKTPPGVSAPAEPLLCKFAD 85
Score = 42.4 bits (99), Expect = 2e-05
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P +M ++EL+++ G+V S +++RD ++ S G GF TE E I
Sbjct: 1 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIS 59
Query: 87 ELNG 90
NG
Sbjct: 60 HFNG 63
Score = 30.1 bits (67), Expect = 0.46
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + PFG V + +++RD + +G GF M + ++ I
Sbjct: 3 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61
Query: 334 NG 335
NG
Sbjct: 62 NG 63
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 57.8 bits (139), Expect = 6e-11
Identities = 29/76 (38%), Positives = 45/76 (59%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L+PE + + F PFG + + +VV+D T K KG+GFV N +A AIQ +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 334 NGYALGDRLLQVSFKT 349
G LG R ++ ++ T
Sbjct: 64 GGQWLGGRQIRTNWAT 79
Score = 50.9 bits (121), Expect = 1e-08
Identities = 20/66 (30%), Positives = 41/66 (62%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T ++++ F+ G + ++++D T +S GYGFV+++ DAE AI ++ G L +
Sbjct: 13 ITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 72
Query: 98 IKVSYA 103
I+ ++A
Sbjct: 73 IRTNWA 78
Score = 37.8 bits (87), Expect = 6e-04
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L +T +D++ F P+G I +R+ V+ +G SKG GF
Sbjct: 3 HVFVGDLSPEITTDDIKAAFAPFGRISDARV---------VKDMATGK------SKGYGF 47
Query: 174 VRFNQHIEAEHAMQELNG 191
V F +AE+A+Q++ G
Sbjct: 48 VSFFNKWDAENAIQQMGG 65
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM2 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contain two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 88
Score = 57.8 bits (139), Expect = 8e-11
Identities = 33/100 (33%), Positives = 51/100 (51%), Gaps = 22/100 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLY+S LP M +++LEN+ +P+G +I++RIL D +S+G+GF
Sbjct: 3 NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANG----------------VSRGVGF 46
Query: 174 VRFNQHIEAEHAMQELNG---TIPEG---ASEPITVKFAN 207
R + E +Q NG P G +EP+ KFA+
Sbjct: 47 ARMESTEKCEVVIQHFNGKYLKTPPGVPAPTEPLLCKFAD 86
Score = 39.3 bits (91), Expect = 2e-04
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P +M ++EL+++ G V S +++RD S G GF TE E I
Sbjct: 2 TNLYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQ 60
Query: 87 ELNGLKLQ 94
NG L+
Sbjct: 61 HFNGKYLK 68
Score = 32.8 bits (74), Expect = 0.047
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + PFG V + +++RD +G GF M + ++ IQ
Sbjct: 4 LYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVS-RGVGFARMESTEKCEVVIQHF 62
Query: 334 NGYAL 338
NG L
Sbjct: 63 NGKYL 67
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 56.8 bits (137), Expect = 9e-11
Identities = 27/75 (36%), Positives = 48/75 (64%), Gaps = 1/75 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + +T++ L+ +F G V++ K+I DK + + YGFV Y+++ DAE A+ L
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59
Query: 89 NGLKLQNKSIKVSYA 103
NG +++N I+V++A
Sbjct: 60 NGRQIENNEIRVNWA 74
Score = 41.8 bits (98), Expect = 2e-05
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL P +++L Q+F G VQNVK++ D + K +GFV +A A+Q+L
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 334 NGYALGDRLLQVSF 347
NG + + ++V++
Sbjct: 60 NGRQIENNEIRVNW 73
Score = 35.2 bits (81), Expect = 0.005
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 16/77 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L +T++ L+ +F+ G + +I+ DK N + GFV
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK----NNKGV------------NYGFV 44
Query: 175 RFNQHIEAEHAMQELNG 191
++Q +AE A+Q LNG
Sbjct: 45 EYHQSHDAEIALQTLNG 61
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 56.8 bits (138), Expect = 1e-10
Identities = 24/73 (32%), Positives = 43/73 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E ++ VL F PFG ++++++ D +T K +GF FV ++A AI ++
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 334 NGYALGDRLLQVS 346
N L R ++V+
Sbjct: 61 NESELFGRTIRVN 73
Score = 45.7 bits (109), Expect = 1e-06
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV + + ++ L F G+++ ++ D T + G+ FV + EDA AI +N
Sbjct: 2 YVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMN 61
Query: 90 GLKLQNKSIKVS 101
+L ++I+V+
Sbjct: 62 ESELFGRTIRVN 73
Score = 36.8 bits (86), Expect = 0.001
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV GL + + ++ L F P+G I +I D ++ R F FV
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLD-YETQKHRGF--------------AFV 45
Query: 175 RFNQHIEAEHAMQELNG 191
F + +A A+ +N
Sbjct: 46 EFEEPEDAAAAIDNMNE 62
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 56.8 bits (138), Expect = 1e-10
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S +IV +P+ +T++ L+ F S GEV K++R + +S +GFV + EDA++A+
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVK 59
Query: 87 ELNGLKLQNKSIKVSYA 103
N + I V A
Sbjct: 60 YFNKTFIDTSKISVELA 76
Score = 37.2 bits (87), Expect = 0.001
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I V NL ++ L + F G V +VKV+R K + FGFV + ++A A++
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDG-KSRRFGFVGFKSEEDAQQAVKYF 61
Query: 334 NGYALGDRLLQVSF 347
N + + V
Sbjct: 62 NKTFIDTSKISVEL 75
Score = 36.0 bits (84), Expect = 0.003
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 18/92 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V LPK++T++ L F G + +++ + G S+ GFV
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR----------DGK------SRRFGFV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F +A+ A++ N T + + I+V+ A
Sbjct: 47 GFKSEEDAQQAVKYFNKTFID--TSKISVELA 76
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 56.9 bits (138), Expect = 1e-10
Identities = 20/70 (28%), Positives = 40/70 (57%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
V +++++++ +F + G+++SC L D T + GYGF+ Y + A+ AI +N L
Sbjct: 8 VHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDL 67
Query: 94 QNKSIKVSYA 103
+ ++V A
Sbjct: 68 GGQQLRVGKA 77
Score = 49.2 bits (118), Expect = 6e-08
Identities = 24/73 (32%), Positives = 43/73 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V ++ P+ ++ + +F FG +++ + DP+T K KG+GF+ N A AI S+
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62
Query: 334 NGYALGDRLLQVS 346
N + LG + L+V
Sbjct: 63 NLFDLGGQQLRVG 75
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 57.3 bits (139), Expect = 1e-10
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
QT T+E L+ +FS G++ +L+RD T S GY FV Y DA RA + + L +
Sbjct: 13 LQT-TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVID 71
Query: 95 NKSIKVSYAR 104
I V + R
Sbjct: 72 GSEIFVDFER 81
Score = 41.9 bits (99), Expect = 3e-05
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 17/97 (17%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
L+V L T+E L +F YG I R+ VR V+G SKG
Sbjct: 3 YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRL---------VRDIVTG------FSKGY 47
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
FV + +A A ++ + + +G+ I V F
Sbjct: 48 AFVEYEHERDALRAYRDAHKLVIDGSE--IFVDFERE 82
Score = 39.9 bits (94), Expect = 2e-04
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L+ +T + L ++F +G ++ +++VRD T KG+ FV
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 56.6 bits (137), Expect = 1e-10
Identities = 16/52 (30%), Positives = 34/52 (65%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+P++ T+E+L+ F G++E +++DK T +S G+G+V +++ A A+
Sbjct: 8 IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
Score = 36.2 bits (84), Expect = 0.002
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 15/80 (18%)
Query: 121 PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHI 180
PK T+EDL F+ +G I I+ DK E SKG G+V+F++
Sbjct: 9 PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGE---------------SKGFGYVKFHKPS 53
Query: 181 EAEHAMQELNGTIPEGASEP 200
+A A++ + + +EP
Sbjct: 54 QAAVALENCDKSFKAVLAEP 73
Score = 31.6 bits (72), Expect = 0.074
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 274 IFVYNLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+FV + P++ + L + F FG ++ V +V+D T + KGFG+V +A A++
Sbjct: 4 LFV--VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 56.4 bits (137), Expect = 1e-10
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+E L LF G V + + +D+ T GYGFV + EDA+ AI +N +KL K I
Sbjct: 11 TEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPI 70
Query: 99 KVS 101
+V+
Sbjct: 71 RVN 73
Score = 52.6 bits (127), Expect = 3e-09
Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + + +LW+LF G V NV + +D T +G+GFV + ++A +AI+ +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 334 NGYALGDRLLQVS 346
N L + ++V+
Sbjct: 61 NMIKLYGKPIRVN 73
Score = 28.7 bits (65), Expect = 0.92
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 15/78 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YV L + +T+E L LF G ++ I D+ V+ +G GFV
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDR---------VTQAH------QGYGFV 45
Query: 175 RFNQHIEAEHAMQELNGT 192
F +A++A++ +N
Sbjct: 46 EFLSEEDADYAIKIMNMI 63
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 56.9 bits (138), Expect = 1e-10
Identities = 24/53 (45%), Positives = 33/53 (62%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
M + + F+ GEV S K+IR+K T +S GYGFV + E AE+A+ LNG
Sbjct: 11 MDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63
Score = 48.0 bits (115), Expect = 1e-07
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 279 LAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
L P ++ ++ F G V +VK++R+ QT K G+GFV ++ A A+QSLNG
Sbjct: 7 LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63
Score = 41.9 bits (99), Expect = 2e-05
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ L M + + + F G + + +I+ +K S G GFV
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNK---------------QTGKSAGYGFV 46
Query: 175 RFNQHIEAEHAMQELNGT-IP 194
F H AE A+Q LNG IP
Sbjct: 47 EFATHEAAEQALQSLNGKPIP 67
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 56.5 bits (137), Expect = 2e-10
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T+EEL+ FS G V+ K+I D+ S GYGFV + EDAE+ I+ + L
Sbjct: 10 IPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEK-ILAMGNLNF 67
Query: 94 QNKSIKVSYA 103
+ K + + A
Sbjct: 68 RGKKLNIGPA 77
Score = 43.8 bits (104), Expect = 5e-06
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 18/77 (23%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V G+P T+E+L + F +G++ +I+ D+ +SKG GFV
Sbjct: 6 FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAG----------------VSKGYGFVT 49
Query: 176 FNQHIEAEH--AMQELN 190
F +AE AM LN
Sbjct: 50 FETQEDAEKILAMGNLN 66
Score = 42.3 bits (100), Expect = 1e-05
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
IFV + P+T + L F FG+V++VK++ D + KG+GFV ++A
Sbjct: 5 IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDA 56
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 56.1 bits (136), Expect = 2e-10
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 37 TMTQEELQHLFSSVGEVESCKLIRDKTTA---QSLGYGFVNYYRTEDAERAIIELNGLKL 93
+T+ L LFS G+++ + K+ Q GY FV + E+AE+A+ LNG
Sbjct: 10 RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTA 69
Query: 94 QNKSIKVSYAR 104
K + V +A
Sbjct: 70 LGKKLVVRWAH 80
Score = 38.0 bits (89), Expect = 5e-04
Identities = 27/94 (28%), Positives = 39/94 (41%), Gaps = 14/94 (14%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L++ L +T+ L LF YG I L K SG + +G F
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHK----------SGPLKGQ--PRGYCF 48
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
V F EAE A++ LNG G + V++A+
Sbjct: 49 VTFETKEEAEKALKSLNGKTALGKK--LVVRWAH 80
Score = 37.6 bits (88), Expect = 7e-04
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVV---RDPQTYKCKGFGFVCMTNYDEAVFA 329
+++ NL TE ++L +LF +G ++ + P + +G+ FV +EA A
Sbjct: 2 LWIGNLDSRLTEFHLL-KLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 330 IQSLNGYALGDRLLQVS 346
++SLNG + L V
Sbjct: 61 LKSLNGKTALGKKLVVR 77
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3). MSSP-2 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence T(C/A)TT, and stimulates DNA
replication in the system using SV40 DNA. MSSP-2 is
identical with Scr3, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-2 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-2 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 56.6 bits (136), Expect = 2e-10
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 22/100 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLY+S LP M +++LE++ +P+G +I++RIL D SGT S+G+GF
Sbjct: 2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRD----------ASGT------SRGVGF 45
Query: 174 VRFNQHIEAEHAMQELNG---TIPEGA---SEPITVKFAN 207
R + E + NG P G +EP+ KFA+
Sbjct: 46 ARMESTEKCEAIITHFNGKYIKTPPGVPAPTEPLLCKFAD 85
Score = 41.6 bits (97), Expect = 3e-05
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P +M ++EL+ + G+V S +++RD + S G GF TE E I
Sbjct: 1 TNLYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIIT 59
Query: 87 ELNG 90
NG
Sbjct: 60 HFNG 63
Score = 30.0 bits (67), Expect = 0.48
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + PFG V + +++RD +G GF M + ++ I
Sbjct: 3 LYISNLPLSMDEQELESMLKPFGQVISTRILRDASG-TSRGVGFARMESTEKCEAIITHF 61
Query: 334 NG 335
NG
Sbjct: 62 NG 63
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 56.5 bits (137), Expect = 2e-10
Identities = 31/84 (36%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 29 LIVNYVPQTMT-QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V+ +P+T L+ LFS VG+ C+L Q G+ FV Y EDAE A
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAEDAEEAQQA 63
Query: 88 LNGLKLQNKSIKVSYARPSSEAIK 111
LNG LQ I+VS+ P
Sbjct: 64 LNGHSLQGSPIRVSFGNPGRPGAS 87
Score = 47.3 bits (113), Expect = 3e-07
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 273 CIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
C+FV L + ++L +LF G ++ P +GF FV ++A A Q
Sbjct: 4 CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQ-PRGFAFVEYATAEDAEEAQQ 62
Query: 332 SLNGYALGDRLLQVSF 347
+LNG++L ++VSF
Sbjct: 63 ALNGHSLQGSPIRVSF 78
Score = 34.9 bits (81), Expect = 0.008
Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 19/94 (20%)
Query: 115 LYVSGLPKHMT-QEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+V LPK L LF G ++ +G P +G F
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP----------NGQP------RGFAF 48
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
V + +AE A Q LNG +G+ PI V F N
Sbjct: 49 VEYATAEDAEEAQQALNGHSLQGS--PIRVSFGN 80
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 56.0 bits (135), Expect = 2e-10
Identities = 21/46 (45%), Positives = 31/46 (67%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
C+FV NL E + LW++FG G ++ V++VRDP+T KGF +V
Sbjct: 1 CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYV 46
Score = 32.2 bits (73), Expect = 0.063
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
+E L +F G +E +++RD T G+ +V + E+A++ LN K
Sbjct: 13 EEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL-LNEKK 64
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 56.0 bits (135), Expect = 2e-10
Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V +P T+E+L+ +FS VG V S +L+ D+ T + GYGF Y E A A+ LNG
Sbjct: 3 VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62
Query: 91 LKLQNKSIKVSYA 103
+L + ++V A
Sbjct: 63 YELNGRQLRVDNA 75
Score = 51.0 bits (122), Expect = 1e-08
Identities = 26/74 (35%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+ E + L +F G V + ++V D +T K KG+GF + + A+ A+++L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 334 NGYALGDRLLQVSF 347
NGY L R L+V
Sbjct: 61 NGYELNGRQLRVDN 74
Score = 34.0 bits (78), Expect = 0.014
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 17/92 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V +P T+E L+++F G +++ R++ D+ +G P KG GF
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE---------TGKP------KGYGFC 45
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ A AM+ LNG E + V A
Sbjct: 46 EYKDQETALSAMRNLNGY--ELNGRQLRVDNA 75
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 55.8 bits (135), Expect = 3e-10
Identities = 28/72 (38%), Positives = 41/72 (56%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T T+EEL+ LF + GE+ L DK T +S G+ FV++ E A +A EL
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 89 NGLKLQNKSIKV 100
+G Q + + V
Sbjct: 62 DGSIFQGRLLHV 73
Score = 51.1 bits (123), Expect = 1e-08
Identities = 27/72 (37%), Positives = 36/72 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL T + L +LF FG + V + D +T + KGF FV + AV A L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 334 NGYALGDRLLQV 345
+G RLL V
Sbjct: 62 DGSIFQGRLLHV 73
Score = 48.4 bits (116), Expect = 1e-07
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T+E+L LF +G I + DK + SKG FV
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDK---------------ETKRSKGFAFV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F A A EL+G+I +G
Sbjct: 47 SFMFPEHAVKAYSELDGSIFQG 68
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 55.8 bits (135), Expect = 3e-10
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV NL + +L++LF G ++ VK+ +DP K K F FV + +AIQ
Sbjct: 3 TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQL 61
Query: 333 LNGYALGDRLLQVS 346
LNG L R L++
Sbjct: 62 LNGIRLFGRELRIK 75
Score = 37.3 bits (87), Expect = 0.001
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+E L LF G +E K+ +D + + FV + AI LNG++L + +
Sbjct: 14 TEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLLNGIRLFGREL 72
Query: 99 KVS 101
++
Sbjct: 73 RIK 75
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 55.7 bits (134), Expect = 3e-10
Identities = 26/75 (34%), Positives = 43/75 (57%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P T TQ++ + L G +E C L+ +TT S GYGFV Y + + A RA +L
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
Query: 89 NGLKLQNKSIKVSYA 103
G +L ++++ V +
Sbjct: 62 LGKQLGSRTLYVHWT 76
Score = 37.2 bits (86), Expect = 8e-04
Identities = 24/70 (34%), Positives = 30/70 (42%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
+ NL P +L PFG ++ +V T KG+GFV D A A L G
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63
Query: 336 YALGDRLLQV 345
LG R L V
Sbjct: 64 KQLGSRTLYV 73
Score = 32.6 bits (74), Expect = 0.041
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L ++ LP TQ+ E L RP+G + R F+ + SKG GFV
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNL--------------ERCFLVYSETTGH-SKGYGFV 46
Query: 175 RFNQHIEAEHAMQELNG 191
+ + A A +L G
Sbjct: 47 EYMKKDSAARAKSDLLG 63
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 55.9 bits (134), Expect = 3e-10
Identities = 22/66 (33%), Positives = 42/66 (63%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T E+++ F+ G++ ++++D T +S GYGFV++Y DAE AI+ + G L +
Sbjct: 13 ITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQ 72
Query: 98 IKVSYA 103
I+ ++A
Sbjct: 73 IRTNWA 78
Score = 55.5 bits (133), Expect = 4e-10
Identities = 28/76 (36%), Positives = 43/76 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L+PE + F PFG + + +VV+D T K KG+GFV N +A AI +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 334 NGYALGDRLLQVSFKT 349
G LG R ++ ++ T
Sbjct: 64 GGQWLGGRQIRTNWAT 79
Score = 38.1 bits (88), Expect = 6e-04
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L +T ED+++ F P+G I +R++ D + SKG GF
Sbjct: 3 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGK---------------SKGYGF 47
Query: 174 VRFNQHIEAEHAMQELNG 191
V F ++AE+A+ + G
Sbjct: 48 VSFYNKLDAENAIVHMGG 65
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 55.3 bits (134), Expect = 4e-10
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P T + L+ FS GE+E +I D+ T +S GYGFV + E AERA +
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62
Query: 89 N 89
N
Sbjct: 63 N 63
Score = 52.6 bits (127), Expect = 4e-09
Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV L T D+ L + F FG ++ V+ D QT K +G+GFV + + A A +
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62
Query: 334 N 334
N
Sbjct: 63 N 63
Score = 43.0 bits (102), Expect = 8e-06
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP H T + L F +G I + ++ D+ +G S+G GFV
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDR---------QTGK------SRGYGFV 47
Query: 175 RFNQHIEAEHAMQELNGTI 193
F AE A ++ N I
Sbjct: 48 TFKDKESAERACKDPNPII 66
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 55.3 bits (134), Expect = 5e-10
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL + + L +LF FG V+ ++V+D T KG FV + A +++
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 334 N-----GYALGDRLLQVSF 347
+ G +L R L V+
Sbjct: 63 DNAEDSGLSLDGRRLIVTL 81
Score = 51.8 bits (125), Expect = 7e-09
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN---- 89
+P T+EEL+ LFS GEV+ ++++DK T S G FV + E A++ + +
Sbjct: 8 LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAED 67
Query: 90 -GLKLQNKSIKVSYA 103
GL L + + V+ A
Sbjct: 68 SGLSLDGRRLIVTLA 82
Score = 41.4 bits (98), Expect = 4e-05
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 15/84 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ LP T+E+L+ LF +G + +RI+ DK + SKG FV
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDK---------------LTGHSKGTAFV 47
Query: 175 RFNQHIEAEHAMQELNGTIPEGAS 198
+F A+ ++ + G S
Sbjct: 48 KFKTKESAQKCLEAADNAEDSGLS 71
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 55.3 bits (134), Expect = 5e-10
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVG--EVESCKLIRDKTTAQSLGYGFVNYYRTEDAER--- 83
LI+ + T+E++ S++ ++ +LIRDK T S G+ FV + EDA +
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64
Query: 84 AIIELNGLKLQNKSIKVSYA 103
A+ L+ + + ++VSYA
Sbjct: 65 ALNNLDPFVIDGRVVRVSYA 84
Score = 41.8 bits (99), Expect = 2e-05
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQ--NVKVVRDPQTYKCKGFGFVCMTNYDEAVF-- 328
+ + L T + + Q +V +V+++RD T +GF FV + ++A
Sbjct: 4 TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63
Query: 329 -AIQSLNGYALGDRLLQVSFK 348
A+ +L+ + + R+++VS+
Sbjct: 64 DALNNLDPFVIDGRVVRVSYA 84
Score = 37.9 bits (89), Expect = 6e-04
Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 17/82 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTI-ITS-RILCDKMASENVRSFVSGTPEIPQISKGIG 172
L + GL T+ED+ ++ I R++ DK + S+G
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDK---------------LTGTSRGFA 49
Query: 173 FVRFNQHIEAEHAMQELNGTIP 194
FV F +A M LN P
Sbjct: 50 FVEFPSLEDATQWMDALNNLDP 71
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 55.1 bits (133), Expect = 5e-10
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL +++ L +LF FG + V V D ++ K KGF +V + ++AV A + L
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 334 NGYALGDRLLQV 345
+G RL+ +
Sbjct: 65 DGKVFQGRLIHI 76
Score = 51.2 bits (123), Expect = 1e-08
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ L V +P + +++L+ LFS GE+ + DK + +S G+ +V + EDA +A
Sbjct: 1 ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Query: 85 IIELNGLKLQNKSIKV 100
EL+G Q + I +
Sbjct: 61 YKELDGKVFQGRLIHI 76
Score = 36.2 bits (84), Expect = 0.002
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP ++DLE LF +G + + DK + SKG +V
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKS---------------GKSKGFAYV 49
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A A +EL+G + +G
Sbjct: 50 LFLDPEDAVKAYKELDGKVFQG 71
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 54.6 bits (132), Expect = 6e-10
Identities = 23/72 (31%), Positives = 41/72 (56%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V+ + T ++L+ +F GEV + RD+ T +S G+ FV +Y DAE A+ +
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 89 NGLKLQNKSIKV 100
+G +L + ++V
Sbjct: 61 DGKELDGRELRV 72
Score = 43.4 bits (103), Expect = 6e-06
Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V NL T + L ++F +G V +V + RD T + +GF FV + +A A+ +++G
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 336 YALGDRLLQV 345
L R L+V
Sbjct: 63 KELDGRELRV 72
Score = 43.4 bits (103), Expect = 6e-06
Identities = 24/82 (29%), Positives = 33/82 (40%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V L T +DL +F YG + I D+ E S+G FV
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRE---------------SRGFAFV 45
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
RF +AE AM ++G +G
Sbjct: 46 RFYDKRDAEDAMDAMDGKELDG 67
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 54.9 bits (132), Expect = 6e-10
Identities = 25/75 (33%), Positives = 40/75 (53%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P + T EE + L + G +E C L+ + T S GYGFV Y + + A +A +EL
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61
Query: 89 NGLKLQNKSIKVSYA 103
G +L ++ +
Sbjct: 62 LGKQLGESTLFAQWM 76
Score = 32.2 bits (73), Expect = 0.065
Identities = 28/77 (36%), Positives = 33/77 (42%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V+ LP T E+ E L R YG I R V S V+G SKG GFV
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNI--ERCFL-------VYSEVTGH------SKGYGFV 46
Query: 175 RFNQHIEAEHAMQELNG 191
+ + A A EL G
Sbjct: 47 EYMKKDSASKARLELLG 63
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 54.6 bits (132), Expect = 6e-10
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 21/79 (26%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL +T+++L +LF P+G I+ V+ IP KG GFV
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIV------------YVK--------IP-PGKGCGFV 42
Query: 175 RFNQHIEAEHAMQELNGTI 193
+F AE A+Q+L GTI
Sbjct: 43 QFVHRAAAEAAIQQLQGTI 61
Score = 47.7 bits (114), Expect = 2e-07
Identities = 26/66 (39%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L P ++ L LFGPFG + VK+ P KG GFV + A AIQ L
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPG---KGCGFVQFVHRAAAEAAIQQL 57
Query: 334 NGYALG 339
G +G
Sbjct: 58 QGTIIG 63
Score = 41.9 bits (99), Expect = 2e-05
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N+ + V + +T++EL+ LF GE+ K+ K G GFV + AE AI
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK------GCGFVQFVHRAAAEAAI 54
Query: 86 IELNGLKLQNKSIKVSY 102
+L G + I++S+
Sbjct: 55 QQLQGTIIGGSRIRLSW 71
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 54.5 bits (132), Expect = 8e-10
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKT-----TAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
T+E L+ F G V S + + K S+GYGFV + E A++A+ L G L
Sbjct: 13 TEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVL 72
Query: 94 QNKSIKVSY 102
++++
Sbjct: 73 DGHALELKL 81
Score = 50.3 bits (121), Expect = 3e-08
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVR-----DPQTYKCKGFGFVCMTNYDEAV 327
+FV NL +T + L + F G V++V + + P G+GFV + + A
Sbjct: 2 TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 328 FAIQSLNGYALGDRLLQVSF 347
A++ L G L L++
Sbjct: 62 KALKRLQGTVLDGHALELKL 81
Score = 39.9 bits (94), Expect = 1e-04
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 10/82 (12%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L T+E L+ F G + + I A + +S G GFV
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTI-----AKKKDPKGPGKL-----LSMGYGFV 52
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F A+ A++ L GT+ +G
Sbjct: 53 EFKSKEAAQKALKRLQGTVLDG 74
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 54.6 bits (131), Expect = 8e-10
Identities = 23/61 (37%), Positives = 36/61 (59%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V VP+T+T++E++ +F G V +I+DK T G FV Y ++A+RAI L
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61
Query: 89 N 89
+
Sbjct: 62 H 62
Score = 39.6 bits (92), Expect = 1e-04
Identities = 24/95 (25%), Positives = 50/95 (52%), Gaps = 18/95 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V +P+ +T++++ +F +G ++ I+ DK +G FV
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGH---------------QQGCCFV 46
Query: 175 RFNQHIEAEHAMQELNG--TIPEGASEPITVKFAN 207
+++ EA+ A++ L+ T+P GAS P+ V++A+
Sbjct: 47 KYSTRDEADRAIRALHNQRTLPGGAS-PVQVRYAD 80
Score = 28.0 bits (62), Expect = 1.9
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
TE V +F G V V +++D +T +G FV + DEA AI++L+
Sbjct: 12 TEQEVR-PMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRALH 62
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 54.3 bits (131), Expect = 9e-10
Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V + ++ E L+ F G V ++I D+ T +S G+G+V++ EDA++AI
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 88 LNGLKLQNKSIKVSYA 103
++G +L + I V ++
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 48.9 bits (117), Expect = 7e-08
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL+ +D L F FG V +V+ D +T + +GFG+V + ++A AI+++
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61
Query: 334 NGYALGDRLLQVSF 347
+G L R + V F
Sbjct: 62 DGKELDGRPINVDF 75
Score = 42.0 bits (99), Expect = 2e-05
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 17/93 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+V L + E L+ F +GT++ +R++ D+ E RS +G G+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDR---ETGRS------------RGFGY 45
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F +A+ A++ ++G +G PI V F+
Sbjct: 46 VDFESPEDAKKAIEAMDGKELDG--RPINVDFS 76
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 54.2 bits (131), Expect = 1e-09
Identities = 22/72 (30%), Positives = 34/72 (47%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IF+ L ++ + +L FG ++ +V+D T KG+ F + AI L
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 334 NGYALGDRLLQV 345
NG LGD+ L V
Sbjct: 63 NGMQLGDKKLTV 74
Score = 48.4 bits (116), Expect = 1e-07
Identities = 20/72 (27%), Positives = 42/72 (58%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + +P +++++++ L S G++++ L++D T S GY F Y ++AI L
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 89 NGLKLQNKSIKV 100
NG++L +K + V
Sbjct: 63 NGMQLGDKKLTV 74
Score = 30.7 bits (70), Expect = 0.20
Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 23/81 (28%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV----SGTPEIPQISKG 170
+++ GLP +++++ ++ L +G +++F S T SKG
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFG---------------KLKAFNLVKDSATGL----SKG 43
Query: 171 IGFVRFNQHIEAEHAMQELNG 191
F + + A+ LNG
Sbjct: 44 YAFCEYLDPSVTDQAIAGLNG 64
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 54.5 bits (132), Expect = 1e-09
Identities = 24/82 (29%), Positives = 39/82 (47%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
GW IFV + E ++ + F FG ++N+ + D +T KG+ + EA AI
Sbjct: 6 GWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAI 65
Query: 331 QSLNGYALGDRLLQVSFKTHKP 352
+ LNG L + + V + K
Sbjct: 66 EGLNGKELLGQTISVDWAFVKG 87
Score = 52.2 bits (126), Expect = 7e-09
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V + +E++ F+ GE+++ L D+ T GY + Y ++A+ AI L
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 89 NGLKLQNKSIKVSYA 103
NG +L ++I V +A
Sbjct: 69 NGKELLGQTISVDWA 83
Score = 30.3 bits (69), Expect = 0.34
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 19/93 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRS-FVSGTPEIPQISKGIGF 173
++V+G+ + +ED+ + F +G I + D+ R+ FV KG
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDR------RTGFV----------KGYAL 52
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ + EA+ A++ LNG E + I+V +A
Sbjct: 53 IEYETKKEAQAAIEGLNGK--ELLGQTISVDWA 83
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 53.8 bits (130), Expect = 1e-09
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
L V +P +T+EE + LFS GEV L ++K G+GF+ +AE+A
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKA 55
Query: 87 ELNGLKLQNKSIKV 100
EL+G+ + + ++V
Sbjct: 56 ELDGIMRKGRQLRV 69
Score = 52.7 bits (127), Expect = 3e-09
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 23/94 (24%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R L+V LP +T+E+ + LF YG + S + +K KG
Sbjct: 1 RCRLFVGNLPNDITEEEFKELFSKYGEV--SEVFLNK-------------------EKGF 39
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
GF+R + AE A EL+G + +G + V+F
Sbjct: 40 GFIRLDTRTNAEKAKAELDGIMRKG--RQLRVRF 71
Score = 50.4 bits (121), Expect = 2e-08
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + + +LF +G V V + ++ KGFGF+ + A A L
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57
Query: 334 NGYALGDRLLQVSF 347
+G R L+V F
Sbjct: 58 DGIMRKGRQLRVRF 71
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including SCAF4,
SCAF8 and similar proteins. The biological role of SCAF4
remains unclear, but it shows high sequence similarity
to SCAF8 (also termed CDC5L complex-associated protein
7, or RNA-binding motif protein 16, or CTD-binding
SR-like protein RA8). SCAF8 is a nuclear matrix protein
that interacts specifically with a highly
serine-phosphorylated form of the carboxy-terminal
domain (CTD) of the largest subunit of RNA polymerase II
(pol II). The pol II CTD plays a role in coupling
transcription and pre-mRNA processing. In addition,
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 77
Score = 53.9 bits (130), Expect = 1e-09
Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 6/76 (7%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + ++ + +T+E+L++LF GE++S +I + G +V +DA RA+ +L
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR------GCAYVCMETRQDAHRALQKL 58
Query: 89 NGLKLQNKSIKVSYAR 104
+KL K IKV++A
Sbjct: 59 RNVKLAGKKIKVAWAP 74
Score = 34.2 bits (79), Expect = 0.009
Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ +L+ + + L LF +G +Q++ ++ +G +VCM +A A+Q L
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP------RGCAYVCMETRQDAHRALQKL 58
Query: 334 NGYALGDRLLQVSFKTHK 351
L + ++V++ +K
Sbjct: 59 RNVKLAGKKIKVAWAPNK 76
Score = 29.6 bits (67), Expect = 0.42
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 25/96 (26%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI-SKGIGF 173
L++ L K +T+EDL+NLF YG I I I +G +
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQ----------------------SIDMIPPRGCAY 42
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
V +A A+Q+L + A + I V +A +
Sbjct: 43 VCMETRQDAHRALQKLRNV--KLAGKKIKVAWAPNK 76
