RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17274
(184 letters)
>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 = 258 bits (661), Expect = 3e-85
Identities = 106/189 (56%), Positives = 138/189 (73%), Gaps = 11/189 (5%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F+L VYG+V RVK + NKK++ALI+MA+ +QA LA+ H++ +++FGK +RV SK Q
Sbjct: 293 LFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN 352
Query: 61 VQLPKEGQPDAGLT--KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELK 118
VQ P+EGQ D GLT KDY++S HRFKKPGS N NI PPS TLHLSNIP SV+E++LK
Sbjct: 353 VQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLK 412
Query: 119 EAFTEKGFT-VKGFKFFPKD---RKMALLQLDSIEEAITALIQMHNHQLSE-----QSHL 169
E F E G VK FKFFPKD KM LL+ +S+E+A+ ALI +++HQL+E HL
Sbjct: 413 ELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHL 472
Query: 170 RVSFSKSNI 178
+VSFS S I
Sbjct: 473 KVSFSTSRI 481
Score = 32.9 bits (75), Expect = 0.089
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITA 154
PSP +H+ N+P V E +L EA G V P R AL++ + E A
Sbjct: 1 PSPVVHVRNLPQDVVEADLVEALIPFG-PVSYVMMLPGKR-QALVEFEDEESAKAC 54
>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 = 138 bits (351), Expect = 2e-43
Identities = 58/76 (76%), Positives = 66/76 (86%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
TLHLSNIP SVTE++LKE FT+ G TVK FKFFPKDRKMAL+Q+ S+EEAI ALI +HN+
Sbjct: 1 TLHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNY 60
Query: 162 QLSEQSHLRVSFSKSN 177
QLSE SHLRVSFSKS
Sbjct: 61 QLSESSHLRVSFSKST 76
>gnl|CDD|241147 cd12703, RRM4_ROD1, RNA recognition motif 4 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM4 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 that 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 = 81
Score = 118 bits (297), Expect = 3e-35
Identities = 58/81 (71%), Positives = 64/81 (79%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
PPS TLHLSNIP SVTED+LK F G +VK FKFF KDRKMAL+QL S+EEAI ALI+
Sbjct: 1 PPSATLHLSNIPPSVTEDDLKGLFLSSGCSVKAFKFFQKDRKMALIQLGSVEEAIEALIE 60
Query: 158 MHNHQLSEQSHLRVSFSKSNI 178
+HNH L E HLRVSFSKS I
Sbjct: 61 LHNHDLGENHHLRVSFSKSTI 81
>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 = 107 bits (267), Expect = 2e-30
Identities = 50/77 (64%), Positives = 64/77 (83%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F+L GVYGDV RVKILYNKKDSALIQMA+ +Q+ LAM H++ +++GK +RV +SKHQ
Sbjct: 31 LFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRVTLSKHQT 90
Query: 61 VQLPKEGQPDAGLTKDY 77
VQLP+EG D GLTKD+
Sbjct: 91 VQLPREGLDDQGLTKDF 107
>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 = 104 bits (260), Expect = 7e-30
Identities = 52/75 (69%), Positives = 61/75 (81%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
TLHLSNIP SV+E++LK F+ G TVKGFKFF KDRKMAL+Q+ S+EEAI +LI +HNH
Sbjct: 1 TLHLSNIPPSVSEEDLKMLFSSNGGTVKGFKFFQKDRKMALIQMGSVEEAIQSLIDLHNH 60
Query: 162 QLSEQSHLRVSFSKS 176
L E HLRVSFSKS
Sbjct: 61 DLGENHHLRVSFSKS 75
>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 = 104 bits (261), Expect = 1e-29
Identities = 48/77 (62%), Positives = 63/77 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F L GVYGDV RVKIL+NKK++AL+QMA+ +QA LAM H++ ++ GK +R+ +SKHQ
Sbjct: 17 LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPLRITLSKHQT 76
Query: 61 VQLPKEGQPDAGLTKDY 77
VQLP+EGQ D GLTKDY
Sbjct: 77 VQLPREGQEDQGLTKDY 93
>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 = 103 bits (259), Expect = 2e-29
Identities = 35/58 (60%), Positives = 49/58 (84%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKH 58
+F+L GVYGDV+RVKIL+NKKD+ALIQMA+ QA A+ H++ +R+ GK++RV +SKH
Sbjct: 17 LFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSKH 74
>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 = 103 bits (258), Expect = 2e-29
Identities = 53/81 (65%), Positives = 62/81 (76%), Gaps = 1/81 (1%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
PPS TLHLSNIP SVTE++L+ F G TVK FKFF +D KMALLQ+ ++EEAI ALI
Sbjct: 1 PPSATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFF-QDHKMALLQMSTVEEAIQALID 59
Query: 158 MHNHQLSEQSHLRVSFSKSNI 178
+HN+ L E HLRVSFSKS I
Sbjct: 60 LHNYNLGENHHLRVSFSKSTI 80
>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 = 78.1 bits (192), Expect = 1e-19
Identities = 34/59 (57%), Positives = 48/59 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQ 59
+F L GVYGDV RVKI++NKK++AL+QMA++ QA LAM H++ R++GK +R +SKHQ