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 55.8 bits (134), Expect = 1e-09
Identities = 33/108 (30%), Positives = 54/108 (50%), Gaps = 4/108 (3%)
Query: 252 LTADLLNNSMLPPKSLHGS----GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP 307
L ++ +N +P S+ GS +F+ L+ T+D L F FG V + KV+ D
Sbjct: 11 LRQNISSNGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR 70
Query: 308 QTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
+T + +GFGFV + A AI ++G L R ++V+ +P P
Sbjct: 71 ETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAP 118
Score = 52.3 bits (125), Expect = 2e-08
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 2/67 (2%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
L+ F+ G+V K+I D+ T +S G+GFVN+ A AI E++G +L + I+V+
Sbjct: 51 LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110
Query: 103 A--RPSS 107
A RPS+
Sbjct: 111 ANDRPSA 117
Score = 33.5 bits (76), Expect = 0.064
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ GL L + F +G ++ ++++ D+ E RS +G GFV
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR---ETGRS------------RGFGFV 81
Query: 175 RFNQHIEAEHAMQELNG 191
FN A A+ E++G
Sbjct: 82 NFNDEGAATAAISEMDG 98
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 53.4 bits (129), Expect = 1e-09
Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 6/67 (8%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T+E L+ FS G + + + ++K GFV + + E A+RAI ELNG +Q
Sbjct: 14 LTEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAELNGTTVQGVQ 67
Query: 98 IKVSYAR 104
+KVS AR
Sbjct: 68 LKVSLAR 74
Score = 36.5 bits (85), Expect = 0.002
Identities = 31/97 (31%), Positives = 41/97 (42%), Gaps = 25/97 (25%)
Query: 110 IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
K LYV G +T+E L+ F P+G II N+ S E K
Sbjct: 2 RKGNTLYVHG--YGLTEEILKKAFSPFGNII------------NI-SM-----EKE---K 38
Query: 170 GIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GFV F + A+ A+ ELNGT +G + V A
Sbjct: 39 NCGFVTFEKMESADRAIAELNGTTVQGVQ--LKVSLA 73
Score = 30.7 bits (70), Expect = 0.17
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
TE+ +L + F PFG + N+ + ++ K GFV + A AI LNG +
Sbjct: 15 TEE-ILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIAELNGTTVQGVQ 67
Query: 343 LQVSF 347
L+VS
Sbjct: 68 LKVSL 72
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 53.3 bits (129), Expect = 2e-09
Identities = 25/66 (37%), Positives = 44/66 (66%), Gaps = 2/66 (3%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P ++T+E+L+ FS G+VE +L+R+K + G+ FV + EDAE A+ +LNGL L
Sbjct: 6 LPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKLNGLVL 63
Query: 94 QNKSIK 99
++++
Sbjct: 64 DGRTLR 69
Score = 49.9 bits (120), Expect = 2e-08
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL P + L + F P+G V+ V++VR+ + +GF FV + ++A A++ L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 334 NGYALGDR 341
NG L R
Sbjct: 59 NGLVLDGR 66
Score = 44.5 bits (106), Expect = 2e-06
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 17/79 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV LP +T+EDL F PYG + R++ +K +G FV
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK-----------------DRPRGFAFV 43
Query: 175 RFNQHIEAEHAMQELNGTI 193
F +AE A+++LNG +
Sbjct: 44 EFASPEDAEAALKKLNGLV 62
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 53.6 bits (129), Expect = 2e-09
Identities = 28/95 (29%), Positives = 50/95 (52%), Gaps = 18/95 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VSGLP +T+E+LE LF+ +G + + R++ + SG P KG+ +V
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLV----------TNRSGKP------KGLAYV 48
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ A A+ +++GT + + I+V +N P
Sbjct: 49 EYENESSASQAVLKMDGTEIKEKT--ISVAISNPP 81
Score = 51.6 bits (124), Expect = 9e-09
Identities = 23/77 (29%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V+ +P ++T+EEL+ LF G V+S +L+ +++ + G +V Y A +A++++
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVLKM 63
Query: 89 NGLKLQNKSIKVSYARP 105
+G +++ K+I V+ + P
Sbjct: 64 DGTEIKEKTISVAISNP 80
Score = 37.8 bits (88), Expect = 7e-04
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTY---KCKGFGFVCMTNYDEAVFAI 330
+FV L L +LF G V++V++V T K KG +V N A A+
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLV----TNRSGKPKGLAYVEYENESSASQAV 60
Query: 331 QSLNGYALGDRLLQVS 346
++G + ++ + V+
Sbjct: 61 LKMDGTEIKEKTISVA 76
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 53.8 bits (130), Expect = 2e-09
Identities = 20/76 (26%), Positives = 36/76 (47%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + T+ +L+ F G ++ +L+RDK T + GY F+ + D + A
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 89 NGLKLQNKSIKVSYAR 104
+G K+ + + V R
Sbjct: 64 DGKKIDGRRVLVDVER 79
Score = 37.6 bits (88), Expect = 9e-04
Identities = 14/45 (31%), Positives = 29/45 (64%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L +T ++ L + F +G ++ +++VRD +T K +G+ F+
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFI 48
Score = 28.4 bits (64), Expect = 1.8
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+ L T+ L F YG I R+ VR +G P +G F+
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRL---------VRDKKTGKP------RGYAFI 48
Query: 175 RFNQHIEAEHAMQELNG 191
F + + A + +G
Sbjct: 49 EFEHERDMKAAYKYADG 65
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 53.0 bits (128), Expect = 3e-09
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
LIV +P T+ +L+ LFS G V + R + G+ FV + DAE+AI +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKGV 60
Query: 89 NGLKLQNKSIKVSYA 103
NG K++ + + V +A
Sbjct: 61 NGKKIKGRPVAVDWA 75
Score = 52.3 bits (126), Expect = 4e-09
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL + + L +LF PFG V V + R P K KGF FV T+ +A AI+ +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 334 NGYALGDRLLQVSF 347
NG + R + V +
Sbjct: 61 NGKKIKGRPVAVDW 74
Score = 36.8 bits (86), Expect = 0.001
Identities = 28/93 (30%), Positives = 40/93 (43%), Gaps = 20/93 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP-QISKGIGF 173
L V LP T+ DL+ LF P+G + I P P KG F
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTI-----------------PRKPDGKKKGFAF 44
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V+F +AE A++ +NG +G P+ V +A
Sbjct: 45 VQFTSKADAEKAIKGVNGKKIKG--RPVAVDWA 75
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 52.7 bits (127), Expect = 3e-09
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+EEL FS G++ LI+ + + F+ + R + A RA+ N L+NK++
Sbjct: 16 TKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVESENHSMLKNKTM 73
Query: 99 KVSY 102
V Y
Sbjct: 74 HVQY 77
Score = 46.9 bits (112), Expect = 4e-07
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV L+P+ L + F G + V +++ F F+ A A++S
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRAN--HTNAFAFIKFEREQAAARAVESE 63
Query: 334 NGYALGDRLLQVSFK 348
N L ++ + V +K
Sbjct: 64 NHSMLKNKTMHVQYK 78
Score = 29.2 bits (66), Expect = 0.69
Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 17/84 (20%)
Query: 110 IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
I + +++V L +T+E+L F +G I+ ++ + + +F
Sbjct: 1 IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI---KRANHTNAF------------ 45
Query: 170 GIGFVRFNQHIEAEHAMQELNGTI 193
F++F + A A++ N ++
Sbjct: 46 --AFIKFEREQAAARAVESENHSM 67
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 52.6 bits (127), Expect = 3e-09
Identities = 29/75 (38%), Positives = 46/75 (61%), Gaps = 6/75 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
SNL +Y +T+E+L+ LF VGEV+ K+ D++ +S G V + + EDAERAI
Sbjct: 6 SNL--HY---DVTEEDLEELFGRVGEVKKVKINYDRS-GRSEGTADVVFEKREDAERAIK 59
Query: 87 ELNGLKLQNKSIKVS 101
+ NG+ L + ++V
Sbjct: 60 QFNGVLLDGQPMQVE 74
Score = 41.8 bits (99), Expect = 2e-05
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL + + L +LFG G V+ VK+ D + + +G V ++A AI+
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61
Query: 334 NGYALGDRLLQVSF 347
NG L + +QV
Sbjct: 62 NGVLLDGQPMQVEL 75
Score = 30.3 bits (69), Expect = 0.23
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 18/91 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L VS L +T+EDLE LF G + +I D+ S+G V
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGR----------------SEGTADV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
F + +AE A+++ NG + +G +P+ V+
Sbjct: 47 VFEKREDAERAIKQFNGVLLDG--QPMQVEL 75
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 51.8 bits (125), Expect = 5e-09
Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T EEL+ LF G V C ++++ YGFV+ EDAE AI L
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53
Query: 89 NGLKLQNKSIKV 100
NG + K I V
Sbjct: 54 NGYEFMGKRINV 65
Score = 48.4 bits (116), Expect = 7e-08
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL T L LF +G V VV++ +GFV M ++A AI++L
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53
Query: 334 NGYALGDRLLQV 345
NGY + + V
Sbjct: 54 NGYEFMGKRINV 65
Score = 38.4 bits (90), Expect = 3e-04
Identities = 27/90 (30%), Positives = 37/90 (41%), Gaps = 25/90 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T E+L LF YGT+ CD + K GFV
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTE----CD-------------------VVKNYGFV 38
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVK 204
+ +AE A++ LNG G + I V+
Sbjct: 39 HMEEEEDAEDAIKALNGYEFMG--KRINVE 66
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 51.9 bits (125), Expect = 6e-09
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSS-VGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
S LIV +P ++T+ EL+ FS GE+ KL+R + +S F+ Y E+A++A
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEEAQKAK 59
Query: 86 IELNGLKLQNKSIKVSYA 103
N + I V +A
Sbjct: 60 DYFNNTYINTSKISVEFA 77
Score = 33.8 bits (78), Expect = 0.018
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 19/93 (20%)
Query: 115 LYVSGLPKHMTQEDLENLF-RPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L V LP +T+ +L+ F + G I ++L + S+ I F
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED----------------GKSRRIAF 46
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ + EA+ A N T + I+V+FA
Sbjct: 47 IGYKTEEEAQKAKDYFNNTYINTSK--ISVEFA 77
Score = 29.5 bits (67), Expect = 0.47
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFG-PFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL + L + F G + +VK++R K + F+ +EA A
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAKDY 61
Query: 333 LNGYALGDRLLQVSF 347
N + + V F
Sbjct: 62 FNNTYINTSKISVEF 76
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 51.0 bits (123), Expect = 7e-09
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
L LFS G VE KL++ K G+ FV + E AE+A+ LNG+ + ++V Y
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Query: 103 A 103
+
Sbjct: 56 S 56
Score = 44.4 bits (106), Expect = 2e-06
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 5/60 (8%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
L++LF PFG V+ +K+++ GF FV + + A A+Q LNG G R L+V +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Score = 30.2 bits (69), Expect = 0.16
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 22/76 (28%)
Query: 131 NLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
LF P+G + ++L K G FV F+ AE A+Q LN
Sbjct: 3 KLFSPFGNVEKIKLLKKK--------------------PGFAFVEFSTEEAAEKAVQYLN 42
Query: 191 GTIPEGASEPITVKFA 206
G + G P+ V ++
Sbjct: 43 GVLFGGR--PLRVDYS 56
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 52.0 bits (125), Expect = 7e-09
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 12/79 (15%)
Query: 38 MTQEELQHLFSSVGE-VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
M + ++ F+S+GE V S K+IR+K T GY FV + AER + +LNG +
Sbjct: 11 MDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPI--- 67
Query: 97 SIKVSYARPSSEAIKRANL 115
P S KR L
Sbjct: 68 --------PGSNPPKRFKL 78
Score = 30.0 bits (68), Expect = 0.35
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 16/87 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYG-TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L++ L +M + ++ F G T+++ +I +R+ ++G P G F
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKI---------IRNKLTGGP------AGYCF 46
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEP 200
V F AE + +LNG G++ P
Sbjct: 47 VEFADEATAERCLHKLNGKPIPGSNPP 73
Score = 29.6 bits (67), Expect = 0.58
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 279 LAPETEDNVLWQLFGPFG-AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
L P ++N + + F G V +VK++R+ T G+ FV + A + LNG
Sbjct: 7 LEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNG 64
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 51.2 bits (123), Expect = 1e-08
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +N L ++F +G V V +V+D +T K KG F+ + ++A +++L
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 334 NGYALGDRLLQVS 346
N L R L+ S
Sbjct: 64 NNKELFGRTLKCS 76
Score = 48.9 bits (117), Expect = 6e-08
Identities = 24/77 (31%), Positives = 44/77 (57%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S + V+ +P ++T +L +FS G+V +++DK T +S G F+ + EDA + +
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
Query: 87 ELNGLKLQNKSIKVSYA 103
LN +L +++K S A
Sbjct: 62 ALNNKELFGRTLKCSIA 78
Score = 44.2 bits (105), Expect = 3e-06
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YVS LP +T DL +F YG ++ I+ DK + SKG+ F+
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRK---------------SKGVAFI 48
Query: 175 RFNQHIEAEHAMQELNGTI 193
F +A ++ LN
Sbjct: 49 LFLDREDAHKCVKALNNKE 67
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 51.4 bits (122), Expect = 1e-08
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 15/85 (17%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
+ + + NLY+ GLP + T +DL L +PYG I++++ + DK ++
Sbjct: 3 DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNK--------------- 47
Query: 168 SKGIGFVRFNQHIEAEHAMQELNGT 192
KG GFV F+ A+ A+ L +
Sbjct: 48 CKGYGFVDFDSPAAAQKAVSALKAS 72
Score = 43.3 bits (101), Expect = 1e-05
Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL + +P T ++L L G++ S K I DKTT + GYGFV++ A++A+
Sbjct: 8 TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVS 67
Query: 87 ELNGLKLQNKSIKVSYARP 105
L +Q + K P
Sbjct: 68 ALKASGVQAQMAKQQEQDP 86
Score = 42.5 bits (99), Expect = 2e-05
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ L P T D L +L P+G + + K + D T KCKG+GFV + A A+ +L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 50.6 bits (122), Expect = 2e-08
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 4/65 (6%)
Query: 38 MTQEELQHLFSSVGEVESCKLIR--DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
T+E++ LFS G+++ ++I D+ T G+ FV YY EDAE A+ LNG KL +
Sbjct: 10 TTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDD 67
Query: 96 KSIKV 100
+ I+V
Sbjct: 68 RIIRV 72
Score = 41.8 bits (99), Expect = 3e-05
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL+ T + +++LF G ++ + + D T GF FV ++A A++ L
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 334 NGYALGDRLLQVSF 347
NG L DR+++V +
Sbjct: 61 NGTKLDDRIIRVDW 74
Score = 36.0 bits (84), Expect = 0.003
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L + T+E + LF G I RI+ M + TP G FV
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDI--KRII---MGLDRFT----KTP------CGFCFV 45
Query: 175 RFNQHIEAEHAMQELNGTI 193
+ +AE+A++ LNGT
Sbjct: 46 EYYTREDAENAVKYLNGTK 64
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by YNL110C
from Saccharomyces cerevisiae, and localizes to the
nucleoplasm and nucleolus. Nop15p has been identified as
a component of a pre-60S particle. It interacts with RNA
components of the early pre-60S particles. Furthermore,
Nop15p binds directly to a pre-rRNA transcript in vitro
and is required for pre-rRNA processing. It functions as
a ribosome synthesis factor required for the 5' to 3'
exonuclease digestion that generates the 5' end of the
major, short form of the 5.8S rRNA as well as for
processing of 27SB to 7S pre-rRNA. Nop15p also play a
specific role in cell cycle progression. Nop15p contains
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 50.6 bits (121), Expect = 2e-08
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I++ +L + L + F FG V+NV+V R +T K +GF+ N + A A +S+
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 334 NGYALGDRLLQV 345
N Y L ++LQV
Sbjct: 62 NNYLLMGKVLQV 73
Score = 49.4 bits (118), Expect = 5e-08
Identities = 21/74 (28%), Positives = 37/74 (50%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + ++P ++EL+ FS G V++ ++ R K T S YGF+ + E A A +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 89 NGLKLQNKSIKVSY 102
N L K ++V
Sbjct: 62 NNYLLMGKVLQVHV 75
Score = 27.5 bits (61), Expect = 2.7
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ LP +++L+ F +GT+ R+ RS +G SK GF+
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRV---------ARSKKTGN------SKHYGFI 46
Query: 175 RFNQHIEAEHAMQELNG 191
+F A A + +N
Sbjct: 47 QFLNPEVAAIAAKSMNN 63
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 50.5 bits (120), Expect = 2e-08
Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 3/81 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + +T+ + LFS +G +SCK+I + T+ Y FV +Y DA A+ +
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59
Query: 89 NGLKLQNKSIKVSYA-RPSSE 108
NG K+ K +KV++A PSS+
Sbjct: 60 NGRKILGKEVKVNWATTPSSQ 80
Score = 28.2 bits (62), Expect = 1.7
Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL+ + + ++ QLF G ++ K++ + + + FV + +A A+ ++
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 59
Query: 334 NGYALGDRLLQVSFKT 349
NG + + ++V++ T
Sbjct: 60 NGRKILGKEVKVNWAT 75
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 50.6 bits (121), Expect = 2e-08
Identities = 26/94 (27%), Positives = 48/94 (51%), Gaps = 17/94 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K T++++E +F PYG + ++ D+M + S+G FV
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM----------------KQSRGCAFV 45
Query: 175 RFNQHIEAEHAMQELNGT-IPEGASEPITVKFAN 207
+++ A+ A++ LNG G +P+ V+FA+
Sbjct: 46 KYSSKEMAQAAIKALNGVYTMRGCDQPLIVRFAD 79
Score = 43.3 bits (102), Expect = 8e-06
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + T++E++ +FS G VE ++RD+ QS G FV Y E A+ AI L
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60
Query: 89 NGLKLQ---NKSIKVSYARP 105
NG+ ++ + V +A P
Sbjct: 61 NGVYTMRGCDQPLIVRFADP 80
Score = 41.0 bits (96), Expect = 5e-05
Identities = 18/62 (29%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L + + + ++F P+G V+++ ++RD + +G FV ++ + A AI++L
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60
Query: 334 NG 335
NG
Sbjct: 61 NG 62
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 50.1 bits (120), Expect = 2e-08
Identities = 21/68 (30%), Positives = 43/68 (63%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL+ + +++ +++ FG +G + +V++ DP + + KGFG+V ++ + A A+ +L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 334 NGYALGDR 341
G L R
Sbjct: 61 GGTDLLGR 68
Score = 43.5 bits (103), Expect = 5e-06
Identities = 15/62 (24%), Positives = 31/62 (50%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++ + F GE+ S +L D + + G+G+V + E A+ A+ L G L + +
Sbjct: 11 DEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPV 70
Query: 99 KV 100
++
Sbjct: 71 RL 72
Score = 34.7 bits (80), Expect = 0.006
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 15/78 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L ++ + F YG I + R+ D SG P KG G+V
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPD---------SGRP------KGFGYV 45
Query: 175 RFNQHIEAEHAMQELNGT 192
F+ A+ A+ L GT
Sbjct: 46 EFSSQEAAQAALDALGGT 63
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 50.0 bits (120), Expect = 2e-08
Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ ++ +P + E+L L S+ G V++C+ + K+ ++ V Y E A++A+ +L
Sbjct: 3 IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVNKL 59
Query: 89 NGLKLQNKSIKVSY 102
NG + + +KVSY
Sbjct: 60 NGHEYEGSKLKVSY 73
Score = 40.0 bits (94), Expect = 1e-04
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 18/75 (24%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
+S +P H+ EDL++L YGT+ C+++ +++ + V+ T E P+
Sbjct: 5 ISNIPPHVRWEDLDSLLSTYGTV----KNCEQVPTKSETATVNVTYESPE---------- 50
Query: 177 NQHIEAEHAMQELNG 191
+A+ A+ +LNG
Sbjct: 51 ----QAQQAVNKLNG 61
Score = 37.3 bits (87), Expect = 8e-04
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVR-DPQTYKCKGFGFVCMTNYDEAVFAIQS 332
I + N+ P L L +G V+N + V +T V + ++A A+
Sbjct: 3 IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAVNK 58
Query: 333 LNGYALGDRLLQVSFKT 349
LNG+ L+VS+
Sbjct: 59 LNGHEYEGSKLKVSYIP 75
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 49.6 bits (119), Expect = 3e-08
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S LIV +P+ + +++L+ LF + G + +L K + +GFV Y E+A++A+
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59
Query: 87 ELNGLKLQNKSIKV 100
N + I V
Sbjct: 60 HFNNSFIDTSKITV 73
Score = 38.1 bits (89), Expect = 4e-04
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 16/78 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V LPK + ++ L LF +GTI ++ K R F GFV
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK--DGKFRKF--------------GFV 46
Query: 175 RFNQHIEAEHAMQELNGT 192
+ EA+ A++ N +
Sbjct: 47 GYKTEEEAQKALKHFNNS 64
Score = 32.3 bits (74), Expect = 0.044
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL +++ L +LF FG + +V++ K + FGFV +EA A++
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDG-KFRKFGFVGYKTEEEAQKALKHF 61
Query: 334 NGYALGDRLLQVSF 347
N + + V
Sbjct: 62 NNSFIDTSKITVEI 75
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 77
Score = 49.7 bits (119), Expect = 4e-08
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+LIV +P T+++L+ FS+ GE+ ++ +D T QS G+GFV + ED + +
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58
Score = 41.6 bits (98), Expect = 3e-05
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V L +T + L F FG + V+V +DP+T + KGFGFV +Y++ V +
Sbjct: 4 VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS--QR 61
Query: 336 YALGDRLLQVSFKTHK 351
+ + R V K
Sbjct: 62 HMIDGRWCDVKIPNSK 77
Score = 33.1 bits (76), Expect = 0.028
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+L V GLP T++DL++ F +G ++ ++ D +G SKG GF
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDP---------KTGQ------SKGFGF 45
Query: 174 VRFNQHIEAEHAMQE 188
VRF + + + +
Sbjct: 46 VRFADYEDQVKVLSQ 60
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 49.5 bits (119), Expect = 4e-08
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ + + +L FS G+V ++IRD+ + +S G +V +Y E A + L G +L
Sbjct: 7 LSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA-LGLTGQRL 65
Query: 94 QNKSIKV 100
+ I V
Sbjct: 66 LGQPIMV 72
Score = 44.5 bits (106), Expect = 2e-06
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ + + L++ F G V++V+++RD + + KG +V + + A+ L
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60
Query: 334 NGYAL 338
G L
Sbjct: 61 TGQRL 65
Score = 31.0 bits (71), Expect = 0.12
Identities = 22/89 (24%), Positives = 32/89 (35%), Gaps = 18/89 (20%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V L + + DL F G + RI+ D+ S SKG+ +V
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDR---------NSRR------SKGVAYVE 47
Query: 176 FNQHIEAEHAMQELNGTIPEGASEPITVK 204
F A+ L G G PI V+
Sbjct: 48 FYDEESVPLAL-GLTGQRLLGQ--PIMVQ 73
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 49.5 bits (119), Expect = 4e-08
Identities = 18/63 (28%), Positives = 34/63 (53%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++ L+ +FS+ G V+ L D+ GY +V + EDAE+AI ++G ++ + +
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70
Query: 99 KVS 101
V
Sbjct: 71 TVE 73
Score = 37.5 bits (88), Expect = 6e-04
Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L +++ ++ L+ +F YGT+ + D+ + +G +V
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDRE---------------VNLPRGYAYV 45
Query: 175 RFNQHIEAEHAMQELNG 191
F +AE A++ ++G
Sbjct: 46 EFESPEDAEKAIKHMDG 62
Score = 37.1 bits (87), Expect = 9e-04
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V L + L ++F +G V++V + D + +G+ +V + ++A AI+ +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 334 NG 335
+G
Sbjct: 61 DG 62
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 49.6 bits (118), Expect = 4e-08
Identities = 20/65 (30%), Positives = 40/65 (61%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ T +S G+ FV + R +D++ A+ NG++L + I
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Query: 99 KVSYA 103
+V Y+
Sbjct: 72 RVDYS 76
Score = 45.3 bits (107), Expect = 1e-06
Identities = 24/79 (30%), Positives = 42/79 (53%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + V VV D +T + +GF FV D++ A++
Sbjct: 1 CLGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60
Query: 333 LNGYALGDRLLQVSFKTHK 351
NG L R ++V + K
Sbjct: 61 ANGMELDGRRIRVDYSITK 79
Score = 29.5 bits (66), Expect = 0.53
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
V GL + T+ DL +F YG + ++ D+ S+G FV F
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGR---------------SRGFAFVYF 48
Query: 177 NQHIEAEHAMQELNGTIPEG 196
+ +++ AM+ NG +G
Sbjct: 49 ERIDDSKEAMEHANGMELDG 68
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 49.2 bits (118), Expect = 5e-08
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL P L F +G +++V V R+P GF FV + +A A+++L
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRAL 56
Query: 334 NGYALGDRLLQVSF 347
+G + ++V
Sbjct: 57 DGRRICGNRVRVEL 70
Score = 42.2 bits (100), Expect = 1e-05
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ EL+ F G + S + R+ G+ FV + DAE A+ L+G ++ +
Sbjct: 12 TKRELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAVRALDGRRICGNRV 66
Query: 99 KVSYARP 105
+V +R
Sbjct: 67 RVELSRG 73
Score = 38.8 bits (91), Expect = 2e-04
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 22/94 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YV L T+ +LE+ F YG + +V +V+ P P G FV
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPL------------RSV--WVARNP--P----GFAFV 41
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
F +AE A++ L+G G + V+ +
Sbjct: 42 EFEDPRDAEDAVRALDGRRICGN--RVRVELSRG 73
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 49.2 bits (118), Expect = 7e-08
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLI---RDKTTAQSLGYGFVNYYRTEDAER 83
+NL V + +T+E L F G + S K++ ++ ++ GFV + DAER
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
A+ EL+G + +K+ + +
Sbjct: 62 ALDELDGKDVMGYELKLGWGKA 83
Score = 47.3 bits (113), Expect = 3e-07
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
NLYV L +T+E L F +G + + +I+ + E R+ G
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC------------G 49
Query: 173 FVRFNQHIEAEHAMQELNGTIPEG 196
FV F +AE A+ EL+G G
Sbjct: 50 FVAFMNRADAERALDELDGKDVMG 73
Score = 46.9 bits (112), Expect = 4e-07
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVV---RDPQTYKCKGFGFVCMTNYDEAVFAI 330
++V NL P+ + VL Q FG FG + +VK++ + + + + GFV N +A A+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 331 QSLNGYALGDRLLQVSF 347
L+G + L++ +
Sbjct: 64 DELDGKDVMGYELKLGW 80
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 48.6 bits (116), Expect = 7e-08
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 30 IVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
+V + P T +E+++ LF G + C + + + FV + +EDA +A+ L+
Sbjct: 4 VVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALH 55
Query: 90 GLKLQNKSIKVSYAR 104
G ++ + V + +
Sbjct: 56 GSRIDGSVLTVEFVK 70
Score = 34.7 bits (80), Expect = 0.006
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 26/93 (27%)
Query: 115 LYVSGL-PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+V G P +ED+E LF P+G ++ CD I K F
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVR----CD-------------------IRKTFAF 38
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F +A A++ L+G+ +G+ +TV+F
Sbjct: 39 VEFEDSEDATKALEALHGSRIDGSV--LTVEFV 69
Score = 33.6 bits (77), Expect = 0.015
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV P T + + +LF PFG + + + F FV + ++A A+++
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEA 53
Query: 333 LNGYALGDRLLQVSFKT 349
L+G + +L V F
Sbjct: 54 LHGSRIDGSVLTVEFVK 70
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 48.6 bits (116), Expect = 9e-08
Identities = 24/72 (33%), Positives = 43/72 (59%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +++ E ++ + Q F PFG ++++ + DP T K KGF FV + A A++ +
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62
Query: 334 NGYALGDRLLQV 345
NG LG R ++V
Sbjct: 63 NGVMLGGRNIKV 74
Score = 37.0 bits (86), Expect = 0.001
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
++ ++ FS G ++S + D T + G+ FV Y E A+ A+ ++NG+ L ++IK
Sbjct: 14 EDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIK 73
Query: 100 V 100
V
Sbjct: 74 V 74
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 48.5 bits (116), Expect = 1e-07
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V +++TQE+L LF + +E C L RD T +S G+ +V Y A A +L
Sbjct: 3 LFVV-VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKL 61
Query: 89 NGLKL 93
NG +
Sbjct: 62 NGFEY 66
Score = 38.8 bits (91), Expect = 2e-04
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV T++ L +LF ++ + RDP T K KGF +V +N A++A +
Sbjct: 2 RLFVVVSKSVTQEQ-LHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60
Query: 333 LNG--YALGDRL 342
LNG Y G+RL
Sbjct: 61 LNGFEYPPGNRL 72
Score = 30.8 bits (70), Expect = 0.16
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 16/77 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V + K +TQE L LF II CD SKG +V
Sbjct: 3 LFVV-VSKSVTQEQLHRLFD----IIPGLEYCDLKRDPY-----------TGKSKGFAYV 46
Query: 175 RFNQHIEAEHAMQELNG 191
++ A +A ++LNG
Sbjct: 47 TYSNPASAIYAKEKLNG 63
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 48.2 bits (115), Expect = 1e-07
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V P+T ++ + ++F P+GAV+ VK++ F FV + + A+ A S+
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53
Query: 334 NGYALGDRLLQVSF 347
+G L + L V++
Sbjct: 54 HGKVLNNNPLYVTY 67
Score = 45.5 bits (108), Expect = 8e-07
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V P ++ ++ +FS G V+ K+I + FV + E A RA +
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53
Query: 89 NGLKLQNKSIKVSY 102
+G L N + V+Y
Sbjct: 54 HGKVLNNNPLYVTY 67
Score = 31.2 bits (71), Expect = 0.11
Identities = 19/89 (21%), Positives = 29/89 (32%), Gaps = 25/89 (28%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV P ++ + +F PYG + E+ IS FV
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAV----------------------KEVKMIS-NFAFV 38
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITV 203
F A A ++G + P+ V
Sbjct: 39 EFESLESAIRAKDSVHGKVLNN--NPLYV 65
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 48.1 bits (115), Expect = 1e-07
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V +P +T+EE + FS G+V +L++D T +S G+GFV + +E A +
Sbjct: 4 VGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVT-FDSESAVERVFSAGM 62
Query: 91 LKLQNKSIKVSYA 103
L+L K ++V A
Sbjct: 63 LELGGKQVEVKRA 75
Score = 47.4 bits (113), Expect = 2e-07
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV L P+ + + F FG V + ++++D T + +GFGFV + + AV + S
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60
Query: 334 NGYALGDRLLQVSFK 348
LG + QV K
Sbjct: 61 GMLELGGK--QVEVK 73
Score = 42.0 bits (99), Expect = 2e-05
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 26/96 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP +T+E+ + F +G ++ ++++ D S+G GFV
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGR---------------SRGFGFV 46
Query: 175 RFNQHIEAE----HAMQELNGTIPEGASEPITVKFA 206
F+ E M EL G + + VK A
Sbjct: 47 TFDSESAVERVFSAGMLELGG-------KQVEVKRA 75
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 48.1 bits (115), Expect = 1e-07
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+F+ L+ ET D+ L F +G + + V++DP T + +GFGFV
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFV 46
Score = 39.7 bits (93), Expect = 1e-04
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
T + L++ FS GE+ C +++D T +S G+GFV + + + A
Sbjct: 12 TDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57
Score = 29.3 bits (66), Expect = 0.68
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 15/72 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ GL T + L+N F +G I C M N + S+G GFV
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITD----CVVMKDPNTKR-----------SRGFGFV 46
Query: 175 RFNQHIEAEHAM 186
F E + AM
Sbjct: 47 TFASASEVDAAM 58
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 47.8 bits (114), Expect = 1e-07
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA--VFAIQ 331
+FV NL+ ET ++ L FG G ++ V+++ + KCKGF FV + A +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 332 SLNGYALGD 340
LNG AL
Sbjct: 61 HLNGRALRV 69
Score = 29.7 bits (67), Expect = 0.36
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T++EL+ F VG + +++ + + + G+ FV++ E A A L G L +++
Sbjct: 11 TEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---LKGKHLNGRAL 67
Query: 99 KVSYA 103
+V Y
Sbjct: 68 RVEYG 72
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 48.1 bits (115), Expect = 2e-07
Identities = 26/77 (33%), Positives = 48/77 (62%), Gaps = 2/77 (2%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVG-EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
N+ +++ +P ++T+E++++ S G E + +L+R KTT S G+ FV + E+A R
Sbjct: 2 NNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR- 60
Query: 85 IIELNGLKLQNKSIKVS 101
+ELN KLQ + K++
Sbjct: 61 WMELNQGKLQLQDYKIT 77
Score = 30.8 bits (70), Expect = 0.17
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 17/78 (21%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYG-TIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ + GLP +T+ED+ N +G R++ K +G S+G
Sbjct: 4 TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKT---------TG------ASRGFA 48
Query: 173 FVRFNQHIEAEHAMQELN 190
FV F EA M ELN
Sbjct: 49 FVEFMSLEEATRWM-ELN 65
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 47.6 bits (114), Expect = 2e-07
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 37 TMTQEELQHLFSSVGEVESCKLIRDKTTAQSL---GYGFVNYYRTEDAERAIIELNGLKL 93
+ +++L+ +FS GEVES ++ + + Q G+ FV + AE A ++LNG +L
Sbjct: 11 KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA-LQLNGTEL 69
Query: 94 QNKSIKVS 101
+ I VS
Sbjct: 70 GGRKISVS 77
Score = 44.6 bits (106), Expect = 2e-06
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKV---VRDPQTYKCKGFGFVCMTNYDEAVFAI 330
I+V NL + +++ L +F FG V+++++ + Q GF FV + A A+
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 331 QSLNGYALGDRLLQVS 346
Q LNG LG R + VS
Sbjct: 63 Q-LNGTELGGRKISVS 77
Score = 39.5 bits (93), Expect = 1e-04
Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 17/90 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCD-KMASENVRSFVSGTPEIPQISKGIGF 173
+YV L + ++DL +F +G + + RI + G F
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLN-------------NGFAF 49
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITV 203
V F AE+A+Q LNGT G I+V
Sbjct: 50 VTFKDASSAENALQ-LNGTELGG--RKISV 76
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 48.1 bits (114), Expect = 2e-07
Identities = 26/79 (32%), Positives = 43/79 (54%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N D+A A +
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70
Query: 333 LNGYALGDRLLQVSFKTHK 351
NG L R ++V F K
Sbjct: 71 ANGMELDGRRIRVDFSITK 89
Score = 45.4 bits (107), Expect = 2e-06
Identities = 18/65 (27%), Positives = 38/65 (58%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ + +S G+ FV + +DA+ A NG++L + I
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81
Query: 99 KVSYA 103
+V ++
Sbjct: 82 RVDFS 86
Score = 30.8 bits (69), Expect = 0.22
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V GL + T+ DL +F YG I I+ D+ + S+G FV
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR---------------SRGFAFV 56
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A + NG +G
Sbjct: 57 YFENVDDAKEAKERANGMELDG 78
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 47.2 bits (113), Expect = 2e-07
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
P+ + ++L+ G+V + RD+ G G V + ED ERA+ +L+G + +
Sbjct: 9 PEGASWQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERALRKLDGTEFR 63
Query: 95 NKSIKV 100
+ ++V
Sbjct: 64 GRRVRV 69
Score = 32.2 bits (74), Expect = 0.044
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 22/88 (25%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
VSGLP+ + +DL++ R G + + + D +G G V F
Sbjct: 5 VSGLPEGASWQDLKDFGRQAGDVTYADVDRD--------------------QEGEGVVEF 44
Query: 177 NQHIEAEHAMQELNGTIPEGASEPITVK 204
+ E A+++L+GT G + V+
Sbjct: 45 TSQEDMERALRKLDGTEFRGRR--VRVE 70
Score = 32.2 bits (74), Expect = 0.051
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 13/74 (17%)
Query: 276 VYNLAPETEDNVLWQLFGPF----GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
V L WQ F G V V RD + G G V T+ ++ A++
Sbjct: 5 VSGLPEGAS----WQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERALR 55
Query: 332 SLNGYALGDRLLQV 345
L+G R ++V
Sbjct: 56 KLDGTEFRGRRVRV 69
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and
2 (NRF-1 and NRF-2), CREB (cAMP-response
element-binding protein), and estrogen-related receptor
alpha (ERRalpha). It interacts indirectly with the
NRF-2beta subunit through host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. Furthermore, like
PGC-1alpha and PGC-1beta, PRC can transactivate a
number of NRF-dependent nuclear genes required for
mitochondrial respiratory function, including those
encoding cytochrome c, 5-aminolevulinate synthase,
Tfam, and TFB1M, and TFB2M. Further research indicates
that PRC may also act as a sensor of metabolic stress
that orchestrates a redox-sensitive program of
inflammatory gene expression. PRC is a multi-domain
protein containing an N-terminal activation domain, an
LXXLL coactivator signature, a central proline-rich
region, a tetrapeptide motif (DHDY) responsible for HCF
binding, a C-terminal arginine/serine-rich (SR) domain,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 91
Score = 47.6 bits (113), Expect = 3e-07
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P MT+ EL+ FS GE+E C + ++ YGFV Y TE+A AI NG KL
Sbjct: 10 IPSRMTRSELKDRFSVFGEIEECTI---HFRSEGDNYGFVTYRYTEEAFAAI--ENGHKL 64
Query: 94 Q 94
+
Sbjct: 65 R 65
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 47.0 bits (112), Expect = 3e-07
Identities = 24/68 (35%), Positives = 35/68 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + + T T+E+L+ LFS G + L DK T + G+ FV Y E A +A EL
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 89 NGLKLQNK 96
+G Q +
Sbjct: 65 DGTVFQGR 72
Score = 42.8 bits (101), Expect = 1e-05
Identities = 25/72 (34%), Positives = 35/72 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NLA + L +LF +G + V + D T K KGF FV + AV A L
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 334 NGYALGDRLLQV 345
+G RLL +
Sbjct: 65 DGTVFQGRLLHL 76
Score = 36.6 bits (85), Expect = 0.002
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ L T+EDLE LF YG + + DK+ + KG FV
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKK---------------PKGFAFV 49
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
+ A A EL+GT+ +G
Sbjct: 50 TYMIPEHAVKAFAELDGTVFQG 71
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 46.9 bits (112), Expect = 4e-07
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V +P Q +L +F + V+S +L+RDK T + G+ +V + E + A +E +G
Sbjct: 6 VGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA-LEYDG 63
Query: 91 LKLQNKSIKVSYA 103
++S++V A
Sbjct: 64 ALFDDRSLRVDIA 76
Score = 32.3 bits (74), Expect = 0.044
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 275 FVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
FV NL T L +F +V++V++VRD +T K KGF +V + + A++ +
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62
Query: 335 GYALGDRLLQV 345
G DR L+V
Sbjct: 63 GALFDDRSLRV 73
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 47.0 bits (112), Expect = 4e-07
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
L V +P+ + +++L+ LF G++ +++DK T G F+ Y E A +A
Sbjct: 8 LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
Score = 44.3 bits (105), Expect = 3e-06
Identities = 30/104 (28%), Positives = 47/104 (45%), Gaps = 21/104 (20%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
+AIK L+V +P+++ ++DL LF +G I +L DK
Sbjct: 3 DDAIK---LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG--------------- 44
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNG--TIPEGASEPITVKFANS 208
+ KG F+ + A A L+ T+P G + PI VK A+S
Sbjct: 45 MHKGCAFLTYCARESALKAQSALHEQKTLP-GMNRPIQVKPADS 87
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 46.4 bits (110), Expect = 4e-07
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V + +QEEL+ LF + G V SC ++R + FV+ A+RAI EL
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54
Query: 89 NGLKLQNKSIKV 100
NG +L + + V
Sbjct: 55 NGRELHGRKLVV 66
Score = 41.0 bits (96), Expect = 3e-05
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV N+ +T L LF +GAV + V+R F FV + A AI+ L
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54
Query: 334 NGYALGDRLLQV 345
NG L R L V
Sbjct: 55 NGRELHGRKLVV 66
Score = 32.5 bits (74), Expect = 0.033
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 23/77 (29%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V + + +QE+L LF YG +++ ++ + FV
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-----------------------RQFAFV 39
Query: 175 RFNQHIEAEHAMQELNG 191
A+ A++ELNG
Sbjct: 40 HLRGEAAADRAIEELNG 56
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 46.8 bits (112), Expect = 5e-07
Identities = 26/73 (35%), Positives = 39/73 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+ D+ + +L G V + K V+DP T K K FGF + + A+ A++ L
Sbjct: 3 VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62
Query: 334 NGYALGDRLLQVS 346
NG LG + L V
Sbjct: 63 NGLELGGKKLLVK 75
Score = 39.1 bits (92), Expect = 2e-04
Identities = 22/71 (30%), Positives = 39/71 (54%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V +P+ ++ + ++ L G+V S K ++D +T + +GF + E A RA+ LNG
Sbjct: 5 VGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLLNG 64
Query: 91 LKLQNKSIKVS 101
L+L K + V
Sbjct: 65 LELGGKKLLVK 75
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 46.1 bits (110), Expect = 5e-07
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 18/90 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V LP +T +DL++LFR G ++ + + D + RS KG G V
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD----NDGRS------------KGFGTV 44
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVK 204
F +A+ A++ NG EG + V+
Sbjct: 45 LFESPEDAQRAIEMFNGYDLEG--RELEVR 72
Score = 42.3 bits (100), Expect = 1e-05
Identities = 30/76 (39%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 274 IFVYNLAPETEDNVLWQ----LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
IFV NL P +V WQ LF G V V D + KGFG V + ++A A
Sbjct: 1 IFVRNL-PF---SVTWQDLKDLFRECGNVLRADVKTDNDG-RSKGFGTVLFESPEDAQRA 55
Query: 330 IQSLNGYALGDRLLQV 345
I+ NGY L R L+V
Sbjct: 56 IEMFNGYDLEGRELEV 71
Score = 39.2 bits (92), Expect = 2e-04
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 9/76 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRD--KTTA--QSLGYGFVNYYRTEDAERA 84
+ V +P ++T ++L+ LF G V +R KT +S G+G V + EDA+RA
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNV-----LRADVKTDNDGRSKGFGTVLFESPEDAQRA 55
Query: 85 IIELNGLKLQNKSIKV 100
I NG L+ + ++V
Sbjct: 56 IEMFNGYDLEGRELEV 71
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 46.4 bits (110), Expect = 6e-07
Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA----VFA 329
+FV L + + L + F FG V+ +V+ D QT K +GFGFV N+D A V
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61
Query: 330 IQSLNGY 336
+NG+
Sbjct: 62 FHPINGH 68
Score = 38.0 bits (88), Expect = 5e-04
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + +L FS G VE ++I DK T + G+GFV + + A++A + +
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV-V 60
Query: 89 NGLKLQNKSIKVSYARPSSE 108
+ ++V A P E
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80
Score = 35.3 bits (81), Expect = 0.005
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 15/71 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V GL + + DL F +G + + ++ DK + +G GFV
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKK---------------RGFGFV 46
Query: 175 RFNQHIEAEHA 185
F H A+ A
Sbjct: 47 YFQNHDSADKA 57
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 46.2 bits (110), Expect = 7e-07
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 17/82 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VS +P DL +F +G I+ I+ N R SKG GFV
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF------NERG-----------SKGFGFV 45
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A ++L+GT+ EG
Sbjct: 46 TFANSADADRAREKLHGTVVEG 67
Score = 45.1 bits (107), Expect = 2e-06
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V N+ D L Q+FG FG + +V+++ + + KGFGFV N +A A + L
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER--GSKGFGFVTFANSADADRAREKL 60
Query: 334 NGYALGDRLLQVSFKT 349
+G + R ++V+ T
Sbjct: 61 HGTVVEGRKIEVNNAT 76
Score = 43.6 bits (103), Expect = 5e-06
Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V+ +P +L+ +F G + ++I ++ S G+GFV + + DA+RA +L
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRAREKL 60
Query: 89 NGLKLQNKSIKVSYA 103
+G ++ + I+V+ A
Sbjct: 61 HGTVVEGRKIEVNNA 75
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 46.2 bits (109), Expect = 7e-07
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + +T+ + LFS +G +SCK+I D TA + Y FV ++ A ++ +
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 89 NGLKLQNKSIKVSYA 103
NG K+ K +KV++A
Sbjct: 60 NGRKIMGKEVKVNWA 74
Score = 28.5 bits (63), Expect = 1.2
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL+ + + ++ QLF G ++ K++ D T + FV + A ++ ++
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 334 NGYALGDRLLQVSF 347
NG + + ++V++
Sbjct: 60 NGRKIMGKEVKVNW 73
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 46.0 bits (110), Expect = 7e-07
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+F+ L+ +T + L + F +G V + +++DP T + +GFGFV
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFV 45
Score = 45.7 bits (109), Expect = 9e-07
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
T+E L+ FS GEV C +++D T +S G+GFV + ++ +
Sbjct: 11 TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL 57
Score = 32.9 bits (76), Expect = 0.029
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 15/63 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ GL T+E L F YG ++ I+ D I S+G GFV
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDP---------------ITGRSRGFGFV 45
Query: 175 RFN 177
F
Sbjct: 46 TFA 48
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 45.8 bits (109), Expect = 7e-07
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
IFV L+PET + + + FG FG + +++ D +T K +GF F+ + +E V I
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS-EEPVKKI 57
Score = 31.6 bits (72), Expect = 0.098
Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V + T+E+++ F G + +L DK T + G+ F+ + +E+ + I+E
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFIT-FDSEEPVKKILET 60
Query: 89 NGLKLQNKSIKVSYA 103
+ K ++V A
Sbjct: 61 QFHVIGGKKVEVKKA 75
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 46.0 bits (110), Expect = 7e-07
Identities = 18/55 (32%), Positives = 30/55 (54%)
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVS 346
F FG V +++ R +T K KG+ FV + + A +++N Y L +RLL+
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74
Score = 44.5 bits (106), Expect = 3e-06
Identities = 21/73 (28%), Positives = 34/73 (46%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + ++P + EL+ FS G V +L R K T +S GY FV + E A+ +
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 89 NGLKLQNKSIKVS 101
N L + +K
Sbjct: 62 NNYLLFERLLKCK 74
Score = 26.4 bits (59), Expect = 6.7
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ LP + +L F +GT+ R+ S + ++ SKG FV
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRL------SRSKKTGK---------SKGYAFV 46
Query: 175 RFNQHIEAEHAMQELNG 191
F A+ + +N
Sbjct: 47 EFESPEVAKIVAETMNN 63
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 46.1 bits (110), Expect = 8e-07
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGP-FGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV +L P+ +D L++ F + + + KVV D Q +G+GFV ++ E A+
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62
Query: 333 LNGY-ALGDRLLQVSFKTHK 351
+ G LG + ++VS K
Sbjct: 63 MQGASGLGGKPIRVSLAIPK 82
Score = 40.4 bits (95), Expect = 8e-05
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 43 LQHLFSSV-GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG-LKLQNKSIKV 100
L FS + K++ D+ S GYGFV + + +RA+ E+ G L K I+V
Sbjct: 18 LYEFFSKRYPSCKGAKVVLDQN-GNSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRV 76
Query: 101 SYARP 105
S A P
Sbjct: 77 SLAIP 81
Score = 33.8 bits (78), Expect = 0.014
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
S+G GFVRF+ E + A+ E+ G G +PI V A
Sbjct: 41 NSRGYGFVRFSDESEQKRALTEMQGASGLG-GKPIRVSLAIP 81
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 46.0 bits (108), Expect = 8e-07
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 15/83 (18%)
Query: 110 IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
+ + NLY+ GLP T +DL L +PYG I++++ + DK ++ K
Sbjct: 2 LSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQ---------------CK 46
Query: 170 GIGFVRFNQHIEAEHAMQELNGT 192
G GFV F+ A+ A+ L
Sbjct: 47 GYGFVDFDSPAAAQKAVASLKAN 69
Score = 42.9 bits (100), Expect = 1e-05
Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL + +P T ++L L G++ S K I DK T Q GYGFV++ A++A+
Sbjct: 5 TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVA 64
Query: 87 ELNGLKLQNKSIK 99
L +Q + K
Sbjct: 65 SLKANGVQAQMAK 77
Score = 41.0 bits (95), Expect = 4e-05
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ L P T D L +L P+G + + K + D T +CKG+GFV + A A+ SL
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 45.4 bits (108), Expect = 1e-06
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV NL + L ++F G V + D + K +G G V + EAV AI
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59
Query: 334 NGYALGDRLLQV 345
NG L DR ++V
Sbjct: 60 NGQMLFDRPMRV 71
Score = 32.3 bits (74), Expect = 0.041
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 16/77 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V+ L + + L+ +F+ G ++ + I DK S+G+G V
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGK----------------SRGMGVV 44
Query: 175 RFNQHIEAEHAMQELNG 191
+F IEA A+ NG
Sbjct: 45 QFEHPIEAVQAISMFNG 61
Score = 28.9 bits (65), Expect = 0.73
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++L+ +F G+V + DK +S G G V + +A +AI NG L ++ +
Sbjct: 11 GWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPM 69
Query: 99 KV 100
+V
Sbjct: 70 RV 71
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 45.5 bits (108), Expect = 1e-06
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ T+++++ FS G+VE L+ DK T + G+GFV + +ED + E++ ++
Sbjct: 7 LSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVT-FESEDVVDKVCEIHFHEI 65
Query: 94 QNKSIKV 100
NK ++
Sbjct: 66 NNKMVEC 72
Score = 36.3 bits (84), Expect = 0.002
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
IFV L+ T ++ + + F FG V++ ++ D QT + +GFGFV + D
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54
Score = 27.4 bits (61), Expect = 2.8
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 15/62 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL + T++D++ F +G + + ++ DK + + +G GFV
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRH---------------RGFGFV 46
Query: 175 RF 176
F
Sbjct: 47 TF 48
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 45.5 bits (107), Expect = 1e-06
Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV---CMTNYDEAVFA 329
+F+ L+ ET D+ L + F +G + + V+RDPQT + +GFGFV C+ D A+ A
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63
Score = 36.6 bits (84), Expect = 0.002
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
T + L+ F G + C ++RD T +S G+GFV Y E+ + A+
Sbjct: 15 TDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 49.5 bits (118), Expect = 2e-06
Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 54/210 (25%)
Query: 22 VNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
V + + + +P + +++++ L S G++++ LI+D T S GY F Y
Sbjct: 291 VLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVT 350
Query: 82 ERAIIELNGLKLQNKSIKVSYA-------RPSSE-----------AIKRANLYVSGLPKH 123
+ AI LNG + + V A + A+ ++ L + G P
Sbjct: 351 DVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTK 410
Query: 124 MTQ--------------------EDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
+ Q ED++ F YG +I I R
Sbjct: 411 VVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVI---------PRPNGDRNS- 460
Query: 164 IPQISKGIG--FVRFNQHIEAEHAMQELNG 191
+ G+G F+ + AE AM+ +NG
Sbjct: 461 ----TPGVGKVFLEYADVRSAEKAMEGMNG 486
Score = 42.6 bits (100), Expect = 2e-04
Identities = 20/82 (24%), Positives = 34/82 (41%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I++ NL ++ + +L FG ++ +++D T KG+ F + AI +L
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
NG GD L V
Sbjct: 358 NGKDTGDNKLHVQRACVGANQA 379
Score = 30.2 bits (68), Expect = 1.6
Identities = 41/238 (17%), Positives = 79/238 (33%), Gaps = 42/238 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ LP ++ ++ ++ L +G D A ++ +G +SKG F
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFG---------DLKAFNLIKDIATG------LSKGYAFC 342
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAM 234
+ + A+ LNG + V+ A G +A N A A
Sbjct: 343 EYKDPSVTDVAIAALNGKDTGD--NKLHVQRAC--VGANQATIDTSNGMAPVTLLAKALS 398
Query: 235 RHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNV--LWQLF 292
+ + L N + + E E+ + F
Sbjct: 399 QSILQIGGKPTKVV-------QLTNLVTGDDLMDDE-----------EYEEIYEDVKTEF 440
Query: 293 GPFGAVQNVKVVR-DPQTYKCKGFG--FVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+G + N+ + R + G G F+ + A A++ +NG DR++ +F
Sbjct: 441 SKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAF 498
Score = 28.3 bits (63), Expect = 7.0
Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 41 EELQHLFSSVGEVESCKLIR-DKTTAQSLGYG--FVNYYRTEDAERAIIELNGLKLQNKS 97
E+++ FS G + + + R + + G G F+ Y AE+A+ +NG K ++
Sbjct: 434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRV 493
Query: 98 IKVSYARPSS 107
+ ++
Sbjct: 494 VVAAFYGEDC 503
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 44.9 bits (107), Expect = 2e-06
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
+FV L + + L + F +G V++V++V D +T K +GF FV +YD
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYD 52
Score = 43.0 bits (102), Expect = 7e-06
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+T+E+L+ FS G VES +++ DK T + G+ FV + + ++ ++
Sbjct: 11 VTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVL 59
Score = 39.5 bits (93), Expect = 1e-04
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V GL + +T+EDL F YG + + I+ DK +G +G FV
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE---------TGKK------RGFAFV 46
Query: 175 RFNQHIEAEHAMQELNGTI 193
F+ + + + + TI
Sbjct: 47 TFDDYDPVDKIVLQKYHTI 65
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 45.0 bits (106), Expect = 2e-06
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 8/77 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + T+T+E L+ F G++E K ++D Y F+++ + A +A+ E+
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55
Query: 89 NGLKLQNKSIKVSYARP 105
NG +L+ ++I++ +A+P
Sbjct: 56 NGKELEGENIEIVFAKP 72
Score = 38.4 bits (89), Expect = 3e-04
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA + +L + FG FG ++ VK K K + F+ D AV A++ +
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 55
Query: 334 NGYALGDRLLQVSF 347
NG L +++ F
Sbjct: 56 NGKELEGENIEIVF 69
Score = 30.0 bits (67), Expect = 0.30
Identities = 26/92 (28%), Positives = 38/92 (41%), Gaps = 25/92 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L +T+E LE F +G + E V+ K F+
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKL------------ERVKKL-----------KDYAFI 40
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F++ A AM+E+NG EG E I + FA
Sbjct: 41 HFDERDGAVKAMEEMNGKELEG--ENIEIVFA 70
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 44.7 bits (105), Expect = 2e-06
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 21/82 (25%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y G+ +T++ + F P+G I+ R+ DK G FV
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDK---------------------GYSFV 41
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
RFN H A HA+ +NGT EG
Sbjct: 42 RFNSHESAAHAIVSVNGTTIEG 63
Score = 37.3 bits (86), Expect = 0.001
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
V +T++ ++ FS G++ ++ DK GY FV + E A AI+ +NG +
Sbjct: 8 VTSGLTEQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVSVNGTTI 61
Query: 94 QNKSIKVSYARPS 106
+ +K + + +
Sbjct: 62 EGHVVKCYWGKET 74
Score = 36.2 bits (83), Expect = 0.002
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 285 DNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYAL 338
+ ++ Q F PFG + V+V D KG+ FV +++ A AI S+NG +
Sbjct: 14 EQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSVNGTTI 61
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 44.1 bits (104), Expect = 3e-06
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T++E++ LF G+V C +I++ YGFV+ A+ AI L
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNL 54
Query: 89 NGLKLQNKSIKV 100
+ KL +I V
Sbjct: 55 HHYKLHGVAINV 66
Score = 39.9 bits (93), Expect = 1e-04
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL PE + + LF +G V ++ K +GFV M + A AI++L
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54
Query: 334 NGYAL 338
+ Y L
Sbjct: 55 HHYKL 59
Score = 34.1 bits (78), Expect = 0.010
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 23/76 (30%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T++++ +LF YG ++ CD I K GFV
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLE----CD-------------------IIKNYGFV 39
Query: 175 RFNQHIEAEHAMQELN 190
+ A+ A++ L+
Sbjct: 40 HMDDKTAADEAIRNLH 55
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 44.2 bits (105), Expect = 3e-06
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T EELQ F S G + ++ DK T Q G+ ++ + E A++ LN + + + I
Sbjct: 12 TPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRGRQI 70
Query: 99 KVS 101
KV+
Sbjct: 71 KVT 73
Score = 35.7 bits (83), Expect = 0.003
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 16/78 (20%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V + T E+L+ F+ GTI ILCDK +G P KG ++
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKF---------TGQP------KGFAYIE 47
Query: 176 FNQHIEAEHAMQELNGTI 193
F E+A+ LN +
Sbjct: 48 FLDKSSVENALL-LNESE 64
Score = 28.4 bits (64), Expect = 1.3
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV N+ T L + F G + + ++ D T + KGF ++ + A+ L
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60
Query: 334 NGYALGDRLLQVS 346
N R ++V+
Sbjct: 61 NESEFRGRQIKVT 73
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 44.1 bits (104), Expect = 3e-06
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V T T +EL+ LF G V C ++D Y FV+ R E+A AI L
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEAL 54
Query: 89 NGLKLQNKSIKV 100
NG +++ + I V
Sbjct: 55 NGKEVKGRRINV 66
Score = 41.0 bits (96), Expect = 3e-05
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 272 WCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
W IFV N++ + L LF FG V V K + FV M +EA+ AI+
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIE 52
Query: 332 SLNGYALGDRLLQV 345
+LNG + R + V
Sbjct: 53 ALNGKEVKGRRINV 66
Score = 27.5 bits (61), Expect = 2.4
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 23/82 (28%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V + T ++L LF +G ++ CDK+ K FV
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVE----CDKV-------------------KDYAFV 39
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
+ EA A++ LNG +G
Sbjct: 40 HMEREEEALAAIEALNGKEVKG 61
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 44.2 bits (104), Expect = 4e-06
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + +L++LF G + V + +D + K K FGFVC + + +AI L
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEG-KPKSFGFVCFKHSESVPYAIALL 62
Query: 334 NGYALGDRLLQVS 346
NG L R ++V
Sbjct: 63 NGIRLYGRPIKVH 75
Score = 35.7 bits (82), Expect = 0.003
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + +E L LF G + + +DK + +GFV + +E AI L
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62
Query: 89 NGLKLQNKSIKVS 101
NG++L + IKV
Sbjct: 63 NGIRLYGRPIKVH 75
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 44.4 bits (105), Expect = 4e-06
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAII 86
+ V +P++ ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63
Query: 87 ELNGLK 92
L+ +K
Sbjct: 64 ALHNMK 69
Score = 39.4 bits (92), Expect = 2e-04
Identities = 30/102 (29%), Positives = 49/102 (48%), Gaps = 21/102 (20%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
AIK ++V +P+ +++DL LF YG + +L D+ P+ S
Sbjct: 1 AIK---MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDR---------SQNPPQ----S 44
Query: 169 KGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
KG FV F +EA++A+ + T+P G PI +K A+
Sbjct: 45 KGCCFVTFYTRKAALEAQNALHNMK-TLP-GMHHPIQMKPAD 84
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 44.2 bits (105), Expect = 4e-06
Identities = 21/59 (35%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKL----IRDKTTAQSLGYGFVNYYRTEDAERAI 85
V +P T+ EL+ F GE+E L D YGFV Y DA RAI
Sbjct: 7 VGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN-------YGFVTYRYACDAFRAI 58
Score = 35.4 bits (82), Expect = 0.006
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTI 139
R +YV +P T+ +L F+P+G I
Sbjct: 2 RRVIYVGKIPIDTTRSELRQRFQPFGEI 29
Score = 28.1 bits (63), Expect = 1.9
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKG--FGFVCMTNYDEAVFAIQ 331
I+V + +T + L Q F PFG ++ + + ++ G +GFV +A AI+
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITL-----HFRDDGDNYGFVTYRYACDAFRAIE 59
Query: 332 SLN 334
N
Sbjct: 60 HGN 62
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 44.9 bits (106), Expect = 4e-06
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
L V +P T+E L FS G V + DK+T ++ G GFV + +
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
Score = 40.7 bits (95), Expect = 1e-04
Identities = 18/56 (32%), Positives = 26/56 (46%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+ +FV NL + + L F FG+V+ V D T + KG GFVC +
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY 56
Score = 36.1 bits (83), Expect = 0.005
Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 15/73 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T+E L F +G++ + + DK +KG GFV
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTG---------------RAKGTGFV 48
Query: 175 RFNQHIEAEHAMQ 187
F ++
Sbjct: 49 CFKDQYTYNACLK 61
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 43.8 bits (104), Expect = 4e-06
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T+ +EL+ FS G+V+SC + DK T S GYGFV+ + + D L
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVS-FSSRDG------L 54
Query: 89 NGLKLQNKSI 98
+ K I
Sbjct: 55 ENALQKQKHI 64
Score = 38.1 bits (89), Expect = 5e-04
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDE 325
+FV NL L + F FG V++ V D +T KG+GFV ++ D
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDG 53
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.9 bits (104), Expect = 4e-06
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQS-LGYGFVNYYRTEDAERA 84
S ++V +P T +EL+ LFS+ GE+++ +L + T S G+GFV++ +DA+RA
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59
Score = 33.5 bits (77), Expect = 0.019
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP-QTYKCKGFGFVCMTNYDEAVFAIQS 332
I V N+ E L +LF FG ++ V++ + T +GFGFV +A A ++
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62
Query: 333 L 333
L
Sbjct: 63 L 63
Score = 26.6 bits (59), Expect = 5.9
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 14/73 (19%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
V +P T ++L LF +G + T R L KM +G GFV F
Sbjct: 5 VRNIPFEATVKELRELFSTFGELKTVR-LPKKMTG-------------TGSHRGFGFVDF 50
Query: 177 NQHIEAEHAMQEL 189
+A+ A + L
Sbjct: 51 ITKQDAKRAFKAL 63
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 43.7 bits (104), Expect = 4e-06
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 8/68 (11%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL--QNK 96
+ EL+ F G + + A ++ Y E A+ A L G L +
Sbjct: 11 SLAELEREFDRFGAIRRIDYDPGRNYA------YIEYESIEAAQAAKEALRGFPLGGPGR 64
Query: 97 SIKVSYAR 104
++V +A
Sbjct: 65 RLRVDFAD 72
Score = 36.8 bits (86), Expect = 0.001
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L P T L + F FGA++ + + + ++ + + A A ++L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG------RNYAYIEYESIEAAQAAKEAL 54
Query: 334 NGYALG--DRLLQVSF 347
G+ LG R L+V F
Sbjct: 55 RGFPLGGPGRRLRVDF 70
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 43.9 bits (103), Expect = 4e-06
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 10/76 (13%)
Query: 274 IFVYNLAPETEDNVLWQLFGPF--GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
++V NL ET ++ + + FG F G V+ VK +RD + FV T+ ++AV A+
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD--------YAFVHFTSREDAVHAMN 55
Query: 332 SLNGYALGDRLLQVSF 347
+LNG L ++V+
Sbjct: 56 NLNGTELEGSCIEVTL 71
Score = 38.9 bits (90), Expect = 3e-04
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 13/78 (16%)
Query: 33 YVPQTM---TQEELQHLFSSV--GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
YV M +++ ++ F G VE K IRD Y FV++ EDA A+
Sbjct: 5 YVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD--------YAFVHFTSREDAVHAMNN 56
Query: 88 LNGLKLQNKSIKVSYARP 105
LNG +L+ I+V+ A+P
Sbjct: 57 LNGTELEGSCIEVTLAKP 74
Score = 28.5 bits (63), Expect = 1.1
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITV 203
FV F +A HAM LNGT EG+ +T+
Sbjct: 41 FVHFTSREDAVHAMNNLNGTELEGSCIEVTL 71
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 43.5 bits (102), Expect = 5e-06
Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 8/77 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + T+T+E L+ FS G++E K ++D Y FV++ + A RA+ E+
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55
Query: 89 NGLKLQNKSIKVSYARP 105
NG +++ + I++ A+P
Sbjct: 56 NGKEIEGEEIEIVLAKP 72
Score = 36.2 bits (83), Expect = 0.002
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA + +L + F FG ++ VK K K + FV D AV A+ +
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEERDAAVRAMDEM 55
Query: 334 NGYALGDRLLQV 345
NG + +++
Sbjct: 56 NGKEIEGEEIEI 67
Score = 27.3 bits (60), Expect = 2.8
Identities = 23/82 (28%), Positives = 31/82 (37%), Gaps = 23/82 (28%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L +T+E LE F +G + E V+ K FV
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKL------------ERVKKL-----------KDYAFV 40
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F + A AM E+NG EG
Sbjct: 41 HFEERDAAVRAMDEMNGKEIEG 62
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 43.6 bits (103), Expect = 5e-06
Identities = 19/37 (51%), Positives = 26/37 (70%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
TQE L+ FS GEV C +++DKTT +S G+GFV +
Sbjct: 12 TQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48
Score = 37.9 bits (88), Expect = 7e-04
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 15/73 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V GL TQE L F YG ++ I+ DK S+G GFV