Sbjct: 18 LFILFGVYGDVHRVKIMFNKKENALVQMADATQAQLAMSHLNGQRLYGKVIRATLSKHQ 76
>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 = 62.2 bits (151), Expect = 2e-13
Identities = 27/58 (46%), Positives = 41/58 (70%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKH 58
+F+L YG+++R+K+L+NK D ALIQM + QA LA+ ++ +FGK+M V SKH
Sbjct: 19 LFNLFSNYGNIVRIKLLHNKPDHALIQMGDGFQAELAVNYLKGAMLFGKRMEVNFSKH 76
>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 = 59.1 bits (144), Expect = 2e-12
Identities = 18/52 (34%), Positives = 36/52 (69%)
Query: 2 FSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
F+L +YG+VLR+K L +K +A++QM + A A+ +++ + +FG+++ V
Sbjct: 18 FNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEV 69
>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 = 56.0 bits (135), Expect = 4e-11
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
PP+ +H+SN+P+ VTE+++ E G V F +K AL++ + E+A AL
Sbjct: 5 PPTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALAC 64
Query: 158 MHNHQLSEQSHLRVSF 173
H L S +R++F
Sbjct: 65 KHASSL-NGSTIRLAF 79
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 46.0 bits (110), Expect = 2e-07
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP-----KDRKMALLQLDSIEEAITALI 156
TL + N+P TE+EL+E F++ G V+ + K + A ++ +S E+A AL
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59
Query: 157 QMHNHQLSEQSHLRV 171
++ +L + L+V
Sbjct: 60 ALNGKEL-DGRPLKV 73
Score = 36.0 bits (84), Expect = 0.001
Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G V V+++ +K K A ++ A A+ ++ + G+ ++V
Sbjct: 23 FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|240873 cd12427, RRM4_hnRNPL_like, RNA recognition motif 4 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM4 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 = 84
Score = 46.1 bits (110), Expect = 2e-07
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 5/68 (7%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTV-KGFKFFPK--DRKMA-LLQLDSIEEAITA 154
PS LH N P + TE++L+E F EKG K FPK +R + L++ +++ EA+ A
Sbjct: 1 PSKVLHFFNAPPTFTEEDLRELFAEKGAPPPSKIKIFPKKSERSSSGLIEFETVAEAVEA 60
Query: 155 LIQMHNHQ 162
L + NH
Sbjct: 61 LA-LCNHT 67
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 45.6 bits (109), Expect = 3e-07
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP---KDRKMALLQLDSIEEAITALIQMH 159
L++ N+P SVTE++L+E F V+G + + R A ++ S E+A AL +++
Sbjct: 1 LYVRNLPPSVTEEDLREFF-SPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLN 59
Query: 160 NHQL 163
L
Sbjct: 60 GLVL 63
>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 = 44.9 bits (107), Expect = 5e-07
Identities = 21/74 (28%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
T+++ N+P +TE+EL+ F+ G ++ + F KD+ A ++ D+ E A TA++ ++
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGA-IEEVRVF-KDKGYAFVRFDTHEAAATAIVAVNGT 59
Query: 162 QLSEQSHLRVSFSK 175
++ Q+ ++ S+ K
Sbjct: 60 SINGQT-VKCSWGK 72
>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 = 45.0 bits (107), Expect = 5e-07
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP----KDRKMALLQLDSIEEAITALIQM 158
L + N+P TE++L+E F++ G ++ + K + A ++ +S E+A AL +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFG-EIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 159 HNHQL 163
+ +L
Sbjct: 60 NGKEL 64
Score = 38.1 bits (89), Expect = 2e-04
Identities = 10/50 (20%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G++ V+I+ +K K A ++ A A+ ++ + G++++V
Sbjct: 22 FGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKV 71
>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 = 43.7 bits (104), Expect = 2e-06
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 99 PSPTLHLSNIPASVTEDELKEAF-TEKGFTVKGFKFFPKDRK-MALLQLDSIEEAITALI 156
P TL ++N+ + TE+EL++ F + GF + K K + ++ + + A AL
Sbjct: 1 PCNTLFVANLGPNTTEEELRQLFSRQPGF--RRLKMHNKGGGPVCFVEFEDVSFATQALN 58
Query: 157 QMHNHQL--SEQSHLRVSFSK 175
+ L S++ +R+ ++K
Sbjct: 59 SLQGAVLSSSDRGGIRIEYAK 79
>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 = 41.7 bits (99), Expect = 6e-06
Identities = 13/55 (23%), Positives = 29/55 (52%)
Query: 2 FSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS 56
+ L +G+V ++K+L K A ++ + A A+ +++ + G+ +RV S
Sbjct: 2 YKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
Score = 33.3 bits (77), Expect = 0.007
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 127 TVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