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDK---------------TTNRSRGFGFV 46
Query: 175 RFNQHIEAEHAMQ 187
+F +
Sbjct: 47 KFKDPNCVGTVLA 59
Score = 35.9 bits (83), Expect = 0.003
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L+ ET L + F +G V + +++D T + +GFGFV
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFV 46
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 43.6 bits (103), Expect = 5e-06
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
+ +L+ FS G V+ K++ D+ S GYGFV + EDA++ + E N L ++K +
Sbjct: 15 NENDLRKFFSQYGTVKEVKIVNDRAGV-SKGYGFVTFETQEDAQKILQEANRLCFRDKKL 73
Query: 99 KVSYA 103
+ A
Sbjct: 74 NIGQA 78
Score = 35.9 bits (83), Expect = 0.003
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV + +T +N L + F +G V+ VK+V D + KG+GFV ++A +Q
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQEA 63
Query: 334 NGYALGDRLLQVS 346
N D+ L +
Sbjct: 64 NRLCFRDKKLNIG 76
Score = 33.6 bits (77), Expect = 0.019
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V G+ + DL F YGT+ +I+ D+ +SKG GFV
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAG----------------VSKGYGFV 48
Query: 175 RFNQHIEAEHAMQELN 190
F +A+ +QE N
Sbjct: 49 TFETQEDAQKILQEAN 64
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 44.1 bits (105), Expect = 6e-06
Identities = 30/103 (29%), Positives = 42/103 (40%), Gaps = 21/103 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGT---------IITSRILCDKMASENVRSFVSGTPEIP 165
L + LPK + ++ L+ LF + I +I+ D + V G
Sbjct: 3 LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDL---KRVDPNGKGK---- 55
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNG--TIPEGASEPITVKFA 206
SKG GFV F H A A++ LN I PI V+FA
Sbjct: 56 --SKGYGFVEFTNHEHALKALRALNNNPEIFGPDKRPI-VEFA 95
Score = 40.3 bits (95), Expect = 1e-04
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 15/76 (19%)
Query: 29 LIVNYVPQTMTQEELQHLF-SSVGE--------VESCKLIRDK------TTAQSLGYGFV 73
L + +P+++ +++L+ LF +V E ++ K++RD +S GYGFV
Sbjct: 3 LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFV 62
Query: 74 NYYRTEDAERAIIELN 89
+ E A +A+ LN
Sbjct: 63 EFTNHEHALKALRALN 78
Score = 39.5 bits (93), Expect = 2e-04
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 15/74 (20%)
Query: 276 VYNLAPETEDNVLWQLF---------GPFGAVQNVKVVRDPQ------TYKCKGFGFVCM 320
+ NL ++ L +LF ++ VK++RD + K KG+GFV
Sbjct: 5 IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64
Query: 321 TNYDEAVFAIQSLN 334
TN++ A+ A+++LN
Sbjct: 65 TNHEHALKALRALN 78
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 43.7 bits (104), Expect = 7e-06
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 51 GEVESCKLIR-DKTTAQSLGYG--FVNYYRTEDAERAIIELNGLKLQNKSIKVS 101
G+V S + R + G G FV + EDA++A + L G K +++ S
Sbjct: 36 GKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVAS 89
Score = 31.4 bits (72), Expect = 0.16
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 295 FGAVQNVKVVRDPQTYKCK---GFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVS 346
+G V +V + R G FV + ++A A +L G R + S
Sbjct: 35 YGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVAS 89
Score = 28.7 bits (65), Expect = 1.4
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 170 GIG--FVRFNQHIEAEHAMQELNG 191
G+G FV F +A+ A L G
Sbjct: 55 GVGKVFVEFADVEDAQKAQLALAG 78
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 47.4 bits (112), Expect = 7e-06
Identities = 24/79 (30%), Positives = 46/79 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +++ E ++ + + F PFG ++++ + DP T K KGF FV + A A++ +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG LG R ++V ++ P
Sbjct: 170 NGQMLGGRNIKVGRPSNMP 188
Score = 46.6 bits (110), Expect = 1e-05
Identities = 42/202 (20%), Positives = 84/202 (41%), Gaps = 31/202 (15%)
Query: 2 MKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRD 61
H++ Q + Q + + V + + ++ ++ F G ++S + D
Sbjct: 84 KAHQQQQLENQQRQQQRQQALAIM-CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWD 142
Query: 62 KTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSS-------------E 108
T + G+ FV Y E A+ A+ ++NG L ++IKV RPS+ E
Sbjct: 143 PATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG--RPSNMPQAQPIIDMVQEE 200
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
A K +YV+ + +++ D++++F +G I+ ++ R+
Sbjct: 201 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL---------ARAPTGRG------H 245
Query: 169 KGIGFVRFNQHIEAEHAMQELN 190
KG GF+ +N A+ +N
Sbjct: 246 KGYGFIEYNNLQSQSEAIASMN 267
Score = 45.4 bits (107), Expect = 3e-05
Identities = 22/81 (27%), Positives = 38/81 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V ++ P+ + + +F FG + ++ R P KG+GF+ N AI S+
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266
Query: 334 NGYALGDRLLQVSFKTHKPLP 354
N + LG + L+V P
Sbjct: 267 NLFDLGGQYLRVGKCVTPPDA 287
Score = 45.1 bits (106), Expect = 4e-05
Identities = 19/70 (27%), Positives = 35/70 (50%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V V +++ +++ +F + GE+ C+L R T GYGF+ Y + AI +N
Sbjct: 209 VASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNL 268
Query: 91 LKLQNKSIKV 100
L + ++V
Sbjct: 269 FDLGGQYLRV 278
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 43.0 bits (102), Expect = 8e-06
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD--EAVFAIQ 331
+FV N+ ED L LF FG ++ + CK GF+ ++ YD A A +
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTL-------YTACKHRGFIMVSYYDIRAARRAKR 56
Query: 332 SLNGYALGDRLLQVSF 347
+L G LG R L + F
Sbjct: 57 ALQGTELGGRKLDIHF 72
Score = 42.6 bits (101), Expect = 1e-05
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 41 EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
EEL+ LF G++ + T + G+ V+YY A RA L G +L + + +
Sbjct: 16 EELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRALQGTELGGRKLDI 70
Query: 101 SYARP 105
++ P
Sbjct: 71 HFSIP 75
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 43.0 bits (102), Expect = 8e-06
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 14/77 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VSGLP + + +L +LFRP+ SR+ + G + P GFV
Sbjct: 3 LFVSGLPSDVKERELAHLFRPFPGYEASRL---VFKEKK------GGEKQPV-----GFV 48
Query: 175 RFNQHIEAEHAMQELNG 191
F+ A AM L G
Sbjct: 49 DFSSAQCAAAAMDALQG 65
Score = 32.6 bits (75), Expect = 0.036
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLI-RDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V+ +P + + EL HLF E+ +L+ ++K + GFV++ + A A+
Sbjct: 3 LFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMDA 62
Query: 88 LNGLKL 93
L G +
Sbjct: 63 LQGYRF 68
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 43.0 bits (101), Expect = 8e-06
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 23/94 (24%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R L+V LP +T+ED + LF YG S + ++ +G
Sbjct: 1 RCRLFVGNLPTDITEEDFKKLFEKYGE--PSEVFINR-------------------DRGF 39
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
GF+R AE A EL+GTI + + P+ ++F
Sbjct: 40 GFIRLESRTLAEIAKAELDGTILK--NRPLRIRF 71
Score = 41.8 bits (98), Expect = 2e-05
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P +T+E+ + LF GE + RD+ G+GF+ AE A EL
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 57
Query: 89 NGLKLQNKSIKVSY 102
+G L+N+ +++ +
Sbjct: 58 DGTILKNRPLRIRF 71
Score = 37.2 bits (86), Expect = 0.001
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + + +LF +G V + RD +GFGF+ + + A A L
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 57
Query: 334 NGYALGDRLLQVSF 347
+G L +R L++ F
Sbjct: 58 DGTILKNRPLRIRF 71
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition, steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway. It binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 76
Score = 43.0 bits (101), Expect = 9e-06
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+F+ L ET D+ L + FG FG V + V+RD T + +GFGF+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49
Score = 41.4 bits (97), Expect = 3e-05
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
T + L+ F GEV C ++RD T +S G+GF+ +
Sbjct: 11 TDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 42.7 bits (101), Expect = 9e-06
Identities = 26/92 (28%), Positives = 37/92 (40%), Gaps = 25/92 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ LP + D+E F+ YG I EI + G GFV
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRI----------------------REI-NLKNGFGFV 38
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F +A+ A+ ELNG E E + V+ A
Sbjct: 39 EFEDPRDADDAVYELNGK--ELCGERVIVEHA 68
Score = 37.7 bits (88), Expect = 6e-04
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
G+GFV + DA+ A+ ELNG +L + + V +AR
Sbjct: 34 GFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
Score = 28.1 bits (63), Expect = 1.3
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ L + + + F +G ++ + + GFGFV + +A A+ L
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREINLKN--------GFGFVEFEDPRDADDAVYEL 53
Query: 334 NGYAL-GDRLL 343
NG L G+R++
Sbjct: 54 NGKELCGERVI 64
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 42.5 bits (101), Expect = 1e-05
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA-ERAIIELNGLKL 93
++T+ +L+ FS G V ++I+ K G+ +++ +E ++ LNG K
Sbjct: 8 SPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLNGTKW 67
Query: 94 QNKSIKVSYAR 104
+ +K+ A+
Sbjct: 68 KGSVLKIEEAK 78
Score = 42.5 bits (101), Expect = 1e-05
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 274 IFVYNLAP-ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L+P TE + L + F FG V +V++++ +GF ++
Sbjct: 2 LFVGGLSPSVTESD-LEERFSRFGTVSDVEIIKKKDAGPDRGFAYI 46
Score = 32.1 bits (74), Expect = 0.069
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTI 139
L+V GL +T+ DLE F +GT+
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTV 26
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 42.2 bits (100), Expect = 1e-05
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 12/63 (19%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL + +++E+L+ +FS G++ L + GYGFV + EDA A+
Sbjct: 7 NLNTDK----VSKEDLEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAAVAG 54
Query: 88 LNG 90
NG
Sbjct: 55 ENG 57
Score = 32.6 bits (75), Expect = 0.030
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 24/78 (30%)
Query: 115 LYVSGLP-KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V L +++EDLE +F YG I+ + KG GF
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISLH-----------------------KGYGF 39
Query: 174 VRFNQHIEAEHAMQELNG 191
V+F+ +A A+ NG
Sbjct: 40 VQFDNEEDARAAVAGENG 57
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 42.5 bits (100), Expect = 1e-05
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 17/94 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K + D+ +F P+G+I +L D+ S+G FV
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNG----------------QSRGCAFV 47
Query: 175 RFNQHIEAEHAMQELNGT-IPEGASEPITVKFAN 207
F A +A++ ++ + EG S P+ VKFA+
Sbjct: 48 TFASRQCALNAIKAMHHSQTMEGCSSPLVVKFAD 81
Score = 38.3 bits (89), Expect = 4e-04
Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ + +N + +F PFG+++ V+RD Q + +G FV + A+ AI+++
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKAM 62
Query: 334 N 334
+
Sbjct: 63 H 63
Score = 33.2 bits (76), Expect = 0.025
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + +++ +F+ G +E C ++RD+ QS G FV + + A AI +
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKAM 62
Query: 89 N 89
+
Sbjct: 63 H 63
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 42.5 bits (100), Expect = 1e-05
Identities = 20/58 (34%), Positives = 34/58 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+FV L +T D+ L + F +G + V+ DP T + +GFGF+ ++ DEA A++
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62
Score = 39.8 bits (93), Expect = 1e-04
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
+ L+ F+ G++ C ++ D T +S G+GF+ + ++A+ A +E + I
Sbjct: 15 SDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA-MEAQPHSIDGNQI 73
Query: 99 KVSYA 103
++ A
Sbjct: 74 ELKRA 78
Score = 34.4 bits (79), Expect = 0.012
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 15/73 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V GL + L F YG + C M N + S+G GF+
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTE----CVVMVDPNTK-----------RSRGFGFI 49
Query: 175 RFNQHIEAEHAMQ 187
F+ EA+ AM+
Sbjct: 50 TFSSADEADEAME 62
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 42.2 bits (100), Expect = 1e-05
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
LIV VP T++EL+ LFS G+V+S +L + K G+ FV + ++A+ A+ L
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Query: 89 NGLKLQNKSIKVSYA 103
L + + + YA
Sbjct: 62 KSTHLYGRHLVLEYA 76
Score = 36.4 bits (85), Expect = 0.002
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP----QTYKCKGFGFVCMTNYDEAVFA 329
+ V N+ E L +LF PFG VK VR P ++ +GF FV EA A
Sbjct: 3 LIVRNVPFEATKKELRELFSPFG---QVKSVRLPKKFDGSH--RGFAFVEFVTKQEAQNA 57
Query: 330 IQSLNGYAL-GDRLL 343
+++L L G L+
Sbjct: 58 MEALKSTHLYGRHLV 72
Score = 33.4 bits (77), Expect = 0.024
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 16/78 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V +P T+++L LF P+G + + R+ + F +G FV
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRL---------PKKFDGS-------HRGFAFV 46
Query: 175 RFNQHIEAEHAMQELNGT 192
F EA++AM+ L T
Sbjct: 47 EFVTKQEAQNAMEALKST 64
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 42.0 bits (99), Expect = 2e-05
Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+++++ F E+ S +L DK T + G+G V++ E + A ++L+G L + I
Sbjct: 12 TEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAA-LKLDGTVLCGRPI 69
Query: 99 KVS 101
+++
Sbjct: 70 RIA 72
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 41.9 bits (99), Expect = 2e-05
Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L+ T+ L QLF +G V K+V + ++ + FGFV M + +EA IQ L
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 334 NGYALGDRLLQV 345
+ L R++ V
Sbjct: 62 HRTELHGRVISV 73
Score = 39.6 bits (93), Expect = 1e-04
Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 15/79 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL+VSGL DL+ LF YG ++ ++I+ + S R F GF
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTN-ARSPGARCF--------------GF 45
Query: 174 VRFNQHIEAEHAMQELNGT 192
V EA +Q L+ T
Sbjct: 46 VTMASVEEAAKCIQHLHRT 64
Score = 37.7 bits (88), Expect = 5e-04
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLG---YGFVNYYRTEDAERA 84
NL V+ + T +L+ LFS G+V K++ T A+S G +GFV E+A +
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIV---TNARSPGARCFGFVTMASVEEAAKC 57
Query: 85 IIELNGLKLQNKSIKV 100
I L+ +L + I V
Sbjct: 58 IQHLHRTELHGRVISV 73
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 42.4 bits (100), Expect = 2e-05
Identities = 18/78 (23%), Positives = 37/78 (47%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
++L V V ++L+ LF G + + D T + G+ +V + DAE A+
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 87 ELNGLKLQNKSIKVSYAR 104
L+ + + I++ +A+
Sbjct: 61 YLDRTRFLGREIEIQFAQ 78
Score = 39.3 bits (92), Expect = 2e-04
Identities = 20/74 (27%), Positives = 39/74 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V N+A T + L +LFG +G + +V + D T + +GF +V + +A A+ L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 334 NGYALGDRLLQVSF 347
+ R +++ F
Sbjct: 63 DRTRFLGREIEIQF 76
Score = 28.9 bits (65), Expect = 1.0
Identities = 26/92 (28%), Positives = 38/92 (41%), Gaps = 17/92 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV + +DL LF YG I+ I D F + P +G +V
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLD---------FYTRRP------RGFAYV 47
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+F +AE A+ L+ T G I ++FA
Sbjct: 48 QFEDVRDAEDALYYLDRTRFLG--REIEIQFA 77
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 42.1 bits (98), Expect = 2e-05
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 15/81 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NLY+ GL T +DL L +PYG I++++ + DK ++ KG
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNK---------------CKGY 45
Query: 172 GFVRFNQHIEAEHAMQELNGT 192
GFV F+ A+ A+ L +
Sbjct: 46 GFVDFDSPSAAQKAVTALKAS 66
Score = 42.1 bits (98), Expect = 2e-05
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ L P T D L +L P+G + + K + D T KCKG+GFV + A A+ +L
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
Score = 40.5 bits (94), Expect = 6e-05
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+NL + + T ++L L G++ S K I DKTT + GYGFV++ A++A+
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
Query: 86 IELNGLKLQNKSIK 99
L +Q + K
Sbjct: 61 TALKASGVQAQMAK 74
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 41.8 bits (99), Expect = 2e-05
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL + L+ LFG +GA++ +++ +T +G FV + +A A L
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61
Query: 334 NGYALGDRLLQVSF 347
+G+ + +R L V +
Sbjct: 62 SGFNVANRYLVVLY 75
Score = 41.4 bits (98), Expect = 3e-05
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N L V +P ++ EEL LF G + IR T ++ G FV Y DA+ A
Sbjct: 2 NRILYVRNLPFKISSEELYDLFGKYGAIRQ---IRIGNTKETRGTAFVVYEDIYDAKNAC 58
Query: 86 IELNGLKLQNKSIKVSY 102
L+G + N+ + V Y
Sbjct: 59 DHLSGFNVANRYLVVLY 75
Score = 34.1 bits (79), Expect = 0.010
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV LP ++ E+L +LF YG I RI K ++G FV
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE------------------TRGTAFV 46
Query: 175 RFNQHIEAEHAMQELNG 191
+ +A++A L+G
Sbjct: 47 VYEDIYDAKNACDHLSG 63
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 41.8 bits (99), Expect = 2e-05
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+V + ++ +EL+ LFS GEV+ + + + + FV +Y AE A+ L
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDAL 58
Query: 89 NGLKLQNKSIKV 100
NG +KV
Sbjct: 59 NGRPFLGGRLKV 70
Score = 36.4 bits (85), Expect = 0.002
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD--EAVFAIQ 331
+ V+NL D L LF FG V++++ + K F YD A A+
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEF-------YDIRAAEAALD 56
Query: 332 SLNGYALGDRLLQV 345
+LNG L+V
Sbjct: 57 ALNGRPFLGGRLKV 70
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 41.9 bits (98), Expect = 2e-05
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+++L+ FS GEV C L D T +S G+GFV + +E ++ +++ KL K I
Sbjct: 11 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-VMDQKEHKLNGKVI 69
Score = 31.9 bits (72), Expect = 0.065
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+F+ L+ +T L F FG V + + DP T + +GFGFV
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV 45
Score = 31.1 bits (70), Expect = 0.13
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 19/83 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ GL T++DL++ F +G ++ + D + S+G GFV
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGR---------------SRGFGFV 45
Query: 175 RFNQHIEAEHAMQE----LNGTI 193
F + + M + LNG +
Sbjct: 46 LFKESESVDKVMDQKEHKLNGKV 68
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 42.0 bits (99), Expect = 2e-05
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 34 VPQTMTQEELQHLFSSVGEVE---SCKLIR--DKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + ++E+L+ V + +R + LG + + E AE+ + +L
Sbjct: 7 LSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKDL 66
Query: 89 NGLKLQNKSIKVSYARP 105
NG +N+ + V P
Sbjct: 67 NGKVFKNRKLFVKLHVP 83
Score = 37.7 bits (88), Expect = 6e-04
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 10/78 (12%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+S L ++EDLE + + + + S+ VR F S GI +
Sbjct: 2 VYISNLSYSSSEEDLEEFLKDF------EPVSVLIPSQTVRGFRSRRVR----PLGIAYA 51
Query: 175 RFNQHIEAEHAMQELNGT 192
F+ +AE +++LNG
Sbjct: 52 EFSSPEQAEKVVKDLNGK 69
Score = 29.7 bits (67), Expect = 0.47
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAV------QNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
+++ NL+ + + L + F V Q V+ R + + G + ++ ++A
Sbjct: 2 VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRS-RRVRPLGIAYAEFSSPEQAE 60
Query: 328 FAIQSLNGYALGDRLLQVSFKTHKP 352
++ LNG +R L V K H P
Sbjct: 61 KVVKDLNGKVFKNRKLFV--KLHVP 83
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 41.5 bits (97), Expect = 2e-05
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 21/82 (25%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y G+ +T++ + F P+G I+ R+ PE KG F+
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVF----------------PE-----KGYSFI 41
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
RF+ H A HA+ +NGT EG
Sbjct: 42 RFSTHESAAHAIVSVNGTTIEG 63
Score = 36.5 bits (84), Expect = 0.002
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 285 DNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
+ ++ Q F PFG + ++V + KG+ F+ + ++ A AI S+NG
Sbjct: 14 EQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSVNG 58
Score = 32.7 bits (74), Expect = 0.038
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T++ ++ FS G++ ++ +K GY F+ + E A AI+ +NG ++
Sbjct: 12 LTEQLMRQTFSPFGQIMEIRVFPEK------GYSFIRFSTHESAAHAIVSVNGTTIEGHV 65
Query: 98 IKVSYAR 104
+K + +
Sbjct: 66 VKCYWGK 72
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 41.6 bits (98), Expect = 3e-05
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 28 NLIVNYVPQTMTQEELQHLF-SSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+IV+ +P+ +T+ +++ F S +G ++ L ++ +S G + + R DA +A
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEG-GKSTGIANITFKRAGDATKAYD 59
Query: 87 ELNGLKLQNKS 97
+ NG
Sbjct: 60 KFNGRIDDGNR 70
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 41.5 bits (97), Expect = 3e-05
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
TQE L+ F GEV+ C ++RD T +S G+GFV +
Sbjct: 13 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 38.8 bits (90), Expect = 3e-04
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+F+ L+ +T L + FG FG V+ V+RDP T + +GFGFV T D+A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV--TFMDQA 53
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 41.5 bits (97), Expect = 3e-05
Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P+ + ++EL +F SVG + +L+ D ++ GY FV Y + +A+RA+ EL
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVREL 62
Query: 89 NGLKLQ 94
N +++
Sbjct: 63 NNYEIR 68
Score = 29.2 bits (65), Expect = 0.70
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V +P+ + +++L +F G I R++ D +N +G FV
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKN---------------RGYAFV 47
Query: 175 RFNQHIEAEHAMQELN 190
+ Q EA+ A++ELN
Sbjct: 48 MYTQKHEAKRAVRELN 63
Score = 27.6 bits (61), Expect = 2.5
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + + ++ L +F G + ++++ D K +G+ FV T EA A++ L
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDG-KNRGYAFVMYTQKHEAKRAVREL 62
Query: 334 NGYAL-GDRLLQV 345
N Y + RLL V
Sbjct: 63 NNYEIRPGRLLGV 75
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 41.6 bits (98), Expect = 3e-05
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 11/79 (13%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ + + ++T+E+L++ FS GE+ES +R+K A FVN+ +A +AI
Sbjct: 5 NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCA------FVNFTNISNAIKAI-- 56
Query: 88 LNGLKLQN--KSIKVSYAR 104
+G+K K K+SY +
Sbjct: 57 -DGVKSHPLFKKFKISYGK 74
Score = 28.5 bits (64), Expect = 1.2
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTI 139
N+Y+ + +T+E L N F YG I
Sbjct: 5 NVYIGNIDDSLTEEKLRNDFSQYGEI 30
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 41.8 bits (98), Expect = 3e-05
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+ ++EL+ GE+ES +++R+K A F+N+ +A A+ LNG K +
Sbjct: 19 LPEKELRKECEKYGEIESIRILREKACA------FINFMNIPNAIAALQTLNGKKPYDTI 72
Query: 98 IKVSYARPS 106
++++Y +
Sbjct: 73 VRINYGKDR 81
Score = 30.3 bits (68), Expect = 0.30
Identities = 14/79 (17%), Positives = 41/79 (51%), Gaps = 11/79 (13%)
Query: 274 IFVYNLAPETEDNVLWQ-----LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
+++ N++ ++ L + +G +++++++R+ K F+ N A+
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE------KACAFINFMNIPNAIA 58
Query: 329 AIQSLNGYALGDRLLQVSF 347
A+Q+LNG D ++++++
Sbjct: 59 ALQTLNGKKPYDTIVRINY 77
Score = 28.3 bits (63), Expect = 1.7
Identities = 21/88 (23%), Positives = 32/88 (36%), Gaps = 21/88 (23%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S + N+ G +++ +++L YG I + RIL E
Sbjct: 2 SRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRIL----------------RE--- 42
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIP 194
K F+ F A A+Q LNG P
Sbjct: 43 --KACAFINFMNIPNAIAALQTLNGKKP 68
>gnl|CDD|241074 cd12630, RRM2_IGF2BP3, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM2 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 76
Score = 41.6 bits (97), Expect = 3e-05
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + E L L + G VESC+ + + + V Y + A +A+ +L
Sbjct: 3 LQIRNIPPHLQWEVLDSLLAQYGTVESCEQVNTDSETAVVN---VTYGNKDQARQALDKL 59
Query: 89 NGLKLQNKSIKVSY 102
NG +L+N S+KV+Y
Sbjct: 60 NGFQLENYSLKVAY 73
Score = 29.6 bits (66), Expect = 0.49
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVR-DPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
+ N+ P + VL L +G V++ + V D +T V N D+A A+ LN
Sbjct: 5 IRNIPPHLQWEVLDSLLAQYGTVESCEQVNTDSETAVVN----VTYGNKDQARQALDKLN 60
Query: 335 GYALGDRLLQVSF 347
G+ L + L+V++
Sbjct: 61 GFQLENYSLKVAY 73
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 41.3 bits (97), Expect = 3e-05
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+F+ L+ +T L + F FG ++ V+RDP T + +GFGFV
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFV 45
Score = 40.9 bits (96), Expect = 5e-05
Identities = 19/41 (46%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
QT T E L+ FS GE++ C ++RD TT +S G+GFV +
Sbjct: 8 WQT-TAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF 47
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 41.8 bits (98), Expect = 3e-05
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
L ++FG +G V+ + R C GF FV M A A+++ NG + R + V +
Sbjct: 18 LKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76
Query: 348 KTHK 351
K
Sbjct: 77 AVQK 80
Score = 39.9 bits (93), Expect = 1e-04
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 29 LIVNYVPQTMTQ-EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
LI+ +P ++ + +L+ +F G+V + R + G+ FV + ++AE A+
Sbjct: 3 LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALEN 61
Query: 88 LNGLKLQNKSIKVSYA 103
NGL++ + + V +A
Sbjct: 62 TNGLEIDGRPVAVDWA 77
Score = 30.6 bits (69), Expect = 0.25
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 127 EDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAM 186
L+ +F YG + + I + G FV + AE A+
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLC----------------GFAFVTMKKRKNAEIAL 59
Query: 187 QELNGTIPEGASEPITVKFA 206
+ NG +G P+ V +A
Sbjct: 60 ENTNGLEIDG--RPVAVDWA 77
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells, and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1) and has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
It represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 41.2 bits (96), Expect = 3e-05
Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T E+++ F G+V+ L+ DKTT + G+GFV + +ED + E++ ++ NK +
Sbjct: 12 TVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVT-FESEDIVEKVCEIHFHEINNKMV 70
Query: 99 K 99
+
Sbjct: 71 E 71
Score = 32.7 bits (74), Expect = 0.037
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV L+ T + Q F FG V + ++ D T + +GFGFV + D
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 26.9 bits (59), Expect = 4.7
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 15/62 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL + T ED++ F +G + + ++ DK + + +G GFV
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRH---------------RGFGFV 46
Query: 175 RF 176
F
Sbjct: 47 TF 48
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM3 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 83
Score = 41.6 bits (97), Expect = 4e-05
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 10/71 (14%)
Query: 37 TMTQEELQHLFSSV--GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
+ T+E ++ F+S+ G VE K IRD Y FV++ EDA A+ LNG +
Sbjct: 19 STTEETIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVDAMNALNGKVID 70
Query: 95 NKSIKVSYARP 105
I+V+ A+P
Sbjct: 71 GSPIEVTLAKP 81
Score = 31.9 bits (72), Expect = 0.073
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 274 IFVYNLAPETEDNVLWQLFGPF--GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
++V NL T + + + F GAV+ VK +RD + FV +N ++AV A+
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVDAMN 62
Query: 332 SLNGYALGDRLLQVSF 347
+LNG + ++V+
Sbjct: 63 ALNGKVIDGSPIEVTL 78
Score = 31.5 bits (71), Expect = 0.12
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
FV F+ +A AM LNG + +G+ PI V A
Sbjct: 48 FVHFSNREDAVDAMNALNGKVIDGS--PIEVTLA 79
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 41.2 bits (96), Expect = 4e-05
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDE 325
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV ++ +E
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE 56
Score = 38.5 bits (89), Expect = 4e-04
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
T E L+ F G + C ++RD T +S G+GFV Y E+ + A+
Sbjct: 15 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 40.5 bits (95), Expect = 5e-05
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
P + +++ LF + G V ++ + F+ + E A+ AI LNG +
Sbjct: 8 PTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIETLNGASVD 63
Query: 95 NKSIKVSY 102
IKV
Sbjct: 64 GNCIKVQR 71
Score = 39.7 bits (93), Expect = 1e-04
Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++ + + +LF G V+ V ++ + + F+ N + A AI++L
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57
Query: 334 NGYALGDRLLQV 345
NG ++ ++V
Sbjct: 58 NGASVDGNCIKV 69
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 40.6 bits (95), Expect = 6e-05
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+V + +++ ++L +F + GE+ K IR+ T + F+ +Y AE A+ L
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEI---KEIRE--TPNKRHHKFIEFYDVRSAEAALKAL 58
Query: 89 NGLKLQNKSIKV 100
N ++ K IK+
Sbjct: 59 NRSEIAGKRIKL 70
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 40.8 bits (95), Expect = 6e-05
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 17/94 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ + K + D+ +F P+G I RIL P+ +S+G FV
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRIL--------------RGPD--GLSRGCAFV 47
Query: 175 RFNQHIEAEHAMQELN-GTIPEGASEPITVKFAN 207
F A+ A++ ++ EG S PI VKFA+
Sbjct: 48 TFTTRAMAQTAIKAMHQAQTMEGCSSPIVVKFAD 81
Score = 31.6 bits (71), Expect = 0.13
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ L + V + + +++ +FS G++E C+++R S G FV + A+ AI
Sbjct: 1 DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59
Score = 29.6 bits (66), Expect = 0.50
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ ++ + +N + +F PFG ++ +++R P +G FV T A AI+++
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAM 62
Query: 334 N 334
+
Sbjct: 63 H 63
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 40.3 bits (95), Expect = 7e-05
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL---- 93
+++EEL +F G VE + K Y FV+Y EDA A LNG +L
Sbjct: 15 VSREELLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAYDALNGKELELPQ 68
Query: 94 QNKSIKVSY 102
QNK + +SY
Sbjct: 69 QNKPLYLSY 77
Score = 28.7 bits (65), Expect = 1.1
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 286 NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGD 340
L ++F +G V+++ + K + FV ++ ++A A +LNG L
Sbjct: 18 EELLRVFEKYGTVEDLVMPPG------KPYCFVSYSSIEDAAAAYDALNGKELEL 66
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 40.4 bits (94), Expect = 7e-05
Identities = 17/49 (34%), Positives = 32/49 (65%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+FV L+P+T + + + FG FG ++N+++ D +T + +GF FV T+
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50
Score = 33.1 bits (75), Expect = 0.029
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
P T T+E+++ F + GE+E+ +L D T + G+ FV Y E ++
Sbjct: 9 PDT-TEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 40.2 bits (94), Expect = 8e-05
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S L V +P +T+EE++ LF G+ + +DK G+GF+ AE A
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDK------GFGFIRLETRTLAEIAKA 55
Query: 87 ELNGLKLQNKSIKVSY 102
EL+ + L+ K ++V +
Sbjct: 56 ELDNMPLRGKQLRVRF 71
Score = 39.5 bits (92), Expect = 2e-04
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 23/94 (24%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R+ L+V LP +T+E++ LF YG I K KG
Sbjct: 1 RSRLFVGNLPPDITEEEMRKLFEKYGK--AGEIFIHK-------------------DKGF 39
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
GF+R AE A EL+ G + + V+F
Sbjct: 40 GFIRLETRTLAEIAKAELDNMPLRG--KQLRVRF 71
Score = 32.5 bits (74), Expect = 0.037
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+ + + +LF +G + + +D KGFGF+ + A A L
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAEL 57
Query: 334 NGYALGDRLLQVSF 347
+ L + L+V F
Sbjct: 58 DNMPLRGKQLRVRF 71
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 40.2 bits (95), Expect = 8e-05
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P+ + ++EL LF G + +L+ D + + GY FV Y E A+RA+ +L+ ++
Sbjct: 9 IPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQLHNYEI 67
Query: 94 QN-KSIKVS 101
+ K + V
Sbjct: 68 RPGKRLGVC 76
Score = 29.1 bits (66), Expect = 0.76
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 16/77 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V +P+ + +++L LF G I R++ D ++G FV
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL----------------NRGYAFV 47
Query: 175 RFNQHIEAEHAMQELNG 191
+ A+ A+++L+
Sbjct: 48 TYTNKEAAQRAVKQLHN 64
>gnl|CDD|241072 cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM2 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. It promotes mRNA
stabilization and functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD. It stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 76
Score = 40.1 bits (93), Expect = 9e-05
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P + E L L + G VE+C+ + + + V Y E +AI++LNG +L
Sbjct: 8 IPPQLRWEVLDGLLAQYGTVENCEQVNTDSETAVVN---VTYGNREQTRQAIMKLNGHQL 64
Query: 94 QNKSIKVSY 102
+N ++KVSY
Sbjct: 65 ENHALKVSY 73
Score = 32.0 bits (72), Expect = 0.075
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVR-DPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
+ N+ P+ VL L +G V+N + V D +T V N ++ AI LN
Sbjct: 5 IRNIPPQLRWEVLDGLLAQYGTVENCEQVNTDSETAVVN----VTYGNREQTRQAIMKLN 60
Query: 335 GYALGDRLLQVSF 347
G+ L + L+VS+
Sbjct: 61 GHQLENHALKVSY 73
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 39.6 bits (93), Expect = 1e-04
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+V+ + ++T++++ LFS++G ++ +L+R G V Y R +DA AI +
Sbjct: 3 LVVSNLHPSVTEDDIVELFSAIGALKRARLVRP-------GVAEVVYVRKDDALTAIDKY 55
Query: 89 NGLKLQNKSIKVS 101
N +L + +K
Sbjct: 56 NNRELDGQPMKCK 68
Score = 30.7 bits (70), Expect = 0.16
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL P TED+++ +LF GA++ ++VR G V D+A+ AI
Sbjct: 3 LVVSNLHPSVTEDDIV-ELFSAIGALKRARLVR-------PGVAEVVYVRKDDALTAIDK 54
Query: 333 LNGYALGDRLLQVS 346
N L + ++
Sbjct: 55 YNNRELDGQPMKCK 68
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 39.9 bits (94), Expect = 1e-04
Identities = 18/74 (24%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ L+V+ + ++ ++++ LF+ G ++ + D++ +SLG V + R DA +A+
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVFERRADALKAMK 59
Query: 87 ELNGLKLQNKSIKV 100
+ NG+ L + +K+
Sbjct: 60 QYNGVPLDGRPMKI 73
Score = 27.6 bits (62), Expect = 2.6
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 16/79 (20%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
L VS L ++ +D++ LF +G + + + D+ SG S G
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR----------SGR------SLGTA 44
Query: 173 FVRFNQHIEAEHAMQELNG 191
V F + +A AM++ NG
Sbjct: 45 DVVFERRADALKAMKQYNG 63
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 43.5 bits (102), Expect = 1e-04
Identities = 37/167 (22%), Positives = 74/167 (44%), Gaps = 21/167 (12%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ + V +P+ + ++EL LF G + +L+ D + Q+ GY FV + E+A+
Sbjct: 56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKE 114
Query: 84 AIIELNGLKLQN-KSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS 142
A+ LN +++ + + V ++ L+V G+PK+ +E++ F
Sbjct: 115 AVKLLNNYEIRPGRLLGVCI------SVDNCRLFVGGIPKNKKREEILEEFS-------- 160
Query: 143 RILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQEL 189
K+ V V + + ++G FV + H A A ++L
Sbjct: 161 -----KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKL 202
Score = 43.1 bits (101), Expect = 2e-04
Identities = 53/195 (27%), Positives = 69/195 (35%), Gaps = 36/195 (18%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGE----VESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
N L V +P+ +EE+ FS V E V DK ++ G+ FV Y A
Sbjct: 138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKK--KNRGFAFVEYESHRAA 195
Query: 82 ERAIIEL--NGLKLQNKSIKVSYARPSSEA-----IKRANLYVSGLPKHMTQEDLENLFR 134
A +L ++L I V +A P E K LYV L T+E +E F
Sbjct: 196 AMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFS 255
Query: 135 PYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIP 194
F G E + + FV F +A AM ELNG
Sbjct: 256 ---------------------EFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKEL 294
Query: 195 EGASEPITVKFANSP 209
EG I V A
Sbjct: 295 EG--SEIEVTLAKPV 307
Score = 42.3 bits (99), Expect = 3e-04
Identities = 69/317 (21%), Positives = 116/317 (36%), Gaps = 83/317 (26%)
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARP-----SSEAIKRANLYVSGLPKHMTQEDLENLF 133
E A +A++E G L ++ + Y P + + ++V +P+ + +++L LF
Sbjct: 20 EAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLF 79
Query: 134 RPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN--- 190
G I R++ D SG ++G FV F EA+ A++ LN
Sbjct: 80 EKAGPIYELRLMMD----------FSGQ------NRGYAFVTFCGKEEAKEAVKLLNNYE 123
Query: 191 --------------------GTIPEGAS-EPITVKFANSPAGRAKALAANLNAQAAAMR- 228
G IP+ E I +F+ G + + A R
Sbjct: 124 IRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRG 183
Query: 229 --------HFAAAMRHFGNPLHHSARFKFAP---------LTADLLNNSMLPPKSLHGSG 271
H AAAM AR K P + D + +
Sbjct: 184 FAFVEYESHRAAAM----------ARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKV 233
Query: 272 WCIFVYNLAPETEDNVLWQLFGPF--GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
++V NL T + ++ + F F G V+ VK +RD + FV + ++AV A
Sbjct: 234 KILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKA 285
Query: 330 IQSLNGYALGDRLLQVS 346
+ LNG L ++V+
Sbjct: 286 MDELNGKELEGSEIEVT 302
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 39.5 bits (92), Expect = 1e-04
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
++++Q F G++ L GYGFV + + DA+ A+ ELNG L + +
Sbjct: 13 EKDIQRFFGGYGKLLEIDLKN--------GYGFVEFEDSRDADDAVYELNGKDLCGERVI 64
Query: 100 VSYAR 104
V +AR
Sbjct: 65 VEHAR 69
Score = 31.4 bits (71), Expect = 0.099
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 23/77 (29%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ L H+ ++D++ F YG ++ EI + G GFV
Sbjct: 2 VYIGRLSYHVREKDIQRFFGGYGKLL----------------------EI-DLKNGYGFV 38
Query: 175 RFNQHIEAEHAMQELNG 191
F +A+ A+ ELNG
Sbjct: 39 EFEDSRDADDAVYELNG 55
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog
of DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 39.8 bits (93), Expect = 1e-04
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI--- 85
+ V + M + E++ F+ G V+ K+I D+T S GYGFV++Y D ++ +
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGV-SKGYGFVSFYDDVDVQKIVESQ 66
Query: 86 IELNGLKLQ 94
I +G KL+
Sbjct: 67 INFHGKKLK 75
Score = 32.9 bits (75), Expect = 0.032
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+FV + ++ + F +G+V+ VK++ D +T KG+GFV +
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYD 55
Score = 32.1 bits (73), Expect = 0.072
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 16/69 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V G+ M + ++ + F YG++ +I+ D+ +SKG GFV
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTG----------------VSKGYGFV 51
Query: 175 RFNQHIEAE 183
F ++ +
Sbjct: 52 SFYDDVDVQ 60
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 39.4 bits (92), Expect = 1e-04
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V N+ P T L LF FG + + D +GF FV + +++A AI L
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56
Query: 334 NGYALGDRLLQVSF 347
G+ + R L+ +
Sbjct: 57 QGFPVHGRPLRCGW 70
Score = 36.7 bits (85), Expect = 0.001
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 32 NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGL 91
N P T TQ +L LF + G + + D+ G+ FV E A AI++L G
Sbjct: 7 NIPPYT-TQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIVQLQGF 59
Query: 92 KLQNKSIKVSYAR 104
+ + ++ + +
Sbjct: 60 PVHGRPLRCGWGK 72
Score = 35.2 bits (81), Expect = 0.006
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 21/76 (27%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
YV +P + TQ DL LF+ +G I+ R Q +G FV+
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGYILEFRH---------------------QPDRGFAFVK 42
Query: 176 FNQHIEAEHAMQELNG 191
+ H +A A+ +L G
Sbjct: 43 LDTHEQAAMAIVQLQG 58
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 39.7 bits (92), Expect = 2e-04
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+F+ L+ +T + L F FG ++ V+RDP T + +GFGFV +
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD 50
Score = 38.9 bits (90), Expect = 2e-04
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
+ + L+ FS GE+ C ++RD TT +S G+GFV +
Sbjct: 12 SPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 39.5 bits (93), Expect = 2e-04
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 273 CIFVYNLA---PETED---NVLWQLFGPFGAVQNVKVVRDPQ--TYKCKGFGFVCMTNYD 324
+ V L E + VL ++F FG + V + P T K KG+ FV +
Sbjct: 3 VVVVDGLPVVGEEKLEKLKKVLRKIFSKFGVGKIVGI-YMPVDETGKTKGYAFVEFATPE 61
Query: 325 EAVFAIQSLNGYAL 338
EA A+++LNGY L
Sbjct: 62 EAKEAVKALNGYKL 75
Score = 30.2 bits (69), Expect = 0.28
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 66 QSLGYGFVNYYRTEDAERAIIELNGLKL 93
++ GY FV + E+A+ A+ LNG KL
Sbjct: 48 KTKGYAFVEFATPEEAKEAVKALNGYKL 75
Score = 30.2 bits (69), Expect = 0.29
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 16/79 (20%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ----ISKGIG 172
V GLP + +E LE L + ++ K + +P +KG
Sbjct: 6 VDGLPV-VGEEKLEKLKK----VLRKIFS--KFGVGKIVGI-----YMPVDETGKTKGYA 53
Query: 173 FVRFNQHIEAEHAMQELNG 191
FV F EA+ A++ LNG
Sbjct: 54 FVEFATPEEAKEAVKALNG 72
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 39.1 bits (91), Expect = 2e-04
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+++L+ FS GEV C + D T +S G+GFV + E+ +++ KL + I
Sbjct: 11 TKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEK-VLDQKEHKLDGRVI 69
Score = 34.1 bits (78), Expect = 0.010
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L+ +T L + F FG V + + DP T + +GFGFV
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFV 45
Score = 31.0 bits (70), Expect = 0.16
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 19/83 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL T++DL+ F +G ++ I D V+G S+G GFV
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDP---------VTGR------SRGFGFV 45
Query: 175 RFNQHIEAEHAMQ----ELNGTI 193
F E + +L+G +
Sbjct: 46 LFKDAASVEKVLDQKEHKLDGRV 68
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 39.3 bits (92), Expect = 2e-04
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P T E+L F + G S +L+ DK T +S G FV + E +A ++L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA-LKL 61
Query: 89 NGLKLQNKSIKV 100
+ L+ + I V
Sbjct: 62 HHTLLKGRKINV 73
Score = 30.8 bits (70), Expect = 0.18
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 15/62 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP T EDL F+ G + R+L DK + SKG FV
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGK---------------SKGCAFV 47
Query: 175 RF 176
F
Sbjct: 48 EF 49
Score = 26.9 bits (60), Expect = 4.5
Identities = 17/45 (37%), Positives = 24/45 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV NL +T L F GA +V+++ D +T K KG FV
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFV 47
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 39.2 bits (91), Expect = 2e-04
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
IFV L PE + + + FG FG ++ +++ DP+T K +GF F+
Sbjct: 7 IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFI 51
Score = 30.7 bits (69), Expect = 0.19
Identities = 15/53 (28%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
P+ T+E+++ F GE+E+ +L D T + G+ F+ ++ ED + ++E
Sbjct: 14 PEA-TEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFIT-FKEEDPVKKVLE 64
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 38.9 bits (91), Expect = 2e-04
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
L V + T+T+EEL+ F G VE I+ Q Y FV + + A RA
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVD-IKRPPRGQGNAYAFVKFLNLDMAHRAK 60
Query: 86 IELNGLKLQNKSIKVSYAR 104
+ ++G + IK+ Y +
Sbjct: 61 VAMSGQYIGRNQIKIGYGK 79
Score = 29.3 bits (66), Expect = 0.64
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + L + F +G V++V + R P+ + + FV N D A A ++
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRG-QGNAYAFVKFLNLDMAHRAKVAM 63
Query: 334 NGYALG 339
+G +G
Sbjct: 64 SGQYIG 69
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 38.9 bits (90), Expect = 2e-04
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 41 EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
E+++ F G+VE L+ DKTT + G+GFV + ED + E++ ++ NK ++
Sbjct: 18 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVT-FENEDVVEKVCEIHFHEINNKMVEC 76
Query: 101 SYA 103
A
Sbjct: 77 KKA 79
Score = 29.6 bits (66), Expect = 0.44
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
IFV L+ T + Q F FG V++ ++ D T + +GFGFV
Sbjct: 6 IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFV 50
Score = 28.9 bits (64), Expect = 1.1
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
+ ++V GL + ED++ F +G + + ++ DK + + R F T E + +
Sbjct: 2 RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRH-RGFGFVTFENEDVVEK 60
Query: 171 IGFVRF----NQHIEAEHA 185
+ + F N+ +E + A
Sbjct: 61 VCEIHFHEINNKMVECKKA 79
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 38.9 bits (90), Expect = 2e-04
Identities = 22/73 (30%), Positives = 39/73 (53%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL V+ + T +L++LFS G+V K++ + + + YGFV +E+A + I
Sbjct: 3 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62
Query: 88 LNGLKLQNKSIKV 100
L+ +L + I V
Sbjct: 63 LHRTELHGRMISV 75
Score = 36.2 bits (83), Expect = 0.002
Identities = 22/72 (30%), Positives = 36/72 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L+ T L LF +G V KVV + ++ + +GFV M+ +EA I L
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 334 NGYALGDRLLQV 345
+ L R++ V
Sbjct: 64 HRTELHGRMISV 75
Score = 31.6 bits (71), Expect = 0.082
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCD 147
NL+VSGL DL+NLF YG ++ ++++ +
Sbjct: 3 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTN 36
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, an abundant eukaryotic nuclear RNA-binding protein
that may modulate splice site selection in pre-mRNA
splicing. hnRNP A1 has been characterized as a splicing
silencer, often acting in opposition to an activating
hnRNP H. It silences exons when bound to exonic elements
in the alternatively spliced transcripts of c-src, HIV,
GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle
between the nucleus and the cytoplasm. Thus, it may be
involved in transport of cellular RNAs, including the
packaging of pre-mRNA into hnRNP particles and transport
of poly A+ mRNA from the nucleus to the cytoplasm. The
cytoplasmic hnRNP A1 has high affinity with AU-rich
elements, whereas the nuclear hnRNP A1 has high affinity
with a polypyrimidine stretch bordered by AG at the 3'
ends of introns. hnRNP A1 is also involved in the
replication of an RNA virus, such as mouse hepatitis
virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 38.8 bits (90), Expect = 3e-04
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 53
>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM3 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. Rod1 contains
four repeats of RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain) and does have RNA binding activities. .
Length = 76
Score = 38.8 bits (90), Expect = 3e-04
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 274 IFVYNLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL P+ + L+ LFG +G V VK++ + K V M + +A A+
Sbjct: 3 LLVSNLNPDAITPHGLFILFGVYGDVHRVKIM-----FNKKENALVQMADATQAQLAMSH 57
Query: 333 LNGYALGDRLLQVSFKTHK 351
LNG L ++++ + H+
Sbjct: 58 LNGQRLYGKVIRATLSKHQ 76
Score = 28.4 bits (63), Expect = 1.5
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+ N P +T L LF G+V K++ +K V A+ A+ L
Sbjct: 4 LVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKEN-----ALVQMADATQAQLAMSHL 58
Query: 89 NGLKLQNKSIKVSYAR 104
NG +L K I+ + ++
Sbjct: 59 NGQRLYGKVIRATLSK 74
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 38.4 bits (89), Expect = 3e-04
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++++L S GEV C + D T +S G+GFV + ++ ++EL KL K I
Sbjct: 12 SKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK-VLELKEHKLDGKLI 70
Query: 99 KVSYAR 104
A+
Sbjct: 71 DPKRAK 76
Score = 32.7 bits (74), Expect = 0.044
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L+ +T L + FG V + + DP T + +GFGFV + +V + L
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKD-AASVDKVLEL 60
Query: 334 NGYALGDRLL 343
+ L +L+
Sbjct: 61 KEHKLDGKLI 70
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 98
Score = 39.1 bits (91), Expect = 3e-04
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 29 LIVNYVPQTMT-QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V+ +P+ EEL +FS + C+L +D+ + G+ V Y E AE +
Sbjct: 5 LCVDKLPKDYEDSEELLQIFSESYKPVFCQLAQDEGSCVG-GFAVVEYETAEQAEEVQLA 63
Query: 88 LNGLKLQNKSIKVSYARPSS 107
++G ++ I++S+ P +
Sbjct: 64 MDGTTIKGSRIQLSFCAPGA 83
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 38.7 bits (90), Expect = 3e-04
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCK-LIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
+ +M+ EL+ F GE+E CK LI+ + YGF+ Y +E A ++ + L+
Sbjct: 10 LSSSMSSTELKKRFEVFGEIEECKVLIKSRGEK----YGFITYRHSEHAALSLGKGASLR 65
Query: 93 LQNK-SIKVSYARP 105
+N+ S ++SY
Sbjct: 66 KRNEPSFQLSYGGL 79
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 38.6 bits (90), Expect = 3e-04
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V+ + Q +T+E+L LFS+ G+V C++ D L + F+ + E A RA + L+G
Sbjct: 7 VSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGA-RAALSLSG 63
Query: 91 LKLQNKSIKVSYARPSSEAI 110
L ++V PS AI
Sbjct: 64 TMLGFYPVRVL---PSKTAI 80
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 38.6 bits (90), Expect = 4e-04
Identities = 25/84 (29%), Positives = 32/84 (38%), Gaps = 18/84 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE----IPQISKG 170
LY+S LP TQ +LE+ F YG V + TP+ +
Sbjct: 3 LYISNLPPDTTQLELESWFTQYG-------------VRPVAFWTLKTPDEDAYVSSKDSI 49
Query: 171 IGFVRFNQHIEAEHAMQELNGTIP 194
GF F H EA A+ LNG
Sbjct: 50 SGFAVFQSHEEAMEALA-LNGRCL 72
Score = 35.2 bits (81), Expect = 0.006
Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 10/88 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESC----KLIRDKTTA--QSLGYGFVNYYRTEDAE 82
L ++ +P TQ EL+ F+ G K + + GF + E+A
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 83 RAIIELNGLKLQNKSIKVSYARPSSEAI 110
A + LNG L ++I+V PSS +
Sbjct: 63 EA-LALNGRCLGERAIEVQ---PSSSRV 86
Score = 33.2 bits (76), Expect = 0.030
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG----AVQNVKVVRDPQT--YKCKGFGFVCMTNYDEAV 327
+++ NL P+T L F +G A +K + K GF +++EA+
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 328 FAIQSLNGYALGDRLLQVS 346
A+ +LNG LG+R ++V
Sbjct: 63 EAL-ALNGRCLGERAIEVQ 80
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 38.0 bits (88), Expect = 4e-04
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
+++++ F G + L R G+GFV + DA+ A+ EL+G +L N+ +
Sbjct: 13 EKDVERFFKGYGRIRDIDLKR--------GFGFVEFDDPRDADDAVYELDGKELCNERVT 64
Query: 100 VSYAR 104
+ +AR
Sbjct: 65 IEHAR 69
Score = 31.5 bits (71), Expect = 0.080
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 152 ENVRSFVSGTPEIPQI--SKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
++V F G I I +G GFV F+ +A+ A+ EL+G E +E +T++ A
Sbjct: 14 KDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDGK--ELCNERVTIEHA 68
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 38.4 bits (89), Expect = 4e-04
Identities = 16/59 (27%), Positives = 32/59 (54%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ + V +P+ + ++EL LF G + +L+ D + Q+ GY F+ + E A+ A+
Sbjct: 2 TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
Score = 29.5 bits (66), Expect = 0.50
Identities = 13/65 (20%), Positives = 34/65 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + + ++ L LF G + +++++ DP + + +G+ F+ + A A++
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
Query: 334 NGYAL 338
+ Y +
Sbjct: 64 DNYEI 68
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 38.2 bits (89), Expect = 5e-04
Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 16/92 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV+G DL F YG ++ R + R F FV
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLV--RCDIPPPRTFQSRPF--------------AFV 45
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ H +AE A +E++G + + V++A
Sbjct: 46 EYESHRDAEDAYEEMHGRRFPDTGDTLHVQWA 77
Score = 32.5 bits (74), Expect = 0.045
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 3/78 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +L + F G + C I T QS + FV Y DAE A E+
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCD-IPPPRTFQSRPFAFVEYESHRDAEDAYEEM 60
Query: 89 NG--LKLQNKSIKVSYAR 104
+G ++ V +A+
Sbjct: 61 HGRRFPDTGDTLHVQWAK 78
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 37.7 bits (88), Expect = 5e-04
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSS 107
GY FV+ A++AI +LNG LQ K I+V ++ P
Sbjct: 35 GYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPKK 73
Score = 35.0 bits (81), Expect = 0.006
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG-AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+++ NL+ + ++ L QLF V +V V + G+ FV + A AI+
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEK 53
Query: 333 LNGYALGDRLLQVSFKTHK 351
LNG L ++++V K
Sbjct: 54 LNGKILQGKVIEVEHSVPK 72
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 38.1 bits (89), Expect = 5e-04
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 25/81 (30%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI-----SK 169
+YV LPK+ T E L+ +F YGT+ +VS +P+ K
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTV----------------VYVS----LPRYKHTGDIK 41
Query: 170 GIGFVRFNQHIEAEHAMQELN 190
G F+ F EA+ A + LN
Sbjct: 42 GFAFIEFETPEEAQKACKHLN 62
Score = 37.0 bits (86), Expect = 0.001
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
+P+ T E L+ +FS G V L R K T G+ F+ + E+A++A LN
Sbjct: 7 LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLN 62
Score = 30.4 bits (69), Expect = 0.25
Identities = 18/61 (29%), Positives = 26/61 (42%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L +F +G V V + R T KGF F+ +EA A + L
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 334 N 334
N
Sbjct: 62 N 62
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 38.0 bits (88), Expect = 5e-04
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P+ M ++EL LF G++ +L+ + + ++ GY FV Y E+A+ AI L
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAIRIL 62
Query: 89 NGLKLQ 94
N +++
Sbjct: 63 NNYEIR 68
Score = 28.7 bits (64), Expect = 0.88
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 313 KGFGFVCMTNYDEAVFAIQSLNGYAL 338
+G+ FV T +EA AI+ LN Y +
Sbjct: 42 RGYAFVMYTTKEEAQLAIRILNNYEI 67
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 37.7 bits (87), Expect = 5e-04
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 13/80 (16%)
Query: 31 VNYVPQTM---TQEELQHLFSSV--GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
V YV M T+E ++ F+ G VE K +RD Y FV+++ EDA A+
Sbjct: 3 VLYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD--------YAFVHFFNREDAVAAM 54
Query: 86 IELNGLKLQNKSIKVSYARP 105
+NG + SI+V+ A+P
Sbjct: 55 SVMNGKCIDGASIEVTLAKP 74
Score = 29.6 bits (66), Expect = 0.40
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 10/76 (13%)
Query: 274 IFVYNLAPETEDNVLWQLFGPF--GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
++V NL T + + F F G V+ VK +RD + FV N ++AV A+
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD--------YAFVHFFNREDAVAAMS 55
Query: 332 SLNGYALGDRLLQVSF 347
+NG + ++V+
Sbjct: 56 VMNGKCIDGASIEVTL 71
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 37.7 bits (87), Expect = 5e-04
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ L V + + T +EL+ F G V C +++D Y FV+ R EDA AI
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 52
Query: 87 ELNGLKLQNKSIKV 100
L+ + Q K + V
Sbjct: 53 GLDNTEFQGKRMHV 66
Score = 28.1 bits (62), Expect = 1.2
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 8/70 (11%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V N++ + L F +G V +V+D + FV M ++AV AI+ L+
Sbjct: 5 VGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDN 56
Query: 336 YALGDRLLQV 345
+ + V
Sbjct: 57 TEFQGKRMHV 66
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a ubiquitously expressed pre-mRNA splicing
factor that enhances messenger RNA (mRNA) splicing in a
cell-specific manner or in a certain developmental
process, such as spermatogenesis. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It may play a more
specific role in meiosis entry and progression. Together
with additional testis-specific RNA-binding proteins,
RBM7 may regulate the splicing of specific pre-mRNA
species that are important in the meiotic cell cycle.
RBM7 contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. .
Length = 75
Score = 38.0 bits (88), Expect = 6e-04
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+ + ++++LF G V VK+ +D K K F FV + +A+ L
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDG-KPKQFAFVNFKHEVSVPYAMNLL 62
Query: 334 NGYALGDRLLQV 345
NG L R L +
Sbjct: 63 NGIKLYGRPLNI 74
Score = 35.3 bits (81), Expect = 0.005
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + +T+E + LF G V K+ +DK + FVN+ A+ L
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNFKHEVSVPYAMNLL 62
Query: 89 NGLKLQNKSIKV 100
NG+KL + + +
Sbjct: 63 NGIKLYGRPLNI 74
Score = 27.6 bits (61), Expect = 2.5
Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 16/77 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L +T+E + LF G +I +I DK G P K FV
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK----------DGKP------KQFAFV 47
Query: 175 RFNQHIEAEHAMQELNG 191
F + +AM LNG
Sbjct: 48 NFKHEVSVPYAMNLLNG 64
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 37.5 bits (88), Expect = 7e-04
Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR--DKTTAQSLGYGFVNYYRTEDAERA 84
S L V P + Q +++ LF GE+ S IR ++ + +V + E A A
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAA 57
Query: 85 IIELNGLKLQNKSIKVSYARP 105
+ LNG + + V + P
Sbjct: 58 VALLNGKLGEGYKLVVKISDP 78
Score = 35.6 bits (83), Expect = 0.004
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSR 143
+ L+V+ P Q D+ +LF YG I++ R
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSIR 31
Score = 34.5 bits (80), Expect = 0.009
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP-QTY-KCKGFGFVCMTNYDEAVFAIQ 331
++V N P + + + LF +G + + +R P + K + F +V T+ + A A+
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59
Query: 332 SLNGYALGDRLLQV 345
LNG L V
Sbjct: 60 LLNGKLGEGYKLVV 73
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 37.7 bits (87), Expect = 7e-04
Identities = 16/51 (31%), Positives = 31/51 (60%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
+FV + +TE++ L F +G + ++++ D Q+ K +GFGFV ++D
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53
Score = 31.6 bits (71), Expect = 0.10
Identities = 11/59 (18%), Positives = 32/59 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V + + + L+ F G++++ ++I D+ + + G+GFV + + ++ +++
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
Score = 27.7 bits (61), Expect = 2.7
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 15/65 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V G+ + + L + F YG I T I+ D+ + + +G GFV
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKK---------------RGFGFV 47
Query: 175 RFNQH 179
F+ H
Sbjct: 48 TFDDH 52
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 37.4 bits (87), Expect = 8e-04
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQV 345
L + F G + V + D +T KGF ++ + D A++ L+G LG L V
Sbjct: 20 LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76
Score = 36.6 bits (85), Expect = 0.002
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 41 EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
L FSS GE+ + D+ T S G+ ++ + + E+A +EL+G L ++ V
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA-LELDGSDLGGGNLVV 76
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 37.8 bits (87), Expect = 8e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV---CMTNYDEAVFA 329
+F+ L+ ET + L + +G + + V+RDP + + +GFGFV CM D A+ A
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63
Score = 33.5 bits (76), Expect = 0.020
Identities = 13/47 (27%), Positives = 28/47 (59%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
T+E L++ + G++ C ++RD + +S G+GFV + + + A+
Sbjct: 15 TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61
Score = 32.8 bits (74), Expect = 0.036
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 15/86 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ GL T+E L N + +G + ++ D + S+G GFV
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR---------------SRGFGFV 49
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEP 200
F+ E + AM TI EP
Sbjct: 50 TFSCMNEVDAAMAARPHTIDGRVVEP 75
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 37.2 bits (87), Expect = 8e-04
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI-- 330
+FV NL ++ L +LF G + +V++V++ + K KG+ +V N + A+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKL 59
Query: 331 --QSLNG 335
+ + G
Sbjct: 60 DRELIKG 66
Score = 33.8 bits (78), Expect = 0.013
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 15/79 (18%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
SNL ++ ++EL+ LFS GE+ +L+++ +S GY +V + E+ E
Sbjct: 5 SNL-----DYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEF---ENEESV-- 53
Query: 87 ELNGLKLQNKSIKVSYARP 105
LKL + IK RP
Sbjct: 54 -QEALKLDRELIK---GRP 68
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 37.3 bits (86), Expect = 8e-04
Identities = 17/45 (37%), Positives = 30/45 (66%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
IFV L+P+T + + + FG FG V+++++ D +T K +GF F+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFI 46
Score = 30.7 bits (69), Expect = 0.16
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+E+++ F + GEVES +L D T + G+ F+ ++ E+ + I+E
Sbjct: 13 EEKIREYFGAFGEVESIELPMDNKTNKRRGFCFIT-FKEEEPVKKIME 59
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 36.9 bits (86), Expect = 0.001
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T++E++ FS GE+E L+ T + G F+ ++TE+A + + L+G +
Sbjct: 6 IPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFIT-FKTEEAAKRALALDGEDM 64
Query: 94 QNKSIKV 100
+ +KV
Sbjct: 65 GGRFLKV 71
Score = 33.1 bits (76), Expect = 0.024
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
TED + F G ++ + ++ P T + +G F+ + A A+ +L+G +G R
Sbjct: 11 TEDEIR-SYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-ALDGEDMGGRF 68
Query: 343 LQV 345
L+V
Sbjct: 69 LKV 71
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 37.7 bits (87), Expect = 0.001
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 269 GSGWCIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
G + V NL E L+ LFG +G VQ VK++ Y K + M + +++
Sbjct: 11 GGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKIL-----YNKKDSALIQMADGNQSQ 65
Query: 328 FAIQSLNGYALGDRLLQVSFKTHK 351
A+ LNG + ++++V+ H+
Sbjct: 66 LAMSHLNGQKMYGKIIRVTLSKHQ 89
Score = 33.1 bits (75), Expect = 0.056
Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 5/94 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+ N + +T + L LF G+V+ K++ +K + + ++ A+ L
Sbjct: 17 LVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDS-----ALIQMADGNQSQLAMSHL 71
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPK 122
NG K+ K I+V+ ++ + + R L GL K
Sbjct: 72 NGQKMYGKIIRVTLSKHQTVQLPREGLDDQGLTK 105
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.0 bits (86), Expect = 0.001
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD--EAVFAI- 330
IFV L P + L + F FG V V V+ D + + +GFGF+ + D + V
Sbjct: 5 IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64
Query: 331 -QSLNG 335
+NG
Sbjct: 65 FHDING 70
Score = 34.3 bits (79), Expect = 0.011
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P +T+ +L+ FS G V ++ D + G+GF+ + +ED+ ++ + +
Sbjct: 10 LPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFIT-FESEDSVDQVVNEHFHDI 68
Query: 94 QNKSIKVSYARP 105
K ++V A P
Sbjct: 69 NGKKVEVKRAEP 80
Score = 29.6 bits (67), Expect = 0.56
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 18/92 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP ++T+ DL F +GT+ ++ D E R +G GF+
Sbjct: 5 IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDH---EKKR------------PRGFGFI 49
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F + + E I + + VK A
Sbjct: 50 TFESEDSVDQVVNEHFHDI---NGKKVEVKRA 78
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 36.7 bits (86), Expect = 0.001
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
L+ LF FG V ++ + T K +G FV + + A A+++L G+ D+ +++ +
Sbjct: 20 LYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQY 76
Score = 32.1 bits (74), Expect = 0.060
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
L LFS G V I T + G FV + E A A+ L G +K +++ Y
Sbjct: 20 LYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQY 76
Query: 103 AR 104
A+
Sbjct: 77 AK 78
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 36.9 bits (85), Expect = 0.002
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + T+E L+ F G + + +++ D+ T S G+GFV++ EDA+ A +
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 89 NGLKLQNKSIKVSYARP 105
++ + + +A+P
Sbjct: 60 EDGEIDGNKVTLDFAKP 76
Score = 32.3 bits (73), Expect = 0.058
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ +T + L + F G++ ++V D T KGFGFV ++ ++A A +++
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 334 N 334
Sbjct: 60 E 60
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 36.4 bits (84), Expect = 0.002
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V VP+ +T+ L+ LF G+V + T S G V++Y DA+RA+ EL
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRGVQ-----TERISEGIVTVHFYDIRDAKRAVREL 58
Query: 89 NGLKLQNKSIKVS 101
G +Q +++ S
Sbjct: 59 CGRHMQQQALGGS 71
Score = 29.4 bits (66), Expect = 0.44
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD--EAVFAIQ 331
+FV N+ + ++ L +LF +G V+ V+ + G V + YD +A A++
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRGVQT-------ERISEGIVTVHFYDIRDAKRAVR 56
Query: 332 SLNGYALGDRLLQVS 346
L G + + L S
Sbjct: 57 ELCGRHMQQQALGGS 71
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form of
the carboxy-terminal domain (CTD) of the largest subunit
of RNA polymerase II (pol II). The pol II CTD plays a
role in coupling transcription and pre-mRNA processing.