V+ K K A ++ + E A A+ ++ + LRV +S
Sbjct: 10 NVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRP-LRVDYS 56
>gnl|CDD|241144 cd12700, RRM3_hnRPLL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM3 of
hnRNP-LL which 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 heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 71
Score = 41.9 bits (98), Expect = 6e-06
Identities = 15/55 (27%), Positives = 36/55 (65%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMI 55
+F+L +YG++ +VK + +AL++M + + A+ H++ +++FGK++ V +
Sbjct: 17 VFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCV 71
>gnl|CDD|241143 cd12699, RRM3_hnRNPL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM3 of hnRNP-L, 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-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 41.9 bits (98), Expect = 9e-06
Identities = 17/58 (29%), Positives = 39/58 (67%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKH 58
+F++ +YG+V +VK + +K +A+++MA+ + A+ H++ +FG+++ V +SK
Sbjct: 17 VFNIFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKLNVCVSKQ 74
>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 = 41.0 bits (97), Expect = 1e-05
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 3/74 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L + + + EL+ F G ++ + R A ++ +SIE A A +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGA-IRRIDY-DPGRNYAYIEYESIEAAQAAKEALRGFP 58
Query: 163 LSEQ-SHLRVSFSK 175
L LRV F+
Sbjct: 59 LGGPGRRLRVDFAD 72
>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 = 40.8 bits (96), Expect = 2e-05
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFK--FFPKDRKMALLQLDSIEEAITALIQMH 159
T+H+ I S++ED+LKE F+ G + + A ++ E A++AL
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL--NL 59
Query: 160 NHQLSEQSHLRVSFSKS 176
+ L LRVS SK+
Sbjct: 60 SGTLLGGHPLRVSPSKT 76
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 41.9 bits (97), Expect = 6e-05
Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 5/98 (5%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTE----KGFTVKGFKFFPKDRKMA 141
K+ Q + TL + N+P VTE++L+E F + K + + K R A
Sbjct: 101 SSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFA 160
Query: 142 LLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNIQ 179
++ +S E A A+ +++ +L E LRV ++ Q
Sbjct: 161 FVEFESEESAEKAIEELNGKEL-EGRPLRVQKAQPASQ 197
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
PSP +H+ +P VTE +L EA +E G + PK ++ AL++ + I +A +
Sbjct: 1 PSPVVHVRGLPDGVTEADLVEALSEFG-PISYVTMMPK-KRQALVEFEDISDAKACVNHA 58
Query: 159 HNHQLSEQSHL-RVSFSKS 176
+ + ++S S
Sbjct: 59 QQNPVYIAGRQAYFNYSTS 77
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 105 LSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALIQMHN 160
+ N+P TE++LK+ F++ G ++ + + + A ++ + E+A AL ++
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFG-PIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNG 61
Query: 161 HQL 163
+L
Sbjct: 62 KEL 64
>gnl|CDD|241149 cd12705, RRM4_hnRPLL, RNA recognition motif 4 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM4 of
hnRNP-LL which 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 heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 85
Score = 37.7 bits (87), Expect = 3e-04
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGF-TVKGFKFF---PKDRKMA-LLQLDSIEEAIT 153
PS LH N+P VTE+ ++ + T FK F P + ++ LL+ +S EA+
Sbjct: 1 PSCVLHYYNVPLCVTEETFQKLCEDHEVSTFIKFKVFDAKPSSKTLSGLLEWESKTEAVE 60
Query: 154 ALIQMHNHQL 163
AL ++++Q+
Sbjct: 61 ALTVLNHYQI 70
>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 = 36.8 bits (86), Expect = 5e-04
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 7/73 (9%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKF-FPKD----RKMALLQLDSIEEAITALIQMHNH 161
NIP TE++L E F+E G V F+ +D + + + IE A +A+ ++ +
Sbjct: 5 NIPYDATEEQLIEIFSEVG-PVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGY 63
Query: 162 QLSEQSHLRVSFS 174
+ + ++ LRV F+
Sbjct: 64 EFNGRA-LRVDFA 75
>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 = 36.8 bits (86), Expect = 5e-04
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 5/73 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L++ N+P S TE++L+E F+E G + K KD A + + ++A+ A+ +M+ +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKK--IKD--YAFVHFEERDDAVKAMEEMNGKE 59
Query: 163 LSEQSHLRVSFSK 175
L E S + VS +K
Sbjct: 60 L-EGSPIEVSLAK 71