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 36.6 bits (84), Expect = 0.002
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ L V V + TQ++L +LF G++ES +I + G +V +DA RA+
Sbjct: 2 STTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPR------GCAYVCMVHRQDAYRAL 55
Query: 86 IELN--GLKLQNKSIKVSYA 103
+L+ K+ +K IK+++A
Sbjct: 56 QKLSSGSYKIGSKVIKIAWA 75
Score = 29.6 bits (66), Expect = 0.50
Identities = 16/66 (24%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN--GYALGDRLLQV 345
L LF FG ++++ ++ +G +VCM + +A A+Q L+ Y +G +++++
Sbjct: 19 LTNLFEEFGQIESINMIPP------RGCAYVCMVHRQDAYRALQKLSSGSYKIGSKVIKI 72
Query: 346 SFKTHK 351
++ +K
Sbjct: 73 AWALNK 78
Score = 28.1 bits (62), Expect = 1.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTI 139
L+V + K TQ+DL NLF +G I
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQI 29
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 36.6 bits (85), Expect = 0.002
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCM--------TNYDE 325
I + L+P T + F PFG ++ ++ DP+T + G V ++
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 326 AVFAIQSLNGYALGDRLLQV 345
A A+ LNG +G + ++V
Sbjct: 61 AKAAVDGLNGRRIGGKRVRV 80
Score = 33.9 bits (78), Expect = 0.018
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT--------ED 80
LI P T ++ H F GE+E +L D T QSLG V + E
Sbjct: 2 LITGLSPLTTPKQIRMH-FRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 81 AERAIIELNGLKLQNKSIKV 100
A+ A+ LNG ++ K ++V
Sbjct: 61 AKAAVDGLNGRRIGGKRVRV 80
Score = 29.6 bits (67), Expect = 0.58
Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 23/85 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ ++GL T + + FRP+G I S + D +G S GI V
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDP---------RTGQ------SLGICRV 45
Query: 175 RF--------NQHIEAEHAMQELNG 191
F H A+ A+ LNG
Sbjct: 46 TFRGDPLRPSAAHEAAKAAVDGLNG 70
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 36.3 bits (84), Expect = 0.002
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++V +P T+++++ LFSS G+++S ++ + K + G+ FV + ++A A+ L
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMNAL 61
Query: 89 NGLKLQNKSIKVSYA 103
L + + + YA
Sbjct: 62 KDTHLLGRRLVLQYA 76
Score = 34.4 bits (79), Expect = 0.009
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 16/78 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V LP T++D+ LF YG + + R+ + Q ++G FV
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRV----------------PKKFDQSARGFAFV 46
Query: 175 RFNQHIEAEHAMQELNGT 192
F+ EA +AM L T
Sbjct: 47 EFSTAKEALNAMNALKDT 64
Score = 30.9 bits (70), Expect = 0.16
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTY--KCKGFGFVCMTNYDEAVFAIQ 331
I V NL E + LF +G +K VR P+ + +GF FV + EA+ A+
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYG---QLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMN 59
Query: 332 SLNG-YALGDRLL 343
+L + LG RL+
Sbjct: 60 ALKDTHLLGRRLV 72
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 36.1 bits (84), Expect = 0.002
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL E + L+ LFG +G V VK++ + K + M + +A A+
Sbjct: 2 LLVSNLNEEMVTPDALFTLFGVYGDVVRVKIL-----FNKKDTALIQMADPQQAQTALTH 56
Query: 333 LNGYALGDRLLQVSFKTH 350
LNG L + L+V+ H
Sbjct: 57 LNGIRLHGKKLRVTLSKH 74
Score = 28.4 bits (64), Expect = 1.3
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCK-LIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L+ N + +T + L LF G+V K L K TA + + A+ A+
Sbjct: 3 LVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTA------LIQMADPQQAQTALTH 56
Query: 88 LNGLKLQNKSIKVSYAR 104
LNG++L K ++V+ ++
Sbjct: 57 LNGIRLHGKKLRVTLSK 73
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 36.0 bits (84), Expect = 0.002
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 273 CIFVYNLAPE-TEDNVLWQLFGPFG-AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
+ + L TE+++ F + +V D + G +V + ++A A+
Sbjct: 1 VVRLRGLPFSATEEDIR-DFFSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRAL 58
Query: 331 QSLNGYALGDRLLQVS 346
+ N +G R ++V
Sbjct: 59 RKHNNK-MGGRYIEVF 73
Score = 33.3 bits (77), Expect = 0.023
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 17/80 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITS-RILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+ + GLP T+ED+ + F I+ D G P G +
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD----------DGRP------TGEAY 45
Query: 174 VRFNQHIEAEHAMQELNGTI 193
V F +A A+++ N +
Sbjct: 46 VEFASPEDARRALRKHNNKM 65
Score = 30.6 bits (70), Expect = 0.18
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 34 VPQTMTQEELQHLFSSVGEVESC-KLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
+P + T+E+++ FS + ++ D + G +V + EDA RA+ + N K
Sbjct: 7 LPFSATEEDIRDFFSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRALRKHNN-K 64
Query: 93 LQNKSIKVS 101
+ + I+V
Sbjct: 65 MGGRYIEVF 73
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 36.1 bits (83), Expect = 0.003
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ + V +P+ + ++EL LF G + +L+ D T + GY FV + E A+ A+
Sbjct: 2 TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 36.1 bits (83), Expect = 0.003
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE+ L F +G ++ ++V+ D Q+ K +GF FV ++D
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHD 53
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 35.7 bits (83), Expect = 0.003
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+++ L + L + F +G V V VV D Q + V + A A+
Sbjct: 9 CVWLDGLDESVTEQYLTRHFSRYGPV--VHVVIDRQRGQA----LVFFDKVEAAQAAVNE 62
Query: 333 LNGYALGDRLLQVSF 347
+ G LG R LQV F
Sbjct: 63 MKGRKLGGRKLQVDF 77
Score = 32.6 bits (75), Expect = 0.044
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ +++T++ L FS G V + R + A V + + E A+ A+ E+ G KL
Sbjct: 15 LDESVTEQYLTRHFSRYGPVVHVVIDRQRGQA------LVFFDKVEAAQAAVNEMKGRKL 68
Query: 94 QNKSIKVSY 102
+ ++V +
Sbjct: 69 GGRKLQVDF 77
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RRMs.
Length = 71
Score = 35.6 bits (83), Expect = 0.003
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++ M ++L +LF G V K ++ K G V + AERAI L
Sbjct: 3 MVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKP-----GTAMVQMGDPQAAERAIEYL 57
Query: 89 NGLKLQNKSIKVSY 102
NG+ L + ++V++
Sbjct: 58 NGVVLFGQKLEVNF 71
Score = 33.3 bits (77), Expect = 0.021
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 274 IFVYNLAPETED-NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ VY L + + + L+ LF +G V +K ++ G V M + A AI+
Sbjct: 2 LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSK-----PGTAMVQMGDPQAAERAIEY 56
Query: 333 LNGYALGDRLLQVSF 347
LNG L + L+V+F
Sbjct: 57 LNGVVLFGQKLEVNF 71
Score = 27.5 bits (62), Expect = 1.9
Identities = 22/78 (28%), Positives = 29/78 (37%), Gaps = 21/78 (26%)
Query: 115 LYVSGLPKH-MTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L V GL K M + L NLF YG ++ + L K G
Sbjct: 2 LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSK--------------------PGTAM 41
Query: 174 VRFNQHIEAEHAMQELNG 191
V+ AE A++ LNG
Sbjct: 42 VQMGDPQAAERAIEYLNG 59
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 36.0 bits (84), Expect = 0.003
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 278 NLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYA 337
L P T D VL Q+F P+GAV+ + + + V + + A A ++LNG
Sbjct: 9 LLYPVTVD-VLHQVFSPYGAVEKILIFEKNTGVQA----LVQFDSVESAENAKKALNGRN 63
Query: 338 L--GDRLLQVSFKTHKPLP 354
+ G L + F K L
Sbjct: 64 IYDGCCTLDIQFSRLKELT 82
Score = 27.5 bits (62), Expect = 2.6
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCK-LIRDKTTA-QSLGYGFVNYYRTEDAERAII 86
+ ++ + +T + L +FS G VE K LI +K T Q+ V + E AE A
Sbjct: 4 VTISNLLYPVTVDVLHQVFSPYGAVE--KILIFEKNTGVQA----LVQFDSVESAENAKK 57
Query: 87 ELNGLKLQNK--SIKVSYARPSS 107
LNG + + ++ + ++R
Sbjct: 58 ALNGRNIYDGCCTLDIQFSRLKE 80
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 35.7 bits (83), Expect = 0.004
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + +T+++L+ F GE+ S ++ + FV + E AE+A L
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ------QCAFVTFTTREAAEKAAERL 57
Query: 89 -NGLKLQNKSIKVSYAR 104
N L + + +K+ + R
Sbjct: 58 FNKLIINGRRLKLKWGR 74
Score = 33.8 bits (78), Expect = 0.015
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRIL 145
LYV GL + +T++DL + F +G I + ++
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV 34
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 35.4 bits (82), Expect = 0.004
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ ++++++L+ FS+ GEV +L D S + FV + E A A + L+G L
Sbjct: 8 IDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSA-LNLSGTLL 64
Query: 94 QNKSIKVS 101
++VS
Sbjct: 65 GGHPLRVS 72
Score = 30.0 bits (68), Expect = 0.35
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 20/94 (21%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+V G+ ++++DL+ F G + R+ D Q S FV
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD-----------------RQHSARFAFVE 46
Query: 176 FNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F E+ + L+GT P+ V + +P
Sbjct: 47 FA-DAESALSALNLSGT--LLGGHPLRVSPSKTP 77
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 36.0 bits (84), Expect = 0.004
Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 10/89 (11%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVG----EVES----CKLIRDKTTAQSLGYGFVNYYR 77
N+N+ V+ +P +T EE +FS G + E+ KL RD+ G Y +
Sbjct: 1 NTNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLK-GDALCCYLK 59
Query: 78 TEDAERAIIELNG-LKLQNKSIKVSYARP 105
E E AI L+G + +KV A+
Sbjct: 60 EESVELAIQLLDGTEIGRGYKMKVERAKF 88
Score = 32.9 bits (76), Expect = 0.039
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIIT 141
N+YVSGLP +T E+ +F G I
Sbjct: 3 NVYVSGLPLDITVEEFVEVFSKCGIIKE 30
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 86
Score = 35.6 bits (82), Expect = 0.004
Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG--AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
I + N+AP T + + P+ +V N+++++D QT + +GF FV +++ EA +Q
Sbjct: 5 IILRNIAPHTVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 332 SLNG 335
L
Sbjct: 65 ILQA 68
Score = 31.8 bits (72), Expect = 0.086
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 53 VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG----LKLQNKSIKVSYAR 104
V + +LI+DK T Q+ G+ FV +A + + L LK+ K+I V +A+
Sbjct: 31 VSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVDFAK 86
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 35.3 bits (81), Expect = 0.004
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++++L+ F+ GEV C + D T +S G+GF+ + E+ +
Sbjct: 12 SKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVL 58
Score = 34.6 bits (79), Expect = 0.007
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L+ +T L F FG V + + DP T + +GFGF+
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFI 46
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 35.7 bits (82), Expect = 0.004
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG--AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
I + N+AP T + + P+ AV N+++++D QT + +GF FV +++ EA +Q
Sbjct: 5 IILRNIAPHTVVDSILTALAPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 332 SLNG 335
L
Sbjct: 65 ILQS 68
Score = 34.9 bits (80), Expect = 0.008
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 53 VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG----LKLQNKSIKVSYAR 104
V + +LI+DK T Q+ G+ FV +A + + L LK+ K+I V +A+
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFAK 86
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 35.2 bits (82), Expect = 0.005
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP------QTYKCKGFGFVCMTNYDEAV 327
++V NL+ + L +FG F V + ++ + KG FV + + A
Sbjct: 4 LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61
Query: 328 FAIQSLNGYALGDRLLQVSF 347
A+ +NGY L + + + F
Sbjct: 62 KALNLVNGYVLKGKPMVIQF 81
Score = 32.9 bits (76), Expect = 0.030
Identities = 27/92 (29%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L K +T+EDL +F G + S M ++R G KG FV
Sbjct: 4 LYVKNLSKRVTEEDLVYIF---GRFVDSSSEEKNMF--DIRLMTEGR------MKGQAFV 52
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
F A A+ +NG + +G +P+ ++F
Sbjct: 53 TFPSEEIATKALNLVNGYVLKG--KPMVIQFG 82
Score = 30.6 bits (70), Expect = 0.23
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSV---GEVESCKL-IRDKTTAQSLGYGFVNYYRTEDA 81
+ L V + + +T+E+L ++F E IR T + G FV + E A
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60
Query: 82 ERAIIELNGLKLQNKSIKVSYA 103
+A+ +NG L+ K + + +
Sbjct: 61 TKALNLVNGYVLKGKPMVIQFG 82
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 35.2 bits (81), Expect = 0.005
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P +T +EL+ +F ++ + S G ++ + +AE+A+ E
Sbjct: 6 LFVKNLPYNITVDELKEVFEDAVDIR----LPSGKDGSSKGIAYIEFKTEAEAEKALEEK 61
Query: 89 NGLKLQNKSIKVSY 102
G ++ +SI V Y
Sbjct: 62 QGAEVDGRSIVVDY 75
Score = 34.0 bits (78), Expect = 0.014
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 19/84 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V LP ++T ++L+ +F I R+ K S SKGI ++
Sbjct: 6 LFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGS----------------SKGIAYI 46
Query: 175 RFNQHIEAEHAMQELNGTIPEGAS 198
F EAE A++E G +G S
Sbjct: 47 EFKTEAEAEKALEEKQGAEVDGRS 70
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two of which are followed
by a glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The subgroup also
includes NAM8, a putative RNA-binding protein that acts
as a suppressor of mitochondrial splicing deficiencies
when overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 35.5 bits (82), Expect = 0.005
Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 37 TMTQEELQHLFSSVGEVE-SCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
M + ++ +++S+G + K+IR + + + GY FV + A+ A+ LNG + N
Sbjct: 10 WMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS-LNGTPIPN 68
Query: 96 --KSIKVSYA 103
++ K+++A
Sbjct: 69 SNRTFKLNWA 78
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 35.6 bits (83), Expect = 0.005
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 28 NLI-VNYVPQTMTQEEL---QHLFSSVGEVESCKLIRDKTTAQSLGYG-----FVNYYRT 78
NL+ V +P + EE+ F G+++ K++ ++ T+ + G +V Y R
Sbjct: 6 NLVYVVGLPPRLADEEVLKKPEYFGQYGKIK--KIVINRNTSYNGSQGPSASAYVTYSRK 63
Query: 79 EDAERAIIELNGLKLQNKSIKVSYA 103
EDA R I ++G L + +K S+
Sbjct: 64 EDALRCIQAVDGFYLDGRLLKASFG 88
Score = 32.5 bits (75), Expect = 0.058
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 274 IFVYNLAPETED-NVL--WQLFGPFGAVQNVKVVRDPQTYKCKGFG----FVCMTNYDEA 326
++V L P D VL + FG +G ++ + V+ +Y +V + ++A
Sbjct: 8 VYVVGLPPRLADEEVLKKPEYFGQYGKIKKI-VINRNTSYNGSQGPSASAYVTYSRKEDA 66
Query: 327 VFAIQSLNGYALGDRLLQVSFKTHK 351
+ IQ+++G+ L RLL+ SF T K
Sbjct: 67 LRCIQAVDGFYLDGRLLKASFGTTK 91
>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast
mitochondrial escape protein 2 (Yme2p) and similar
proteins. This subfamily corresponds to the RRM of
Yme2p, also termed protein RNA12, an inner mitochondrial
membrane protein that plays a critical role in
mitochondrial DNA transactions. It may serve as a
mediator of nucleoid structure and number in
mitochondria of the yeast Saccharomyces cerevisiae.
Yme2p contains an exonuclease domain, an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal domain. .
Length = 86
Score = 35.3 bits (82), Expect = 0.005
Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 6/89 (6%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ + V + ++QEEL LF G+++ I Y V + R A A
Sbjct: 4 STTIRVEFEGPELSQEELYSLFRPYGKIKD---ITPPPPDSLPRYATVTFRRIRGAISAK 60
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIKRAN 114
L+G +L ++ E RA+
Sbjct: 61 NCLHGFELNEGKTRL---HIQYEPKLRAH 86
Score = 33.0 bits (76), Expect = 0.040
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 124 MTQEDLENLFRPYGTII 140
++QE+L +LFRPYG I
Sbjct: 16 LSQEELYSLFRPYGKIK 32
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 35.1 bits (81), Expect = 0.006
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 5/78 (6%)
Query: 28 NLIVNYVPQTMTQEELQH----LFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
L V + +T+EE+ FS G + S K+ + A Y FV +Y A R
Sbjct: 2 TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61
Query: 84 AIIELNGLKL-QNKSIKV 100
A NG L Q +KV
Sbjct: 62 AQKACNGKWLFQGSPLKV 79
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 35.1 bits (81), Expect = 0.006
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYAR 104
G F N+ E+A+ + LNG ++ + ++V Y R
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
Score = 30.1 bits (68), Expect = 0.32
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 313 KGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFK 348
+G F + +EA +++LNGY + R L+V +K
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYK 78
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 34.8 bits (80), Expect = 0.007
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T EEL+ FS G + ++ DK + GY ++ + T D+ A + L+ + + I
Sbjct: 12 TAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIE-FATRDSVEAAVALDESSFRGRVI 70
Query: 99 KV 100
KV
Sbjct: 71 KV 72
Score = 29.8 bits (67), Expect = 0.40
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 17/77 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++YV + T E+LE F G I ILCDK SG P KG +
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKF---------SGHP------KGYAY 45
Query: 174 VRFNQH--IEAEHAMQE 188
+ F +EA A+ E
Sbjct: 46 IEFATRDSVEAAVALDE 62
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 35.1 bits (81), Expect = 0.007
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 29 LIVNYVPQTMTQEELQ----HLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ V +P + + +EL+ FS G + K++RD + Y FV + +DA+ A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA 61
Query: 85 IIELNGLKLQNKSIKVSYAR 104
+ + G L + I+ A+
Sbjct: 62 LAKGQGTILDGRHIRCERAK 81
Score = 32.0 bits (73), Expect = 0.076
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 273 CIFVYNLAPETEDNVL----WQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
C+FV +L D+ L + F +G + VKV+RD ++ + + FV TN D+A
Sbjct: 4 CVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKN 60
Query: 329 AI 330
A+
Sbjct: 61 AL 62
Score = 27.4 bits (61), Expect = 3.7
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 22/88 (25%)
Query: 113 ANLYVSGLPKHMTQEDLE----NLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
A ++V+ LP + ++LE F YGT++ ++L D P
Sbjct: 3 ACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWR----------QRP------ 46
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEG 196
FV+F +A++A+ + GTI +G
Sbjct: 47 --YAFVQFTNDDDAKNALAKGQGTILDG 72
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 34.9 bits (80), Expect = 0.007
Identities = 16/69 (23%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ + +P+ + ++EL L +G++ +++ D + GY FV + ++A+ AI
Sbjct: 2 CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIK 60
Query: 87 ELNGLKLQN 95
+LN +++N
Sbjct: 61 QLNNYEIRN 69
Score = 30.3 bits (68), Expect = 0.31
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IF+ L + ++ L L G + ++++ D +G+ FV +N EA AI+ L
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQL 62
Query: 334 NGYALGD-RLLQV 345
N Y + + RLL V
Sbjct: 63 NNYEIRNGRLLGV 75
Score = 29.6 bits (66), Expect = 0.49
Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ LP+ + +++L L G I R++ D + ++G FV
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN----------------NRGYAFV 47
Query: 175 RFNQHIEAEHAMQELN 190
F+ EA++A+++LN
Sbjct: 48 TFSNKQEAKNAIKQLN 63
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in a family that represents a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), at
their N-terminus, and an RS domain at their C-terminus.
Length = 70
Score = 34.4 bits (79), Expect = 0.008
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++N+ P +L+ F G++ + ++ R+ + FV Y EDA +A+
Sbjct: 3 FVINFDPINTRTRDLERHFEPYGKLVNVRIRRN--------FAFVQYETQEDATKALEST 54
Query: 89 NGLKLQNKSIKVSYA 103
N K+ ++ I V YA
Sbjct: 55 NMSKVLDRVISVEYA 69
Score = 32.5 bits (74), Expect = 0.033
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 274 IFVYNLAP-ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV N P T L + F P+G + NV++ R+ F FV ++A A++S
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRN--------FAFVQYETQEDATKALES 53
Query: 333 LNGYALGDRLLQVSF 347
N + DR++ V +
Sbjct: 54 TNMSKVLDRVISVEY 68
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 34.5 bits (80), Expect = 0.008
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 29 LIVNYVPQTMTQ-----EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
LIV VP + L+ LFSS GE+ + + S V + E+A
Sbjct: 1 LIVTNVPSEVFTNAELKAALESLFSSYGEIATFVYLP------SFRRARVVFSSPEEAAL 54
Query: 84 AIIELNGLKLQNKSIKVSYA 103
A IEL+G + ++V +
Sbjct: 55 ARIELHGTVFEGSVLRVYFG 74
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 34.5 bits (80), Expect = 0.008
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTII 140
+YV G PK T +D++ F +G +
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVN 27
Score = 34.1 bits (79), Expect = 0.011
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
P+ T +++Q F G+V + ++ RD G FV + EDA+ +E LK +
Sbjct: 8 PKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFK-GSVFVEFKTEEDAK-KFLEKEKLKYK 65
Query: 95 NKSIKVS 101
K + V
Sbjct: 66 EKELTVM 72
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 34.6 bits (79), Expect = 0.008
Identities = 18/78 (23%), Positives = 36/78 (46%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
++L V V E+L+ F G + + D T + G+ ++ + DAE A+
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60
Query: 87 ELNGLKLQNKSIKVSYAR 104
LN + + I++ +A+
Sbjct: 61 NLNRKWVCGRQIEIQFAQ 78
Score = 34.2 bits (78), Expect = 0.013
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+A T L + FG +G + +V V D T + +GF ++ + +A A+ +L
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 334 NGYALGDRLLQVSF 347
N + R +++ F
Sbjct: 63 NRKWVCGRQIEIQF 76
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 35.0 bits (80), Expect = 0.009
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQH----LFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
N + +N + + +EEL+ LFS G V ++ T + G FV + A
Sbjct: 1 NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSA 57
Query: 82 ERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
A+ +L G K +++ YA+ S+ + +
Sbjct: 58 TNALRQLQGFPFYGKPMRIQYAKTDSDIVSK 88
Score = 27.7 bits (61), Expect = 3.0
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 288 LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
L+ LF FG V ++ ++ T K +G FV A A++ L G+ + +++ +
Sbjct: 22 LYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSATNALRQLQGFPFYGKPMRIQY 78
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence show that the
RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 35.0 bits (80), Expect = 0.009
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 274 IFVYNLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL PE L+ LFG +G VQ VK++ + K V M + ++A A+
Sbjct: 2 LLVSNLNPERVTPQCLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMSH 56
Query: 333 LNGYALGDRLLQVSFKTHK 351
LNG L + L+++ H+
Sbjct: 57 LNGQKLHGKPLRITLSKHQ 75
Score = 31.5 bits (71), Expect = 0.15
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 5/94 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+ N P+ +T + L LF G+V+ K++ +K V A+ A+ L
Sbjct: 3 LVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSHL 57
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPK 122
NG KL K ++++ ++ + + R GL K
Sbjct: 58 NGQKLHGKPLRITLSKHQTVQLPREGQEDQGLTK 91
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 34.2 bits (78), Expect = 0.010
Identities = 25/72 (34%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV NL + L ++F G V+ + D + K +G G V EAV AI
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQPIEAVQAISMF 61
Query: 334 NGYALGDRLLQV 345
NG L DR + V
Sbjct: 62 NGQFLFDRPMHV 73
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 34.1 bits (78), Expect = 0.010
Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 23/94 (24%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R L+V LP +T+++ + LF YG + +K KG
Sbjct: 1 RCRLFVGNLPADITEDEFKKLFAKYGE--PGEVFINK-------------------GKGF 39
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
GF++ AE A EL+ T G + V+F
Sbjct: 40 GFIKLESRALAEIAKAELDDTPMRG--RQLRVRF 71
Score = 31.0 bits (70), Expect = 0.15
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V +P +T++E + LF+ GE + + K G+GF+ AE A EL
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGK------GFGFIKLESRALAEIAKAEL 57
Query: 89 NGLKLQNKSIKVSY 102
+ ++ + ++V +
Sbjct: 58 DDTPMRGRQLRVRF 71
Score = 27.2 bits (60), Expect = 2.7
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + ++ +LF +G V + K KGFGF+ + + A A L
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAEL 57
Query: 334 NGYALGDRLLQVSF 347
+ + R L+V F
Sbjct: 58 DDTPMRGRQLRVRF 71
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 34.1 bits (78), Expect = 0.011
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIR-DKTTAQSLGYGFVNYYRTEDAERAIIE 87
L+VN + + +++ LQ +F E IR + + GY FV + EDA+ A+
Sbjct: 4 LVVNNLSYSASEDSLQEVF------EKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNS 57
Query: 88 LNGLKLQNKSIKVSY 102
N +++ +SI++ +
Sbjct: 58 CNNTEIEGRSIRLEF 72
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 34.5 bits (80), Expect = 0.011
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN----KSIKVSYAR 104
D ++GY F+N+ E AE+ NG K +N K ++YAR
Sbjct: 36 DFKNKCNVGYAFINFVNPEYAEKFYKAFNGKKWKNFKSKKVCDITYAR 83
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 34.2 bits (78), Expect = 0.013
Identities = 21/74 (28%), Positives = 40/74 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+A +T L + FG +G + +V V D T + +GF +V + +A A+ +L
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 334 NGYALGDRLLQVSF 347
+ + R +++ F
Sbjct: 63 DRKWICGRQIEIQF 76
Score = 28.8 bits (64), Expect = 1.2
Identities = 18/78 (23%), Positives = 36/78 (46%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S+L V + E+L+ F G + + D T + G+ +V + DAE A+
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60
Query: 87 ELNGLKLQNKSIKVSYAR 104
L+ + + I++ +A+
Sbjct: 61 NLDRKWICGRQIEIQFAQ 78
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 34.2 bits (78), Expect = 0.014
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 21 DVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTED 80
D NL + + +++ EL+ F G +E +I+ Q Y F+ + +
Sbjct: 3 DDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDM 61
Query: 81 AERAIIELNGLKLQNKSIKVSYAR 104
A RA + ++G + IK+ Y +
Sbjct: 62 AHRAKVAMSGRVIGRNPIKIGYGK 85
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 34.2 bits (78), Expect = 0.015
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N L + + T+T+ +L+ F G + I+ Q+ YGF+ + + A RA
Sbjct: 7 NRTLFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMAHRAK 65
Query: 86 IELNGLKLQNKSIKVSYAR 104
+ ++G L+ IK+ Y +
Sbjct: 66 LAMSGKVLRRNPIKIGYGK 84
Score = 29.1 bits (65), Expect = 0.76
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL + L + F FG + V + R P + +GF+ N D A A ++
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKR-PGRGQTSTYGFLKFENLDMAHRAKLAM 68
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G L +++ + P
Sbjct: 69 SGKVLRRNPIKIGYGKATP 87
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 33.5 bits (76), Expect = 0.017
Identities = 13/34 (38%), Positives = 24/34 (70%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCD 147
NL+VSGL + DL+NLF YG +++++++ +
Sbjct: 1 NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTN 34
Score = 33.5 bits (76), Expect = 0.020
Identities = 21/72 (29%), Positives = 36/72 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L+ T+ L LFG +G V + KVV + ++ K +G V M++ E I L
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 334 NGYALGDRLLQV 345
+ L + + V
Sbjct: 62 HRTELHGQQISV 73
Score = 32.3 bits (73), Expect = 0.053
Identities = 19/73 (26%), Positives = 35/73 (47%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL V+ + +L++LF G+V S K++ + + + YG V + + R I
Sbjct: 1 NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60
Query: 88 LNGLKLQNKSIKV 100
L+ +L + I V
Sbjct: 61 LHRTELHGQQISV 73
>gnl|CDD|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF9 and
similar proteins. This subfamily corresponds to the
RRM2 of serine/arginine-rich splicing factor SRSF1,
SRSF9 and similar proteins. SRSF1, also termed ASF-1, is
a shuttling SR protein involved in constitutive and
alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9, also termed SRp30C, has been
implicated in the activity of many elements that control
splice site selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. SRSF9 can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 74
Score = 33.6 bits (77), Expect = 0.017
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+IV+ +P T + ++L+ G+V + RD G G V + R ED + A+ +L
Sbjct: 3 VIVSGLPPTGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFLRYEDMKYAVKKL 55
Query: 89 NGLKLQNKSIKVSYAR 104
+ K ++ + SY R
Sbjct: 56 DDSKFRSHEGETSYIR 71
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 33.8 bits (77), Expect = 0.018
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + L ++F G V ++ D + K +G G V EAV AI
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILED-KDGKSRGIGTVTFEQPIEAVQAISMF 61
Query: 334 NGYALGDRLLQV 345
NG L DR + V
Sbjct: 62 NGQLLFDRPMHV 73
Score = 31.5 bits (71), Expect = 0.097
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 16/81 (19%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ ++V+ L + + L+ +F G ++ + IL DK S+GIG
Sbjct: 1 STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGK----------------SRGIG 44
Query: 173 FVRFNQHIEAEHAMQELNGTI 193
V F Q IEA A+ NG +
Sbjct: 45 TVTFEQPIEAVQAISMFNGQL 65
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 33.8 bits (77), Expect = 0.020
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQ--NVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
I + NL P + + + P+ + NV+V++D QT +GF F+ ++ EA +Q
Sbjct: 5 IILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQ 64
Query: 332 SL 333
L
Sbjct: 65 IL 66
>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM2 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C, an essential splicing
regulatory serine/arginine (SR) protein that has been
implicated in the activity of many elements that control
splice site selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. SRSF9 can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. SRSF9 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by an unusually short C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 76
Score = 33.4 bits (76), Expect = 0.020
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+IV+ +P + + ++L+ G+V + +D G G V + R ED E A+ +L
Sbjct: 3 VIVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGVVEFLRKEDMEYALRKL 55
Query: 89 NGLKLQNKSIKVSYARPSSE 108
+ K ++ + SY R E
Sbjct: 56 DDTKFRSHEGETSYIRVMPE 75
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 33.4 bits (77), Expect = 0.021
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V G+PK T+E++ F + +V V +P+ ++G FV
Sbjct: 4 LFVGGIPKTKTKEEILEEFSKVTEGVV-----------DVI--VYRSPDDKNKNRGFAFV 50
Query: 175 RFNQHIEAEHA 185
+ H A A
Sbjct: 51 EYESHRAAAMA 61
Score = 28.4 bits (64), Expect = 1.5
Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGE-VESCKLIR---DKTTAQSLGYGFVNY--YRT- 78
N L V +P+T T+EE+ FS V E V + R DK + G+ FV Y +R
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNR--GFAFVEYESHRAA 58
Query: 79 EDAERAIIELNGLKLQNKSIKVSYA 103
A R ++ + L + V +A
Sbjct: 59 AMARRKLVP-GRILLWGHEVAVDWA 82
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 33.4 bits (77), Expect = 0.022
Identities = 26/94 (27%), Positives = 34/94 (36%), Gaps = 19/94 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L Q+DLE F+ G ++ RI D SKG G V
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR----------------SKGFGHV 45
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
F A+ A+ E +G G I V A
Sbjct: 46 EFATEEGAQKAL-EKSGEELLG--REIRVDLATE 76
Score = 33.1 bits (76), Expect = 0.030
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + Q++L+ F GEV ++ +D S G+G V + E A++A +E
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR-SKGFGHVEFATEEGAQKA-LEK 59
Query: 89 NGLKLQNKSIKVSYARP 105
+G +L + I+V A
Sbjct: 60 SGEELLGREIRVDLATE 76
Score = 32.3 bits (74), Expect = 0.050
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL+ E + L + F G V +V++ +D + KGFG V + A A++
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDG-RSKGFGHVEFATEEGAQKALE-K 59
Query: 334 NGYALGDRLLQV 345
+G L R ++V
Sbjct: 60 SGEELLGREIRV 71
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 33.5 bits (76), Expect = 0.023
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 27 SNLI-VNYVPQTMTQEELQHLFSSVG-EVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
SN+I + +PQ T+ +++ G + +L+R+K++ QS G+ FV + +DA R
Sbjct: 2 SNIIMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATR 60
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 33.5 bits (77), Expect = 0.023
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCK--------LIRDKTTAQSLGYGFVNYYRTEDAE 82
V+ +P T+++L F S+G ++ K L +DK T + G V Y A
Sbjct: 3 VSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAAS 62
Query: 83 RAIIELNGLKLQNKSIKVSYA 103
AI N +IKVS A
Sbjct: 63 AAIEWFNNKDFMGNTIKVSLA 83
Score = 31.2 bits (71), Expect = 0.14
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVK--------VVRDPQTYKCKGFGFVCMTNYDE 325
+FV NL P T + L + FG G ++ K + +D T + KG V +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 326 AVFAIQSLNGYALGDRLLQVS 346
A AI+ N ++VS
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVS 81
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in
Saccharomyces cerevisiae protein Nrd1,
Schizosaccharomyces pombe Rpb7-binding protein seb1 and
similar proteins. This subfamily corresponds to the
RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous
nuclear ribonucleoprotein (hnRNP)-like RNA-binding
protein encoded by gene NRD1 (for nuclear pre-mRNA
down-regulation) from yeast S. cerevisiae. It is
implicated in 3' end formation of small nucleolar and
small nuclear RNAs transcribed by polymerase II, and
plays a critical role in pre-mRNA metabolism. Nrd1
contains an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a short arginine-, serine-, and glutamate-rich
segment similar to the regions rich in RE and RS
dipeptides (RE/RS domains) in many metazoan splicing
factors, and a proline- and glutamine-rich C-terminal
domain (P+Q domain) similar to domains found in several
yeast hnRNPs. Disruption of NRD1 gene is lethal to
yeast cells. Its N-terminal domain is sufficient for
viability, which may facilitate interactions with RNA
polymerase II where Nrd1 may function as an auxiliary
factor. By contrast, the RRM, RE/RS domains, and P+Q
domain are dispensable. Seb1 is an RNA-binding protein
encoded by gene seb1 (for seven binding) from fission
yeast S. pombe. It is essential for cell viability and
bound directly to Rpb7 subunit of RNA polymerase II.
Seb1 is involved in processing of polymerase II
transcripts. It also contains one RRM motif and a
region rich in arginine-serine dipeptides (RS domain).