>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 = 36.6 bits (85), Expect = 7e-04
Identities = 18/76 (23%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S +++ NI S+TE++L+ F++ G ++ + + + A + +I AI A+ +
Sbjct: 3 SRNVYIGNIDDSLTEEKLRNDFSQYG-EIESVNYLRE-KNCAFVNFTNISNAIKAIDGVK 60
Query: 160 NHQLSEQSHLRVSFSK 175
+H L ++ ++S+ K
Sbjct: 61 SHPLFKKF--KISYGK 74
>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 = 34.5 bits (80), Expect = 0.003
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
+ + N+P TE+EL+E F + G ++ P R +AL++ +A A +
Sbjct: 2 VILVKNLPFGTTEEELRELFEKFG-SLGRL-LLPPSRTIALVEFLEPSDARKAFKSL 56
>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 = 34.9 bits (81), Expect = 0.003
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
P+ + L + SVTE L F+ G V + R AL+ D +E A A+ +M
Sbjct: 6 PTNCVWLDGLDESVTEQYLTRHFSRYGPVVH--VVIDRQRGQALVFFDKVEAAQAAVNEM 63
Query: 159 HNHQLSEQSHLRVSF 173
+L L+V F
Sbjct: 64 KGRKLGG-RKLQVDF 77
>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 = 34.5 bits (80), Expect = 0.004
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
T+ L N+ +V E+++K F + G V+ + FP D + AL++ +S +A A + ++
Sbjct: 2 TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFP-DHEGALVEFESPSDAGKASLSLNGS 60
Query: 162 QL 163
Q
Sbjct: 61 QF 62
>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 = 34.1 bits (79), Expect = 0.004
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
P+ L L N+P T++ L+ F + GF K + P+ R +A ++ ++ E+A AL
Sbjct: 1 PNKILFLQNLPEETTKEMLEMLFNQFPGF--KEVRLVPR-RGIAFVEFETEEQATVALQA 57
Query: 158 MHNHQLSEQSHLRVS 172
+ +++ +++S
Sbjct: 58 LQGFKITPGHAMKIS 72
>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 = 34.1 bits (79), Expect = 0.005
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 17/65 (26%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG-----FTVK--------GFKF----FPKDRKMALLQ 144
TL + N+P T+++L+E F+E G F VK GF + +D K AL +
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 145 LDSIE 149
+
Sbjct: 61 KKKTK 65
>gnl|CDD|241148 cd12704, RRM4_hnRNPL, RNA recognition motif 4 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM4 of hnRNP-L, 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-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both hnRNP-L and PTB are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 33.8 bits (77), Expect = 0.008
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGF----TVKGFKFFPKDRKMALLQLDSIEEAITA 154
PS LH N P VTE+ E E G +VK F + LL+ +S +A+
Sbjct: 1 PSNVLHFFNAPPDVTEENFSEICDELGVKRPASVKVFSGKSERSSSGLLEWESKSDALET 60
Query: 155 LIQMHNHQL 163
L M+++Q+
Sbjct: 61 LAFMNHYQM 69
>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 = 33.4 bits (77), Expect = 0.010
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 25/88 (28%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTV--------------KGFKFFPKDRKMALLQLDS 147
L++ N+P +VTE++LK+ F + G V +GF F +++++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFG-EVTSARVITDRETGRSRGFGF---------VEMET 50
Query: 148 IEEAITALIQMHNHQLSEQSHLRVSFSK 175
EEA A+ +++ ++ L V+ ++
Sbjct: 51 AEEANAAIEKLNGTDFGGRT-LTVNEAR 77
>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 = 33.3 bits (77), Expect = 0.011
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 105 LSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLS 164
+SN+ VT D L + F+ G K F AL+Q DS+E A A ++ +
Sbjct: 6 ISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNIY 65
Query: 165 EQS-HLRVSFSKSN 177
+ L + FS+
Sbjct: 66 DGCCTLDIQFSRLK 79
>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 = 32.6 bits (75), Expect = 0.018
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 13/76 (17%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDS---IEEAITAL--IQ 157
L + N+P +TE+E KE F++ G + F K++ ++LD+ E+A L I
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSE--VFLNKEKGFGFIRLDTRTNAEKAKAELDGIM 61
Query: 158 MHNHQLSEQSHLRVSF 173
Q LRV F
Sbjct: 62 RKGRQ------LRVRF 71
>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 = 32.3 bits (74), Expect = 0.019
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V+ KI+ N + + MA +A + H+ + + G+ + V
Sbjct: 23 YGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73
>gnl|CDD|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM1 of hnRNP-L, 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-L shows significant sequence homology to
polypyrimidine tract-binding protein (PTB or hnRNP I).