Length = 79
Score = 33.3 bits (76), Expect = 0.024
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
L V M + +L+ F GEV+SC L DK + FV Y DAE A
Sbjct: 4 RTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKR------HAFVKMYNRRDAENARE 57
Query: 87 ELN 89
+
Sbjct: 58 AME 60
Score = 29.8 bits (67), Expect = 0.37
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 285 DNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGD 340
+ L FG FG VQ+ + D K FV M N +A A +++ Y GD
Sbjct: 17 EYDLRSGFGRFGEVQSCILNND------KRHAFVKMYNRRDAENAREAMEQYKSGD 66
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 33.1 bits (75), Expect = 0.024
Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 19/77 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VSGLP + +L LFRP+ S I K+ S+ + +GFV
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLI---KLTSK----------------QPVGFV 44
Query: 175 RFNQHIEAEHAMQELNG 191
F+ EAE A LNG
Sbjct: 45 SFDSRSEAEAAKNALNG 61
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 33.5 bits (76), Expect = 0.026
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + FG +G +++V V R+P GF FV + +A A++ L
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 61
Query: 334 NGYAL 338
+G L
Sbjct: 62 DGRTL 66
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 32.9 bits (76), Expect = 0.027
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL ET +L LF F + V++V +G FV ++A A+Q+L
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58
Query: 334 NGY 336
G+
Sbjct: 59 QGF 61
Score = 31.0 bits (71), Expect = 0.12
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 23/79 (29%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS-KGIGF 173
L++ LP+ T+E LE LF + G E+ + +GI F
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQF----------------------PGFKEVRLVPRRGIAF 42
Query: 174 VRFNQHIEAEHAMQELNGT 192
V F +A A+Q L G
Sbjct: 43 VEFETEEQATVALQALQGF 61
Score = 29.8 bits (68), Expect = 0.31
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 13/80 (16%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N L + +P+ T+E L+ LF+ + +L+ + G FV + E E+A
Sbjct: 2 NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRR------GIAFVEF---ETEEQAT 52
Query: 86 IELNGL----KLQNKSIKVS 101
+ L L ++K+S
Sbjct: 53 VALQALQGFKITPGHAMKIS 72
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 32.9 bits (75), Expect = 0.030
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q + +I N P T++ E L+ +F G+V K +R+ T FV ++ DA +A
Sbjct: 1 QGTLVIFNLDP-TVSSETLRSIFQVYGDV---KELRE--TPCKREQRFVEFFDVRDAAKA 54
Query: 85 IIELNGLKLQNKSIKV 100
+ +NG ++ K + +
Sbjct: 55 LRAMNGKEISGKPVVI 70
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 32.9 bits (76), Expect = 0.031
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ + NL P+ ++ L L PFG V NV ++R K V M + + A +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRG------KNQALVEMDSVESAKSMVDYY 55
Query: 334 --NGYALGDRLLQVSFKTH 350
+ R + + + H
Sbjct: 56 LTVPALIRGRRVYIQYSNH 74
Score = 29.5 bits (67), Expect = 0.43
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDK------MASENV-RSFVSGTPEIPQI 167
L++ LP +T+ DL L P+G + +L K M S +S V +P +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPAL 61
Query: 168 SKG-IGFVRFNQH 179
+G +++++ H
Sbjct: 62 IRGRRVYIQYSNH 74
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 33.1 bits (75), Expect = 0.032
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P +T ++L+ FS G V ++ + +S G G V + E AE+A +
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRLM 59
Query: 89 NGLKLQNKSIKVSYAR 104
NG+K+ + I V R
Sbjct: 60 NGIKINGREIDVRLDR 75
Score = 28.8 bits (64), Expect = 0.81
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 17/78 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V LP +T + L+ F G ++ + I KM EN +S KG G V
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEI---KM--ENGKS------------KGCGTV 44
Query: 175 RFNQHIEAEHAMQELNGT 192
RF+ AE A + +NG
Sbjct: 45 RFDSPESAEKACRLMNGI 62
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 32.9 bits (75), Expect = 0.033
Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG--AVQNVKVVRDPQTYKCK---GFGFVCMTNYDEAVF 328
+FV NL T + L F VK DP+ GFGFV ++A
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 329 AIQSLNGYALGDRLLQVSF 347
A+++++G+ L L V F
Sbjct: 63 ALKAMDGFVLDGHTLVVKF 81
Score = 32.1 bits (73), Expect = 0.078
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 67 SLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYAR 104
S+G+GFV + E A+ A+ ++G L ++ V ++
Sbjct: 46 SMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83
Score = 30.6 bits (69), Expect = 0.22
Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 16/96 (16%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP--QISKG 170
A L+V L T + L + F+ + +R+ K + P+ P +S G
Sbjct: 1 ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARV---KTKPD---------PKRPGQTLSMG 48
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GFV F +A+ A++ ++G + +G + + VKF+
Sbjct: 49 FGFVGFKTKEQAQAALKAMDGFVLDGHT--LVVKFS 82
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 32.7 bits (75), Expect = 0.035
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
L+ +F G + L+ K YG+ Y E AERAI L+G ++ +KV
Sbjct: 16 LEDVFCRFGGLIDVYLVPGKN------YGYAKYADRESAERAITTLHGKEVNGVKLKV 67
Score = 28.4 bits (64), Expect = 0.90
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 275 FVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
V N +P + +L +F FG + +V +V K +G+ + + A AI +L+
Sbjct: 4 IVCNPSPPPDY-ILEDVFCRFGGLIDVYLVPG------KNYGYAKYADRESAERAITTLH 56
Query: 335 G 335
G
Sbjct: 57 G 57
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal Rrp7 domain. .
Length = 102
Score = 33.4 bits (77), Expect = 0.036
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVES 55
++N VP T+E L+ LFS G+VES
Sbjct: 4 FVLN-VPPYCTEESLKRLFSRCGKVES 29
Score = 27.7 bits (62), Expect = 4.0
Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG--IG 172
L+V +P + T+E L+ LF G + S L +K S I KG +
Sbjct: 3 LFVLNVPPYCTEESLKRLFSRCGK-VESVELQEKPGPAESEDLTSKFFPPKPI-KGFKVA 60
Query: 173 FVRFNQHIEAEHAMQELNGT---IPEGASEPITV 203
+V F + A+ +L T I S PI
Sbjct: 61 YVVFKKPSSLSRAL-KLKSTEPFILSTESHPILT 93
>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 32.2 bits (74), Expect = 0.037
Identities = 15/45 (33%), Positives = 18/45 (40%), Gaps = 8/45 (17%)
Query: 313 KGFGFVCMTNYDEAVFAIQS-----LNGYALGDRLLQVSFKTHKP 352
KGFGF+ + + VF S L GD V FK P
Sbjct: 9 KGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDE---VEFKVVSP 50
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 32.6 bits (75), Expect = 0.039
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
+ED L ++F +G V +V VV K KG V + A A+++ G
Sbjct: 17 SED-ELRKIFSKYGDVSDV-VVSS----KKKGSAIVEFASKKAAEAAVENECGLP--SNP 68
Query: 343 LQVSF 347
L VS+
Sbjct: 69 LLVSW 73
Score = 29.5 bits (67), Expect = 0.47
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGL 91
+++EL+ +FS G+V ++ K G V + + AE A+ GL
Sbjct: 16 YSEDELRKIFSKYGDVSDV-VVSSKKK----GSAIVEFASKKAAEAAVENECGL 64
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 32.6 bits (74), Expect = 0.042
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P T + L+ F+ G V + + +S G G V + E AERA +
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRMM 59
Query: 89 NGLKLQNKSIKVSYAR 104
NG KL + I V R
Sbjct: 60 NGYKLNGREIDVRIDR 75
Score = 28.4 bits (63), Expect = 1.5
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV NL + +L F G V + + K KG G V + + A A + +
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRMM 59
Query: 334 NGYALGDRLLQV 345
NGY L R + V
Sbjct: 60 NGYKLNGREIDV 71
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 32.5 bits (74), Expect = 0.046
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YV LP + ++DLE+LF YG I + +N R V FV
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIEL-------KNRRGLVP-----------FAFV 43
Query: 175 RFNQHIEAEHAMQELNG 191
RF +AE A+ NG
Sbjct: 44 RFEDPRDAEDAVFGRNG 60
Score = 31.3 bits (71), Expect = 0.11
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V +P + +++L+ LF G + +L K + + FV + DAE A+ NG
Sbjct: 4 VGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60
Query: 91 LKLQNKSIKVSY 102
++V +
Sbjct: 61 YDFGQCRLRVEF 72
Score = 29.4 bits (66), Expect = 0.53
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V NL + + L LF +G ++++++ F FV + +A A+
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP---FAFVRFEDPRDAEDAVFGR 58
Query: 334 NGYALGDRLLQVSF 347
NGY G L+V F
Sbjct: 59 NGYDFGQCRLRVEF 72
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 32.4 bits (74), Expect = 0.047
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 31 VNYVPQTMTQEELQHLF-SSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
++ +P + ++L+ LF VGEV +L +D+ +S G G V + E ++A+ +N
Sbjct: 4 ISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKALETMN 62
Query: 90 GLKLQNKSIKV 100
+L+ + + V
Sbjct: 63 RYELKGRKLVV 73
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 32.2 bits (74), Expect = 0.055
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++V +P T+EEL+ LF G + L +T A V + DA +A L
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIA------LVEFLEPSDARKAFKSL 56
Query: 89 NGLKLQN 95
+ ++
Sbjct: 57 AYKRFKH 63
Score = 28.7 bits (65), Expect = 0.83
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 21/76 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V LP T+E+L LF +G++ R+L + S+ I V
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSL--GRLL---LPP----------------SRTIALV 41
Query: 175 RFNQHIEAEHAMQELN 190
F + +A A + L
Sbjct: 42 EFLEPSDARKAFKSLA 57
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 32.4 bits (74), Expect = 0.055
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL + L + FG + +K+V++ K FV + A+ + +L
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVTTL 59
Score = 32.0 bits (73), Expect = 0.079
Identities = 12/61 (19%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ + +P++ ++EEL+ G ++ K++++K FV++ +A + +
Sbjct: 5 NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEK------NIAFVHFLSIANAIKVVTT 58
Query: 88 L 88
L
Sbjct: 59 L 59
Score = 30.1 bits (68), Expect = 0.35
Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 21/76 (27%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
N+Y+ LP+ ++E+L +G I +I+ + K I F
Sbjct: 5 NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE---------------------KNIAF 43
Query: 174 VRFNQHIEAEHAMQEL 189
V F A + L
Sbjct: 44 VHFLSIANAIKVVTTL 59
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 32.2 bits (74), Expect = 0.057
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQ--SLGYGFVNYYRTEDAERA 84
V V T+E+++ LF +G++E +L FV Y ED A
Sbjct: 4 VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVA 59
>gnl|CDD|240972 cd12528, RRM2_MEI2_fungi, RNA recognition motif 2 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM2 of fungal Mei2-like proteins.The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 81
Score = 32.5 bits (74), Expect = 0.058
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
LQ+L S+ G++++ K + + ++ ++ T DA+ A+ ELNG + N
Sbjct: 25 LQNLLSTFGDLKAFKSLP--SQQDNVKEFICEFFDTRDADNAVDELNGRVVDN 75
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 32.2 bits (74), Expect = 0.063
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV NL P T + L QLF + +K+ KG G VC +++ FA Q+
Sbjct: 4 TLFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQA 56
Query: 333 LN 334
LN
Sbjct: 57 LN 58
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 32.0 bits (73), Expect = 0.064
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
L+V LP +T+++L+ F+ +G ++ RI
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRI 35
Score = 31.2 bits (71), Expect = 0.13
Identities = 13/61 (21%), Positives = 27/61 (44%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ L V +P +T++EL+ F G V ++ + +GFV + E ++ +
Sbjct: 3 SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62
Query: 86 I 86
Sbjct: 63 A 63
Score = 31.2 bits (71), Expect = 0.15
Identities = 20/75 (26%), Positives = 32/75 (42%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + ++ L + F FG V V++ + FGFV + + + +
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65
Query: 334 NGYALGDRLLQVSFK 348
Y GD L V K
Sbjct: 66 PIYFRGDHRLNVEEK 80
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein
1 (scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase,
or COMPASS component SET1, or lysine
N-methyltransferase 2, which is encoded by SET1 from
the yeast S. cerevisiae. It is a nuclear protein that
may play a role in both silencing and activating
transcription. scSet1p is closely related to the SET
domain proteins of multicellular organisms, which are
implicated in diverse aspects of cell morphology,
growth control, and chromatin-mediated transcriptional
silencing. scSet1p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a conserved SET domain that may play a role in DNA
repair and telomere function. .
Length = 110
Score = 32.7 bits (75), Expect = 0.073
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYY 76
++V + +++ +++ FSS GE+ + D TA LG + YY
Sbjct: 2 PVEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYY 52
>gnl|CDD|241073 cd12629, RRM2_IGF2BP2, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM2 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, a ubiquitously expressed
RNA-binding protein involved in the stimulation of
insulin action. It is predominantly nuclear. SNPs in
IGF2BP2 gene are implicated in susceptibility to type 2
diabetes. IGF2BP2 plays an important role in cellular
motility; it regulates the expression of PINCH-2, an
important mediator of cell adhesion and motility, and
MURF-3, a microtubule-stabilizing protein, through
direct binding to their mRNAs. IGF2BP2 may be involved
in the regulation of mRNA stability through the
interaction with the AU-rich element-binding factor
AUF1. In addition, IGF2BP2 binds initially to nascent
beta-actin transcripts and facilitates the subsequent
binding of the shuttling IGF2BP1. IGF2BP2 contains four
hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. .
Length = 76
Score = 32.0 bits (72), Expect = 0.073
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P + E L L + G VE+ + + T + V Y E+A+ A+ +L+G +
Sbjct: 8 IPPHLQWEVLDGLLAQYGTVENVEQVNTDTETAVVN---VTYATKEEAKVAVEKLSGHQF 64
Query: 94 QNKSIKVSY 102
++ S KVSY
Sbjct: 65 EDYSFKVSY 73
Score = 28.1 bits (62), Expect = 1.6
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVR-DPQTYKCKGFGFVCMTNYDEAVFAIQS 332
I + N+ P + VL L +G V+NV+ V D +T V +EA A++
Sbjct: 3 IQIRNIPPHLQWEVLDGLLAQYGTVENVEQVNTDTETAVVN----VTYATKEEAKVAVEK 58
Query: 333 LNGYALGDRLLQVSF 347
L+G+ D +VS+
Sbjct: 59 LSGHQFEDYSFKVSY 73
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 34.4 bits (79), Expect = 0.075
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 8/92 (8%)
Query: 260 SMLPPKSLHGSGWCIFVYNLAPETED-NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
S P G G + V L E + + L+ LF +G V+ VK +++ K +
Sbjct: 266 SYGPAGG--GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALI 318
Query: 319 CMTNYDEAVFAIQSLNGYALGDRLLQVSFKTH 350
M + +A A+ LNG L + L+V
Sbjct: 319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ 350
Score = 33.6 bits (77), Expect = 0.15
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++ + + + L +LF G VE K +++K + A+ A+ L
Sbjct: 279 MVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKK-----ETALIEMADPYQAQLALTHL 333
Query: 89 NGLKLQNKSIKV 100
NG+KL K ++V
Sbjct: 334 NGVKLFGKPLRV 345
>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato
(cpo) coding RNA-binding protein and similar proteins.
This subfamily corresponds to the RRM of Cpo, an
RNA-binding protein encoded by Drosophila couch potato
(cpo) gene. Cpo contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It may
control the processing of RNA molecules required for the
proper functioning of the peripheral nervous system
(PNS). .
Length = 83
Score = 32.0 bits (72), Expect = 0.080
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 14/77 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VSGLP +L LFR Y S + K+ S+N ++ + +GFV
Sbjct: 4 LFVSGLPMDAKPRELYLLFRAYKGYEGSLL---KVTSKNGKT-----------TSPVGFV 49
Query: 175 RFNQHIEAEHAMQELNG 191
F AE A Q+L G
Sbjct: 50 TFETRAGAEAAKQDLQG 66
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 31.4 bits (72), Expect = 0.083
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 34 VPQTMTQEELQHLFSS-VGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
V T+ +E+++ F +V +L D A V + DA +A + LNG +
Sbjct: 8 VSDTVNEEQIKAFFEKIGPDVRKIELFPDHEGA------LVEFESPSDAGKASLSLNGSQ 61
Query: 93 LQNKSIKV 100
K+IK+
Sbjct: 62 FGGKTIKI 69
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 31.9 bits (73), Expect = 0.085
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
L V + ++ E L+ FS GEVE +I D +S G G V + R A+ AI
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDD-RGRSTGEGIVEFSRKPGAQAAI 57
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 31.9 bits (73), Expect = 0.090
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ N P T T ++L FS GEV+ ++ D+T Q Y FV + A ++L
Sbjct: 8 YVGNLDPTT-TADQLLEFFSQAGEVKYVRMAGDET--QPTRYAFVEFAEQTSVINA-LKL 63
Query: 89 NGLKLQNKSIKVSYAR 104
NG + +KV+++
Sbjct: 64 NGAMFGGRPLKVNHSN 79
Score = 30.3 bits (69), Expect = 0.27
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V NL P T + L + F G V+ V++ D + FV + A++ L
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR--YAFVEFAEQTSVINALK-L 63
Query: 334 NGYALGDRLLQV 345
NG G R L+V
Sbjct: 64 NGAMFGGRPLKV 75
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 31.9 bits (72), Expect = 0.093
Identities = 22/83 (26%), Positives = 50/83 (60%), Gaps = 8/83 (9%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSV-GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
++ L ++ +PQ++T+E+L+ LF++ G V++ K +D A + E+A +A
Sbjct: 3 SATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHKMA------LLQMSTVEEAIQA 56
Query: 85 IIELNGLKL-QNKSIKVSYARPS 106
+I+L+ L +N ++VS+++ +
Sbjct: 57 LIDLHNYNLGENHHLRVSFSKST 79
>gnl|CDD|241142 cd12698, RRM3_PTBPH3, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subgroup corresponds to the RRM3 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 31.4 bits (71), Expect = 0.11
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQ--SLGYGFVNYYRTEDAERAII 86
L+ N P+ + ++L +LFS+ G + KL+ +K +G GF AE A+
Sbjct: 5 LVSNLNPEKIDADKLFNLFSNYGNIVRIKLLHNKPDHALIQMGDGF-------QAELAVN 57
Query: 87 ELNGLKLQNKSIKVSYAR 104
L G L K ++V++++
Sbjct: 58 YLKGAMLFGKRMEVNFSK 75
Score = 27.2 bits (60), Expect = 3.5
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 112 RANLYVSGL-PKHMTQEDLENLFRPYGTIITSRILCDK 148
R L VS L P+ + + L NLF YG I+ ++L +K
Sbjct: 1 RCTLLVSNLNPEKIDADKLFNLFSNYGNIVRIKLLHNK 38
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 31.3 bits (71), Expect = 0.11
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P + + E++ LF G + L K + GY F+ + DAE AI
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58
Query: 89 NGLKLQNKSIKV 100
+G + ++V
Sbjct: 59 DGYDFDGQRLRV 70
>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to the
RRM2 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D member
3, known previously as PMP-70) and/or PXF (peroxisomal
farnesylated protein, known previously as PEX19). It
associates with LIM kinase 2 (LIMK2) and may serve as a
relatively common target of human autoantibodies
reactive to cytoplasmic vesicle-like structures. LKAP
contains two RNA recognition motifs (RRMs), also known
as RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). However, whether those RRMs are bona fide RNA
binding sites remains unclear. Moreover, there is no
evidence of LAKP localization in the nucleus. Therefore,
if the RRMs are functional, their interaction with RNA
species would be restricted to the cytoplasm and
peroxisomes.
Length = 89
Score = 31.5 bits (72), Expect = 0.12
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 277 YNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQT---YKCKGFGFVCMTNYDEAVFAIQSL 333
Y L+ + L F G V +V + PQT V + N +A +AI L
Sbjct: 14 YRLSRKELQQTLTNQFKRHGKVLSVSLR--PQTDGSLVAS----VRVPNLQDAQYAISQL 67
Query: 334 NGYALGDRLLQVSFKT 349
+ +G + + VS+
Sbjct: 68 HRRKIGSKRILVSYAQ 83
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 31.2 bits (71), Expect = 0.12
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 18/77 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YV LP + + D+E+LF YG I + ++++ G P FV
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPI----------KAIDLKNRRRGPP--------FAFV 43
Query: 175 RFNQHIEAEHAMQELNG 191
F +AE A++ +G
Sbjct: 44 EFEDPRDAEDAVRGRDG 60
Score = 28.1 bits (63), Expect = 1.2
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKV---VRDPQTYKCKGFGFVCMTNYDEAVFAI 330
I+V NL + + + LF +G ++ + + R P F FV + +A A+
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGP------PFAFVEFEDPRDAEDAV 55
Query: 331 QSLNGYALGDRLLQVSF 347
+ +GY L+V F
Sbjct: 56 RGRDGYDFDGYRLRVEF 72
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 31.1 bits (71), Expect = 0.14
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQ--------NVKVVRDPQTYKCKGFGFVCMTNYDE 325
I++ L + ++ L +LFG G ++ +K+ D +T + KG V +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59
Query: 326 AVFAIQSLNGYALGDRLLQVSF 347
A AI+ NGY ++VS
Sbjct: 60 AQAAIEWFNGYEFRGNKIKVSL 81
Score = 28.8 bits (65), Expect = 0.98
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 35 PQTMTQEELQHLFSSVGEVES--------CKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
P +T++ L LF +G ++ K+ DK T G V Y A+ AI
Sbjct: 7 PDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPK-GEATVTYDDPSAAQAAIE 65
Query: 87 ELNGLKLQNKSIKVS 101
NG + + IKVS
Sbjct: 66 WFNGYEFRGNKIKVS 80
>gnl|CDD|130586 TIGR01523, ATPase-IID_K-Na, potassium and/or sodium efflux P-type
ATPase, fungal-type. Initially described as a calcium
efflux ATPase , more recent work has shown that the S.
pombe CTA3 gene is in fact a potassium ion efflux pump.
This model describes the clade of fungal P-type ATPases
responsible for potassium and sodium efflux. The degree
to which these pumps show preference for sodium or
potassium varies. This group of ATPases has been
classified by phylogentic analysis as type IID. The
Leishmania sequence (GP|3192903), which falls between
trusted and noise in this model, may very well turn out
to be an active potassium pump.
Length = 1053
Score = 33.8 bits (77), Expect = 0.14
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 18 YQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGE 52
Y SD+ ++ + I +P+ +T +E QH VGE
Sbjct: 7 YFSDIADEAAEFIGTSIPEGLTHDEAQHRLKEVGE 41
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 31.1 bits (71), Expect = 0.14
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 34 VPQTMTQEELQHLFSSVGEVE-SCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
+P +T+ E+ F+ + E ++ DKT ++LG +V + EDA RA L+ K
Sbjct: 7 IPFDVTKGEVLAFFAGIAIAEQGIHILYDKTG-KTLGEAYVEFVSEEDAMRA-ERLHRKK 64
Query: 93 LQNKSIKVS 101
L+ + I +
Sbjct: 65 LKGREILLR 73
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 30.8 bits (70), Expect = 0.14
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 51 GEVESC-KLIRDKTTAQSL--GYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
GEV K+ D ++ G ++ + R+EDA RAI++LNG + +K
Sbjct: 17 GEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 31.1 bits (71), Expect = 0.16
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 14/76 (18%)
Query: 265 KSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
++L+ G I + + E+ +L + FG +G +++++V+ KG FV
Sbjct: 2 RTLYVGG--IKAGSALKQIEE-ILRRHFGEWGDIEDIRVLPS------KGIAFVRYKYRA 52
Query: 325 EAVFAI-----QSLNG 335
A FA QSL+G
Sbjct: 53 SAEFAKEAMADQSLDG 68
Score = 28.0 bits (63), Expect = 2.0
Identities = 28/102 (27%), Positives = 41/102 (40%), Gaps = 36/102 (35%)
Query: 115 LYVSGLPKHMTQEDLENL----FRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
LYV G+ + +E + F +G I E++R +P SKG
Sbjct: 4 LYVGGIKAGSALKQIEEILRRHFGEWGDI------------EDIRV-------LP--SKG 42
Query: 171 IGFVRFNQHIEAEHAM-----QELNGTIPEGASEPITVKFAN 207
I FVR+ AE A Q L+G E + V++AN
Sbjct: 43 IAFVRYKYRASAEFAKEAMADQSLDG------GEVLNVRWAN 78
>gnl|CDD|224594 COG1680, AmpC, Beta-lactamase class C and other penicillin binding
proteins [Defense mechanisms].
Length = 390
Score = 33.4 bits (76), Expect = 0.17
Identities = 26/114 (22%), Positives = 37/114 (32%), Gaps = 10/114 (8%)
Query: 211 GRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGS 270
G A A A L + A M F A+ + G L A L D P G
Sbjct: 261 GSALAGAGGLFSTARDMARFGQALLNGGVLLGRQL-LP-AMLVPDFTTGGQAPGLGGEGL 318
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
G+ ++V P FG G + DP+ + V ++N
Sbjct: 319 GYGLWVV---PGGAGPASPGAFGHTGGFGTFIAI-DPE----RNLAVVLLSNRP 364
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate
probable RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 31.2 bits (70), Expect = 0.18
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 42 ELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+L+ FS+VG+V ++I D+ + +S G +V + + A I L G +L
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGLTGQRL 67
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 30.7 bits (69), Expect = 0.18
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYAR 104
GYGFV + DA+ A+ ELNG L + + V +AR
Sbjct: 34 GYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR 69
Score = 30.0 bits (67), Expect = 0.30
Identities = 24/95 (25%), Positives = 39/95 (41%), Gaps = 25/95 (26%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+Y+ L + D+E F+ YG I+ E+ + G GFV
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKIL----------------------EV-DLKNGYGFV 38
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F+ +A+ A+ ELNG + E + V+ A P
Sbjct: 39 EFDDLRDADDAVYELNGK--DLCGERVIVEHARGP 71
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 30.5 bits (69), Expect = 0.19
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 59 IRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
++D S +G+V++ ED E+A +EL G KL IK+ A
Sbjct: 32 VQDVRIGSSKKFGYVDFESAEDLEKA-LELTGKKLLGNEIKLEKA 75
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 30.9 bits (70), Expect = 0.19
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
++VS LP +T+ED+ N +G I+ ++
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKV 39
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 31.1 bits (71), Expect = 0.20
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 22 VNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
VN ++ L+V VP ++EL LF+ G +E +L+ + + + + + A
Sbjct: 6 VNSESRYLLVQGVPALGVEKELLELFALYGTIEEYRLLDEYPCEEFTEVYLIKFETIQSA 65
Query: 82 ERAIIELNGLKLQNKS-----IKVSYARPSSEAI 110
A KL +S + V YA P E +
Sbjct: 66 RFA-----KRKLDERSFFGGLLHVCYA-PEYETV 93
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 31.1 bits (71), Expect = 0.21
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVK---VVRDPQTYKCKGF 315
+FV NL T+ L +LF FG +++V+ V + K
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVA 47
Score = 30.3 bits (69), Expect = 0.31
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 18/84 (21%)
Query: 34 VPQTMTQEELQHLFSSVGEVES---------CKLIRDKTTAQSLGY----GFVNYY---- 76
+P T +++L+ LF G +ES K + K A + VN Y
Sbjct: 8 LPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFK 67
Query: 77 RTEDAERAIIELNGLKLQNKSIKV 100
E AE+A ++LNG + + I+V
Sbjct: 68 EEESAEKA-LKLNGTEFEGHHIRV 90
Score = 27.6 bits (62), Expect = 3.0
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 23/95 (24%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ----ISK 169
++V LP ++DL+ LF+ +G I + R RS ++P+ I K
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRF----------RSVPVKEKKLPKKVAAIKK 51
Query: 170 GI--------GFVRFNQHIEAEHAMQELNGTIPEG 196
+V F + AE A+ +LNGT EG
Sbjct: 52 KFHDKKDNVNAYVVFKEEESAEKAL-KLNGTEFEG 85
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 30.7 bits (70), Expect = 0.21
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 39 TQEELQHLFSSVG--EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE-LNGLKLQN 95
T E+L+ + G +V+S K K +S G+ +V + +E A A+ E L G +
Sbjct: 11 TDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFA-SEAAAAAVKEKLEGREFNG 69
Query: 96 KSIKVSY 102
K V+Y
Sbjct: 70 KKCVVTY 76
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 70
Score = 30.5 bits (69), Expect = 0.21
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+++ +P +T++E+ L S +V+ C + + K TAQ V + A RAI +L
Sbjct: 2 IVIRNLPADVTKQEVHDLLSDY-QVKYCDVDKSKRTAQ------VTLLNGDQASRAIAKL 54
Query: 89 NGLKLQNKSIKV 100
+ + + I V
Sbjct: 55 HQSSYKERKISV 66
Score = 27.1 bits (60), Expect = 3.7
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 311 KCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQV 345
K K V + N D+A AI L+ + +R + V
Sbjct: 32 KSKRTAQVTLLNGDQASRAIAKLHQSSYKERKISV 66
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 30.3 bits (69), Expect = 0.23
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRD----KTTAQSLGYGFVNYYRTEDAERA 84
L+V ++P +++++ + L G S +++ K TA F + + A +A
Sbjct: 2 LLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTA------FATFDNEQAASQA 54
Query: 85 IIELNGLKLQNKSIKVSYA 103
+ L+ LK+ K + V YA
Sbjct: 55 LSRLHQLKILGKRLVVEYA 73
Score = 27.6 bits (62), Expect = 2.2
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V +L PE ++ L FGA +V+V+ + K K F N A A+
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFGA-SSVRVMS--RRGKLKNTAFATFDNEQAASQALSR 57
Query: 333 LNGYALGDRLLQVSF 347
L+ + + L V +
Sbjct: 58 LHQLKILGKRLVVEY 72
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 30.8 bits (69), Expect = 0.24
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 42 ELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+L+ FS+VG+V ++I D+ + +S G +V + AI
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 30.8 bits (69), Expect = 0.26
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 7/89 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQH----LFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
N + +N + + + ++EL+ +FS G++ + R + + G FV + A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSA 59
Query: 82 ERAIIELNGLKLQNKSIKVSYARPSSEAI 110
A+ + G +K +++ YA+ S+ I
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYAKTDSDII 88
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding protein
with multiple splicing (RBP-MS). The biological function
of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 76
Score = 30.4 bits (68), Expect = 0.26
Identities = 25/77 (32%), Positives = 34/77 (44%), Gaps = 19/77 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VSGLP + +L LFRP+ S I K+ S+ + +GFV
Sbjct: 4 LFVSGLPVDIKPRELYLLFRPFKGYEGSLI---KLTSK----------------QPVGFV 44
Query: 175 RFNQHIEAEHAMQELNG 191
F+ AE A LNG
Sbjct: 45 TFDSRAGAEAAKNALNG 61
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand
effect modulator 6, a member of a family of
transcription coactivators that plays a central role in
the regulation of cellular energy metabolism. As an
inducible transcription coactivator, PGC-1alpha can
interact with a broad range of transcription factors
involved in a wide variety of biological responses,
such as adaptive thermogenesis, skeletal muscle fiber
type switching, glucose/fatty acid metabolism, and
heart development. PGC-1alpha stimulates mitochondrial
biogenesis and promotes oxidative metabolism. It
participates in the regulation of both carbohydrate and
lipid metabolism and plays a role in disorders such as
obesity, diabetes, and cardiomyopathy. PGC-1alpha is a
multi-domain protein containing an N-terminal
activation domain region, a central region involved in
the interaction with at least a nuclear receptor, and a
C-terminal domain region. The N-terminal domain region
consists of three leucine-rich motifs (L1, NR box 2 and
3), among which the two last are required for
interaction with nuclear receptors, potential nuclear
localization signals (NLS), and a proline-rich region
overlapping a putative repression domain. The
C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 30.7 bits (69), Expect = 0.28
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 38 MTQEELQHLFSSVGEVESCKL-IRDKTTAQSLGYGFVNYYRTEDAERAI 85
T+ EL+ F GE+E C + +RD + YGF+ Y T DA A+
Sbjct: 14 TTRTELRDRFEVFGEIEECTVNLRDDGDS----YGFITYRYTCDAFAAL 58
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 156
Score = 31.5 bits (71), Expect = 0.30
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 49 SVGEVESCKLI---RDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
S G V+ K+ T +S GYGF+ + + A A+ LNG + K I
Sbjct: 67 SGGVVKQAKVETEKAGSTAGRSRGYGFMEFISHKYALMALRWLNGHAVTVKKI 119
Score = 29.6 bits (66), Expect = 1.7
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 296 GAVQNVKVV---RDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYAL 338
G V+ KV + +G+GF+ ++ A+ A++ LNG+A+
Sbjct: 69 GVVKQAKVETEKAGSTAGRSRGYGFMEFISHKYALMALRWLNGHAV 114
>gnl|CDD|241211 cd12767, RRM2_SRSF1, RNA recognition motif 2 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM2
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, a
splicing regulatory serine/arginine (SR) protein
involved in constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation. SRSF1
is a shuttling SR protein and contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
separated by a long glycine-rich spacer, and a
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 76
Score = 30.1 bits (67), Expect = 0.32
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
++V+ +P + + ++L+ G+V + RD G G V + R ED A+
Sbjct: 1 YRVVVSGLPPSGSWQDLKDHMREAGDVCYADVFRD-------GTGVVEFVRKEDMTYAVR 53
Query: 87 ELNGLKLQNKSIKVSYAR 104
+L+ K ++ + +Y R
Sbjct: 54 KLDNTKFRSHEGETAYIR 71
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 77
Score = 29.9 bits (67), Expect = 0.38
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 314 GFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
G V M NY EA+ AI LN +G R +++S
Sbjct: 43 GTAIVAMENYYEAMAAINELNDRPIGPRKVKLSL 76
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 30.0 bits (67), Expect = 0.41
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + F +G ++ V + R+P GF FV + +A A++ L
Sbjct: 2 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 56
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G + ++V T P
Sbjct: 57 DGKVICGSRVRVELSTGMP 75
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 75
Score = 29.7 bits (67), Expect = 0.48
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 313 KGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVS 346
G V + EA+ A++ LNG +G R ++++
Sbjct: 42 TGEATVAFDTHREAMAAVRELNGRPIGTRKVKLT 75
Score = 27.4 bits (61), Expect = 3.1
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 169 KGIGFVRFNQHIEAEHAMQELNG 191
G V F+ H EA A++ELNG
Sbjct: 42 TGEATVAFDTHREAMAAVRELNG 64
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 29.7 bits (67), Expect = 0.48
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSR 143
++V GLP++ T+E + +F G II R
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEIIAIR 37
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 29.9 bits (68), Expect = 0.51
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 115 LYVSGLP-KHMTQEDLENLFRPYGTIITSRILC-DKMASENVRSFVSGTPEIPQISKGIG 172
+ LP + T E + LF G I RIL + +++ + S P++ K
Sbjct: 3 VVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGT--KECA 60
Query: 173 FVRFNQHIEAEHAMQELNG 191
V F + A A++EL+
Sbjct: 61 VVEFEKLEAARKAVEELSA 79
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed
RNA-binding motif, single-stranded-interacting protein
4, an RNA-binding protein that is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. For instance, DND1
binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and
cell cycle regulator and tumor suppressor, LATS2 (large
tumor suppressor, homolog 2 of Drosophila). It helps
maintain their protein expression through blocking the
inhibitory function of microRNAs (miRNA) from these
transcripts. DND1 may also impose another level of
translational regulation to modulate expression of
critical factors in embryonic stem (ES) cells. DND1
interacts specifically with apolipoprotein B editing
complex 3 (APOBEC3), a multi-functional protein
inhibiting retroviral replication. The DND1-APOBEC3
interaction may play a role in maintaining viability of
germ cells and for preventing germ cell tumor
development. DND1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 78
Score = 29.4 bits (66), Expect = 0.52
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S + + +PQ + ++ L LF SVG + +L+ + + G+ + Y A AI
Sbjct: 2 SEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKYSDRRGASAAIA 60
Query: 87 ELNGLKLQ 94
L+ +L
Sbjct: 61 TLHNYELP 68
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 29.6 bits (66), Expect = 0.54
Identities = 21/85 (24%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKL-IRDKTTAQSLGYGFVNYYRTEDAE 82
+++ +++ +P +T+ +++ L S + + + + T S G+ FV +Y +DA
Sbjct: 3 KESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDAT 62
Query: 83 RAIIELNGLKL--QNKSIKVSYARP 105
+E N KL Q K+I + Y+ P
Sbjct: 63 SW-MEANQKKLVIQGKTIAMHYSNP 86
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 29.6 bits (66), Expect = 0.56
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
L V +PQ ++ E L+ FS G+VE +I D + G G V + A +A+
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDD-RGRPTGKGIVEFAGKPSARKAL 57
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 29.0 bits (65), Expect = 0.61
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F N + + + +LFG +G V V D ++ GF FV M + +A AI+ L
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRV----DMKS----GFAFVYMEDERDAEDAIRGL 54
Query: 334 NGYALG 339
+ + G
Sbjct: 55 DNFEFG 60
Score = 29.0 bits (65), Expect = 0.74
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL--QNKS 97
Q E++ LF G V+ + K+ G+ FV DAE AI L+ + Q +
Sbjct: 14 QSEIERLFGKYGRVDRVDM---KS-----GFAFVYMEDERDAEDAIRGLDNFEFGRQRRR 65
Query: 98 IKVSYAR 104
++V +A+
Sbjct: 66 LRVEWAK 72
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 29.4 bits (66), Expect = 0.62
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V V T EEL+ F G V ++ DK + G+ ++ + E A + L+
Sbjct: 4 VGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA-LALDE 62
Query: 91 LKLQNKSIKVSYAR 104
+ + IKV R
Sbjct: 63 SLFRGRQIKVMPKR 76
Score = 27.8 bits (62), Expect = 1.8
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 16/83 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++YV + T E+LE F G++ ILCDK SG P KG +
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF---------SGHP------KGFAY 45
Query: 174 VRFNQHIEAEHAMQELNGTIPEG 196
+ F+ A+ L+ ++ G
Sbjct: 46 IEFSDKESVRTAL-ALDESLFRG 67
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 29.2 bits (65), Expect = 0.63
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
I N + + +++ +FS G V C + + GY FV Y A A+I
Sbjct: 5 FIGNLNTAVVKKSDVETIFSKYGRVVGCSVHK--------GYAFVQYSNERHARGAVIGE 56
Query: 89 NGLKLQNKSIKVSYA 103
NG L +++ ++ A
Sbjct: 57 NGRVLAGQTLDINMA 71
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 29.0 bits (65), Expect = 0.70
Identities = 13/46 (28%), Positives = 27/46 (58%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+L+V LP+++ +E + F+ YG + + +IL + + V +FV
Sbjct: 1 HLWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVD 46
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 29.2 bits (66), Expect = 0.77
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 43 LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
L+ + GEVE K+ T + LG V + + A+R + +LN + K IKV
Sbjct: 19 LKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKV 76
Score = 26.9 bits (60), Expect = 6.5
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 285 DNV----LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
DN+ L + +G V+ VK+ P+T K G V + A ++ LN
Sbjct: 12 DNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQ 66
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 29.0 bits (65), Expect = 0.77
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
TE++V + FG FG V +V++ + + FGFV N +
Sbjct: 12 TEEDV-SEYFGQFGPVLDVRIPYQQK----RMFGFVTFENAE 48
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 28.8 bits (64), Expect = 0.84
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKL-IRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ L + + +T E+L+ LF KL + + +S GY FV+Y A RAI
Sbjct: 2 NKLYIGNLSPAVTAEDLRQLFGDR------KLPLTGQVLLKS-GYAFVDYPDQNWAIRAI 54
Query: 86 IELNG-LKLQNKSIKVSYARP 105
L+G ++L K ++V Y+ P
Sbjct: 55 ETLSGKVELHGKVMEVDYSVP 75
Score = 28.4 bits (63), Expect = 1.4
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL+P L QLFG + K+ Q G+ FV + + A+ AI++L
Sbjct: 4 LYIGNLSPAVTAEDLRQLFG------DRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETL 57
Query: 334 NGYA-LGDRLLQVSFKTHK 351
+G L ++++V + K
Sbjct: 58 SGKVELHGKVMEVDYSVPK 76
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 28.9 bits (65), Expect = 0.90
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 66 QSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVS 101
Q G V + D +RAI +L+G +L + IK+
Sbjct: 35 QRPNEGVVEFATYSDMKRAIEKLDGTELNGRKIKLI 70
>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins
related to the La autoantigen. This subfamily
corresponds to the RRM of plant La-like proteins related
to the La autoantigen. A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes. Members in this family
contain an LAM domain followed by an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 29.0 bits (65), Expect = 0.91
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYK 311
+ NL + L ++FG G+V+NV+ + DP
Sbjct: 3 VVAENLPEDHSIENLEEIFGTVGSVKNVR-ICDPGRVG 39
Score = 27.9 bits (62), Expect = 2.8
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 22/87 (25%)
Query: 30 IVNYVPQTMTQEELQHLFSSVGEVES---CKLIRDKTTAQSLGYG------------FVN 74
+ +P+ + E L+ +F +VG V++ C R + + + V
Sbjct: 4 VAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHALVE 63
Query: 75 YYRTEDAERAIIEL-------NGLKLQ 94
Y E AE+A+ EL +GL+++
Sbjct: 64 YETVEAAEKAVTELSDEGNWRSGLRVR 90
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM1 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 75
Score = 28.4 bits (63), Expect = 1.1
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
V N+ E +N L QL PFG V + ++R K + M + A+ A+Q
Sbjct: 5 VRNVGHEISENDLLQLVQPFGVVTKLVMLR------AKNQALLQMQDVSSAISALQ 54
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site
of the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65
(also termed U2AF2). U2AF35 contains two N-terminal
zinc fingers, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 28.9 bits (65), Expect = 1.2
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 19/83 (22%)
Query: 22 VNEQNSNLIVNYVPQTMTQEELQ----HLFSSV--------GEVES---CKLIRDKTTAQ 66
N QNS + + ++ ELQ + V GE+E C + D
Sbjct: 11 QNPQNSPQSADGLKVKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMNVCDNLGDHL--- 67
Query: 67 SLGYGFVNYYRTEDAERAIIELN 89
+G +V + R EDAE+A+ +LN
Sbjct: 68 -VGNVYVKFRREEDAEKAVNDLN 89
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 28.4 bits (64), Expect = 1.3
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 57 KLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
KL++ + A FV + E+ ++A+ L+G K + + + A+P
Sbjct: 37 KLLKRQDFA------FVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79
Score = 26.4 bits (59), Expect = 6.4
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 311 KCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQV 345
K + F FV + +E A++ L+G+ R+L
Sbjct: 40 KRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSA 74
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 28.4 bits (64), Expect = 1.3
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 117 VSGLPKHMTQEDLENLFRPYGTII 140
V LPK T+ + F+ G I
Sbjct: 5 VKNLPKDTTENKIRQFFKDCGEIR 28
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM2 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 27.9 bits (62), Expect = 1.5
Identities = 14/60 (23%), Positives = 33/60 (55%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
V+ +++T+E LQ F + ++E+ L +D + + Y F+ + +++ A A+ + G
Sbjct: 3 VSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHITG 62
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 28.0 bits (62), Expect = 1.7
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 7/62 (11%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ LP T+E+L L +P+G I+ ++ C+ A+ N ++FV E +++ I V
Sbjct: 5 LHLRNLPWECTEEELIELCKPFGKIVNTK--CNVGANRN-QAFV----EFADLNQAIAMV 57
Query: 175 RF 176
+
Sbjct: 58 SY 59
>gnl|CDD|241107 cd12663, RRM1_RAVER1, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM1 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 71
Score = 28.0 bits (62), Expect = 1.8
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 311 KCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFK 348
K KG FV + N ++A AI+ + L DR + V +
Sbjct: 33 KYKGTAFVTLLNGEQAESAIKEFHQSVLRDREISVQLQ 70
Score = 27.6 bits (61), Expect = 2.5
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+++ +P ++ +E+ L E++ C + + K TA FV E AE AI E
Sbjct: 3 ILIKGLPADISNQEVHDLLGDY-ELKYCFVDKYKGTA------FVTLLNGEQAESAIKEF 55
Query: 89 NGLKLQNKSIKV 100
+ L+++ I V
Sbjct: 56 HQSVLRDREISV 67
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTI 139
+YV LP + +D+E+LF YG I
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAI 26
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 27.6 bits (62), Expect = 1.8
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V + + MT+E+L+ FS GEV + + + FV + E A+ E
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFR-----AFAFVTFADPEVAQSLCGE- 56
Query: 89 NGLKLQNKSIKVSYAR 104
++ S+ VS A
Sbjct: 57 -DHIIKGVSVHVSNAE 71
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 27.9 bits (62), Expect = 2.0
Identities = 23/83 (27%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCK--------LIRDKTTAQSLGYGFVNYYRT 78
S + V + +T EEL F G V+ K + DK T + G V+Y
Sbjct: 1 STIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDP 60
Query: 79 EDAERAIIELNGLKLQNKSIKVS 101
A+ A+ +G Q +KVS
Sbjct: 61 PSAKAAVEWFDGKDFQGSKLKVS 83
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 27.8 bits (62), Expect = 2.0
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + + +T T +L+ F GE+ I K + Y F+ Y +A+ ++
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIID---IDIKKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 89 NGLKLQNKSIKV 100
+G L N +K+
Sbjct: 62 DGEYLGNNRVKL 73
Score = 27.8 bits (62), Expect = 2.2
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV 158
L++ L K T DL F +G II I K +F+
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDI--KKQGGNPAYAFI 46
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 28.0 bits (63), Expect = 2.3
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFG-FVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+G V NV V + FV ++ DEA+ A+++LNG G R + F
Sbjct: 27 CEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGRKVTARF 83
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 28.0 bits (63), Expect = 2.4
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 72 FVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
FV + R E A +A+++LNG +++K S+
Sbjct: 55 FVEFERVESAIKAVVDLNGRFFGGRTVKASF 85
>gnl|CDD|235379 PRK05261, PRK05261, putative phosphoketolase; Provisional.
Length = 785
Score = 29.8 bits (68), Expect = 2.4
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 22/53 (41%)
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
I+ LNG K+ N +I AR ++ E+LE LFR YG
Sbjct: 198 ILHLNGYKIANPTI---LAR-------------------ISDEELEALFRGYG 228
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 27.3 bits (61), Expect = 2.5
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P ++ ++ L GE K D +++ + F + E+ + + NG +L
Sbjct: 8 IPLDVSDYTIEDLIKEFGEPVYSK-FYDHKDSRTAVFEFED---PSILEKVVEKYNGKEL 63
Query: 94 QNKSIKV 100
I+V
Sbjct: 64 NGAKIEV 70
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 27.3 bits (61), Expect = 2.7
Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+++ VP + + +L+ G V + + A + G V++Y AE A+ ++
Sbjct: 4 LLLSGVPPHIPETQLRRDLEQWGAVRAV-----QMDAMAEGIVTVHFYDLRHAEDALRDI 58
Query: 89 NGLKLQN 95
L
Sbjct: 59 RAQHLFQ 65
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 27.6 bits (61), Expect = 2.7
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
L+V LP + + +L+ F+ YG ++ RI
Sbjct: 6 LFVGNLPHDVDKSELKEFFQQYGNVVELRI 35
>gnl|CDD|143383 cd07878, STKc_p38beta_MAPK11, Catalytic domain of the
Serine/Threonine Kinase, p38beta Mitogen-Activated
Protein Kinase. Serine/Threonine Kinases (STKs),
p38beta subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
p38beta subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. p38 kinases are mitogen-activated protein
kinases (MAPKs), serving as important mediators of
cellular responses to extracellular signals. They are
activated by the MAPK kinases MKK3 and MKK6, which in
turn are activated by upstream MAPK kinase kinases
including TAK1, ASK1, and MLK3, in response to cellular
stresses or inflammatory cytokines. Vertebrates contain
four isoforms of p38, named alpha, beta, gamma, and
delta. p38beta, also called MAPK11, is widely expressed
in tissues and shows more similarity with p38alpha than
with the other isoforms. Both are sensitive to
pyridinylimidazoles and share some common substrates
such as MAPK activated protein kinase 2 (MK2) and the
transcription factors ATF2, c-Fos and, ELK-1. p38beta is
involved in regulating the activation of the
cyclooxygenase-2 promoter and the expression of
TGFbeta-induced alpha-smooth muscle cell actin.
Length = 343
Score = 29.2 bits (65), Expect = 2.9
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 12/69 (17%)
Query: 94 QNKSIKVSYARPSSEAIKR-----ANLYVSGLPKHMTQEDLENLFR---PYGTIITSRIL 145
Q K I PS E +K+ A Y+ LP HM Q+DL+ +FR P + ++L
Sbjct: 224 QLKRIMEVVGTPSPEVLKKISSEHARKYIQSLP-HMPQQDLKKIFRGANPLAIDLLEKML 282
Query: 146 ---CDKMAS 151
DK S
Sbjct: 283 VLDSDKRIS 291
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding protein
12 (RBM12) and similar proteins. This subfamily
corresponds to the RRM3 of RBM12. RBM12, also termed
SH3/WW domain anchor protein in the nucleus (SWAN), is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 101
Score = 28.0 bits (62), Expect = 3.0
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 1/89 (1%)
Query: 265 KSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
+S H G+C+++ L E E+ + F V++ + K G GFV N
Sbjct: 3 RSPHELGFCVYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 62
Query: 325 EAVFAIQSLNGYALGDRLLQVSFKTHKPL 353
+ A+ Y +G+R +QV T K +
Sbjct: 63 DYKAALCRHKQY-MGNRFIQVHPITKKAM 90
>gnl|CDD|178624 PLN03075, PLN03075, nicotianamine synthase; Provisional.
Length = 296
Score = 29.3 bits (66), Expect = 3.0
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 10/53 (18%)
Query: 229 HFAAAMRHFGNPLHHSARF-------KFAPLTADLLN-NSMLPPKSLH--GSG 271
HF+ + F NPL H F K + L DLL+ + P + GSG
Sbjct: 81 HFSTILGSFDNPLDHLNLFPYYNNYLKLSKLEFDLLSQHVNGVPTKVAFVGSG 133
>gnl|CDD|221781 pfam12805, FUSC-like, FUSC-like inner membrane protein yccS. This
family has similarities to the fusaric acid resistance
protein family. The proteins are lodged in the inner
membrane.
Length = 284
Score = 29.1 bits (66), Expect = 3.1
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 219 NLNAQAAAMRHFAAAMRHFGNPLHHSARFKFA 250
L QA A R A A+ P HS R + A
Sbjct: 214 LLELQAQACREIAQAILL-RKPYQHSPRLRRA 244
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 27.2 bits (61), Expect = 3.3
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 115 LYVSGLPK-HMTQEDLENLFRPYGTIITSRIL 145
+ +S LP+ T+ +L L P+G + L
Sbjct: 3 VRLSNLPEGGYTEAELLKLAEPFGKVDHYIFL 34
Score = 26.5 bits (59), Expect = 5.3
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 9/72 (12%)
Query: 280 APETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYAL- 338
TE +L +L PFG V + + + F+ M + ++A + Y L
Sbjct: 11 GGYTEAELL-KLAEPFGKVDHYIFLPNRNK------AFIEMESPEDAQALVSFYKTYPLT 63
Query: 339 -GDRLLQVSFKT 349
G + ++V+ T
Sbjct: 64 IGGKSIKVALST 75
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 27.3 bits (60), Expect = 3.3
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
V NL+P + +L Q F FG V+ V+ D + + G GFV
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRG-RPTGKGFV 45
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 92
Score = 27.5 bits (61), Expect = 3.4
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
P +L+ FS + C+L + Q G+ + Y E AE + +GL L
Sbjct: 12 PSLCDVGDLREAFSKIHAPTFCQLACGQD-GQLKGFAVLEYESAEMAEMVQQQADGLSLA 70
Query: 95 NKSIKVSYARP 105
I+VS+ P
Sbjct: 71 GSHIRVSFCAP 81
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 28.9 bits (65), Expect = 3.5
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 19/73 (26%)
Query: 195 EGASEPITVKFANSPAGRAKALAANLNAQAAAM-----------RHFAAAMRHFGNPLH- 242
EGA + V + S A+ALA L +A A+ FA A HFG P+
Sbjct: 28 EGAR--VVVNYHQSED-AAEALADELGDRAIALQADVTDREQVQAMFATATEHFGKPITT 84
Query: 243 --HSA--RFKFAP 251
++A F F
Sbjct: 85 VVNNALADFSFDG 97
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 27.5 bits (61), Expect = 3.5
Identities = 25/96 (26%), Positives = 37/96 (38%), Gaps = 21/96 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPY-GTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+Y + + K +TQ D++ F G + R+L D S I F
Sbjct: 7 IYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTR-----------------IAF 49
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
V F AE A+ LN + S PI V + +P
Sbjct: 50 VEF---AMAESAIAALNCSGAVLGSLPIRVSPSKTP 82
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 27.1 bits (61), Expect = 3.8
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 23/87 (26%)
Query: 33 YV---PQTMTQEELQHLFSSV-----------GEVESCKLIRDKTTAQSLGYGFVNYYRT 78
YV P +T+EEL F+ V S ++ +K + FV +
Sbjct: 5 YVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN------FAFVEFRTV 58
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARP 105
E+A A+ L+G+ + + +K+ RP
Sbjct: 59 EEATAAL-ALDGIIFKGQPLKIR--RP 82
>gnl|CDD|233854 TIGR02409, carnitine_bodg, gamma-butyrobetaine hydroxylase.
Members of this protein family are gamma-butyrobetaine
hydroxylase, both bacterial and eukarytotic. This enzyme
catalyzes the last step in the conversion of lysine to
carnitine. Carnitine can serve as a compatible solvent
in bacteria and also participates in fatty acid
metabolism.
Length = 366
Score = 29.0 bits (65), Expect = 4.0
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 12/70 (17%)
Query: 180 IEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGN 239
+ ++H + EL+ +G E + ++F N + + ++ F AA R F
Sbjct: 257 LRSKHPVIELD---DDG--EVVKIRFNN------ASRDTIFDVPVERVQDFYAAYRRFVE 305
Query: 240 PLHHSARFKF 249
L S RFKF
Sbjct: 306 -LIESPRFKF 314
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 26.9 bits (60), Expect = 4.2
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 9/76 (11%)
Query: 34 VPQTMTQEELQHLFSSV-GEVESCKLIR-DKTTAQSLGYGFVNYYRTEDAERAIIELNGL 91
+P ++T+E+L+ LF+ G V++ K D+ A + E+A A+I L+
Sbjct: 7 IPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMA------LIQMGSVEEAIEALIALHNY 60
Query: 92 KL-QNKSIKVSYARPS 106
+L ++ ++VS+++ +
Sbjct: 61 QLSESSHLRVSFSKST 76
>gnl|CDD|224311 COG1393, ArsC, Arsenate reductase and related proteins,
glutaredoxin family [Inorganic ion transport and
metabolism].
Length = 117
Score = 27.6 bits (62), Expect = 4.7
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 30 IVNYVPQTMTQEELQHLFSSVG-EVESCKLIRDK-TTAQSLG 69
++Y+ ++EEL+ + S +G VE +LI + TT + L
Sbjct: 30 FIDYLKTPPSREELKKILSKLGDGVE--ELINTRGTTYRELN 69
>gnl|CDD|202408 pfam02812, ELFV_dehydrog_N, Glu/Leu/Phe/Val dehydrogenase,
dimerisation domain.
Length = 131
Score = 27.8 bits (63), Expect = 4.9
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 121 PKHMTQEDLENLFRPYGTIITSRILCDKM 149
PK ++ +LE L R +G + S I +
Sbjct: 79 PKGLSDAELERLTRAFGRELESIIGPGRD 107
>gnl|CDD|239275 cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed
of TRX-fold arsenic reductases and similar proteins
including the transcriptional regulator, Spx. ArsC
catalyzes the reduction of arsenate [As(V)] to arsenite
[As(III)], using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX), through a
single catalytic cysteine. This family of predominantly
bacterial enzymes is unrelated to two other families of
arsenate reductases which show similarity to
low-molecular-weight acid phosphatases and
phosphotyrosyl phosphatases. Spx is a general regulator
that exerts negative and positive control over
transcription initiation by binding to the C-terminal
domain of the alpha subunit of RNA polymerase.
Length = 105
Score = 27.1 bits (61), Expect = 5.0
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 30 IVNYVPQTMTQEELQHLFSSVG-EVESCKLIRDK-TTAQSLG 69
++Y+ + T+EEL+ L + +G VE L + T + LG
Sbjct: 28 FIDYLKEPPTKEELKELLAKLGLGVE--DLFNTRGTPYRKLG 67
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 28.4 bits (64), Expect = 5.2
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 208 SPAGRAKALAANLNAQAAAMRHFAAAMRHFGN 239
+ G A AL A+L A A AAA+ FG
Sbjct: 53 AAGGEALALTADLETYAGAQAAMAAAVEAFGR 84
>gnl|CDD|217984 pfam04244, DPRP, Deoxyribodipyrimidine photo-lyase-related protein.
This family appears to be related to pfam00875.
Length = 223
Score = 28.3 bits (64), Expect = 5.4
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 225 AAMRHFAAAMRHFGNPLHH 243
+AMRHFA +R G+ + +
Sbjct: 49 SAMRHFAEELRAAGHTVIY 67
>gnl|CDD|173123 PRK14660, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 125
Score = 27.5 bits (61), Expect = 5.5
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 200 PITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRH 236
P + + S A RA+ LAA A+ A M+ +R
Sbjct: 33 PGEIAYCTSKANRAERLAARFAAKEAVMKAIGTGLRE 69
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 28.2 bits (63), Expect = 5.8
Identities = 10/39 (25%), Positives = 24/39 (61%)
Query: 267 LHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVR 305
++ G+ V NL+P+ + ++ F GA+++V+++R
Sbjct: 1 MYPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIR 39
>gnl|CDD|117248 pfam08675, RNA_bind, RNA binding domain. This domain corresponds
to the RNA binding domain of Poly(A)-specific
ribonuclease (PARN).
Length = 75
Score = 26.6 bits (58), Expect = 6.0
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
KR ++ PK DL LF +G I S I ++ +FVS
Sbjct: 6 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-------DDTSAFVS 47
>gnl|CDD|241160 cd12716, RRM1_2_NP220, RNA recognition motif 1 and 2 in vertebrate
nuclear protein 220 (NP220). This subgroup corresponds
to RRM1 and RRM2 of NP220, also termed zinc finger
protein 638 (ZN638), or cutaneous T-cell
lymphoma-associated antigen se33-1, or zinc finger
matrin-like protein, a large nucleoplasmic DNA-binding
protein that binds to cytidine-rich sequences, such as
CCCCC (G/C), in double-stranded DNA (dsDNA). NP220
contains multiple domains, including MH1, MH2, and MH3,
domains homologous to the acidic nuclear protein matrin
3; RS, an arginine/serine-rich domain commonly found in
pre-mRNA splicing factors; PstI-HindIII, a domain
essential for DNA binding; acidic repeat, a domain with
nine repeats of the sequence LVTVDEVIEEEDL; and a
Cys2-His2 zinc finger-like motif that is also present in
matrin 3. It may be involved in packaging, transferring,
or processing transcripts. This subgroup corresponds to
the domain of MH2 that contains two tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 76
Score = 26.3 bits (58), Expect = 6.1
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 115 LYVSGLP-KHMTQEDLENLFRPYGTIITSRIL 145
+ +S LP K ++E++ NL +P+G + IL
Sbjct: 3 VLISNLPEKGYSEEEIYNLAKPFGKLKDILIL 34
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 26.3 bits (58), Expect = 6.1
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
I N + +++E+L +FS+ GE+ L YGFV + E AI
Sbjct: 3 FIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAINCE 54
Query: 89 NGLKLQNKSIKVSYARP 105
G ++ + + + ++P
Sbjct: 55 QGKMIRGRKLHLEVSKP 71
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 28.3 bits (64), Expect = 6.3
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 5/32 (15%)
Query: 210 AGRAKALAANLNAQ-----AAAMRHFAAAMRH 236
RA ALA LNA+ A A AAA+
Sbjct: 161 PARAAALADELNARFPAARATAGSDLAAALAA 192
>gnl|CDD|241145 cd12701, RRM4_PTBP1, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM4 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 76
Score = 26.6 bits (58), Expect = 6.4
Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 34 VPQTMTQEELQHLFSSVG-EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLK 92
+P ++++E+L+ LFSS G V+ K + + G V E+A +++I+L+
Sbjct: 7 IPPSVSEEDLKMLFSSNGGTVKGFKFFQKDRKMALIQMGSV-----EEAIQSLIDLHNHD 61
Query: 93 L-QNKSIKVSYARPS 106
L +N ++VS+++ +
Sbjct: 62 LGENHHLRVSFSKST 76
>gnl|CDD|185193 PRK15293, PRK15293, putative fimbrial protein SthD; Provisional.
Length = 185
Score = 27.7 bits (61), Expect = 6.9
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 197 ASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAM 234
A+ P T+K N PA KA A + N ++A+A+
Sbjct: 74 ATIPFTIKMTNCPATTTKA-AISFNGVPYPDPNYASAI 110
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 26.2 bits (58), Expect = 7.2
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTI 139
++V GLP +T+ DL +G I
Sbjct: 5 VHVRGLPDGVTEADLVEALSEFGPI 29
>gnl|CDD|185698 cd09021, Aldose_epim_Ec_YphB, aldose 1-epimerase, similar to
Escherichia coli YphB. Proteins similar to Escherichia
coli YphB are uncharacterized members of the
aldose-1-epimerase superfamily. Aldose 1-epimerases or
mutarotases are key enzymes of carbohydrate metabolism,
catalyzing the interconversion of the alpha- and
beta-anomers of hexose sugars such as glucose and
galactose. This interconversion is an important step
that allows anomer specific metabolic conversion of
sugars. Studies of the catalytic mechanism of the best
known member of the family, galactose mutarotase, have
shown a glutamate and a histidine residue to be critical
for catalysis; the glutamate serves as the active site
base to initiate the reaction by removing the proton
from the C-1 hydroxyl group of the sugar substrate, and
the histidine as the active site acid to protonate the
C-5 ring oxygen.
Length = 273
Score = 28.0 bits (63), Expect = 7.5
Identities = 12/28 (42%), Positives = 13/28 (46%)
Query: 245 ARFKFAPLTADLLNNSMLPPKSLHGSGW 272
RF FA L N+ P LHG GW
Sbjct: 53 GRFLFAGREVALPPNTADEPHPLHGDGW 80
>gnl|CDD|238969 cd02011, TPP_PK, Thiamine pyrophosphate (TPP) family,
Phosphoketolase (PK) subfamily, TPP-binding module; PK
catalyzes the conversion of D-xylulose 5-phosphate and
phosphate to acetyl phosphate,
D-glyceraldehyde-3-phosphate and H2O. This enzyme
requires divalent magnesium ions and TPP for activity.
Length = 227
Score = 27.7 bits (62), Expect = 7.6
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 22/53 (41%)
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
I+ LNG K+ N +I AR ++ E+LE LFR YG
Sbjct: 118 ILHLNGYKISNPTI---LAR-------------------ISHEELEALFRGYG 148
>gnl|CDD|202042 pfam01912, eIF-6, eIF-6 family. This family includes eukaryotic
translation initiation factor 6 as well as presumed
archaebacterial homologues.
Length = 197
Score = 27.9 bits (63), Expect = 7.7
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 6/41 (14%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVG-EVESCKLIRDKTTA 65
NSN ++ VP T T EEL HL S+ VE + +K TA
Sbjct: 61 NSNGLL--VPSTATDEELDHLKESLDVNVE---RLEEKLTA 96
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 26.8 bits (60), Expect = 7.9
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
F FG V KV + + + +G +V + +EA+ A + NG + L F
Sbjct: 49 FEKFGEVVQFKVCCNYEPH-LRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCEF 103
>gnl|CDD|218765 pfam05820, DUF845, Baculovirus protein of unknown function
(DUF845). This family consists of several highly
related Baculovirus proteins of unknown function.
Length = 119
Score = 26.9 bits (60), Expect = 8.0
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 137 GTIITSRILCDKMASENVRSFVSG 160
GT+I +LCD+ + +R FV G
Sbjct: 78 GTLIKVLVLCDECCKKELRDFVEG 101
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 28.1 bits (62), Expect = 8.7
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 63 TTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
+TA G ++ Y EDA R I E++G L + +K +Y
Sbjct: 161 STASHAGV-YITYSTKEDAARCIAEVDGSLLDGRVLKATY 199
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the E3
component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to have
distinct functions (ferric leghemoglobin reductase and
NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 28.0 bits (63), Expect = 8.8
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 57 KLIRDKTTAQSLGYGFVNYYRTED-AERAIIELNGLKLQN--KSIKVSYARPS-SEAIKR 112
K+I DK T + LG + + TE +E A+ ++ ++I + P+ SEAIK
Sbjct: 393 KIIADKKTGEILGAHIIGPHATELISEAALAMELEGTVEELARTI---HPHPTLSEAIKE 449
Query: 113 ANLYVSGLPKH 123
A L G P H
Sbjct: 450 AALAALGKPIH 460
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 28.3 bits (63), Expect = 9.0
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 9/43 (20%)
Query: 100 VSYARPSSEAIKRANLY---------VSGLPKHMTQEDLENLF 133
V YA P A KR N + + G + +T +L LF
Sbjct: 881 VGYAHPYFHAAKRRNCFPGDTRILVNIDGNVERITLRELYELF 923
>gnl|CDD|234405 TIGR03936, sam_1_link_chp, radical SAM-linked protein. This model
describes an uncharacterized protein encoded adjacent
to, or as a fusion protein with, an uncharacterized
radical SAM protein.
Length = 209
Score = 27.5 bits (62), Expect = 9.6
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNA 222
+ + I+ E ++ LN +PEG I V +A +L A ++A
Sbjct: 66 IELTEEIDPEEVLERLNAVLPEG----IEVLEVEEVPDKAPSLMALIDA 110
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.388
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,882,632
Number of extensions: 1691207
Number of successful extensions: 3149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2794
Number of HSP's successfully gapped: 963
Length of query: 356
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 258
Effective length of database: 6,590,910
Effective search space: 1700454780
Effective search space used: 1700454780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.0 bits)