Both, hnRNP-L and PTB, are localized in the nucleus but
excluded from the nucleolus. hnRNP-L is an RNA-binding
protein with three RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 32.7 bits (74), Expect = 0.020
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
SP +H+ + V E +L EA E G T+ PK R+ AL++ + + A A+
Sbjct: 1 ASPVVHVRGLIDGVVEADLVEALQEFG-TISYVVVMPKKRQ-ALVEFEDMNGACNAVNYA 58
Query: 159 HNHQLSEQSH 168
++Q+ H
Sbjct: 59 ADNQIYIAGH 68
>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 = 32.2 bits (74), Expect = 0.021
Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 110 ASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHL 169
+TE+ LK+AF+ G + K++ + + +E A A+ +++ + L
Sbjct: 12 YGLTEEILKKAFSPFGNIIN--ISMEKEKNCGFVTFEKMESADRAIAELNG-TTVQGVQL 68
Query: 170 RVSFSK 175
+VS ++
Sbjct: 69 KVSLAR 74
>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 = 32.5 bits (74), Expect = 0.021
Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHN 160
T+++ NIP T+ +L F G+ ++ F+ P DR A ++LD+ E+A A++Q+
Sbjct: 2 TVYVGNIPPYTTQADLIPLFQNFGYILE-FRHQP-DRGFAFVKLDTHEQAAMAIVQLQG 58
>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 = 32.5 bits (75), Expect = 0.022
Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 108 IPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITALIQMHNH 161
+P + TE++++ F E G ++ +D+ A ++ S EEA A+ +H
Sbjct: 7 LPKTATEEDVRALFEEYG-NIEEV-TIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGK 64
Query: 162 QLSE 165
Sbjct: 65 VTMP 68
>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 = 32.1 bits (74), Expect = 0.027
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFK---------FFPKDRKMALLQLDSIEEAIT 153
L++ N+P +TE+EL + F + + ++ A ++ ++EEA
Sbjct: 4 LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEATA 63
Query: 154 AL----IQMHNHQL 163
AL I L
Sbjct: 64 ALALDGIIFKGQPL 77
>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 = 32.3 bits (74), Expect = 0.028
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S TL + ++ VTE++LK F E G ++ P R A + +++ ++A AL ++
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYG-EIQSIDMIPP-RGCAYVCMETRQDAHRALQKLR 59
Query: 160 NHQLSEQS 167
N +L+ +
Sbjct: 60 NVKLAGKK 67
>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 = 32.0 bits (73), Expect = 0.034
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK------DRKMALLQLDSIEEAI 152
PS + ++++PAS ++DEL+ A TE F+ G F K R A +Q + ++A
Sbjct: 1 PSACVFVASLPASKSDDELEAAVTEH-FSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAK 59
Query: 153 TALIQMHNHQLSEQSHLRVSFSKSN 177
AL + L + H+R +K N
Sbjct: 60 NALAKGQGTILDGR-HIRCERAKVN 83
>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 = 31.7 bits (72), Expect = 0.036
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 102 TLHLSNIPASVTEDELKEAFTE 123
TL + N+P ++T DELKE F +
Sbjct: 5 TLFVKNLPYNITVDELKEVFED 26
>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 = 31.4 bits (72), Expect = 0.042
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ--MHN 160
LHL N+P VTE +L + G V + AL+++DS+E A +++ +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFG-KVTNVLLLRG-KNQALVEMDSVESA-KSMVDYYLTV 58
Query: 161 HQLSEQSHLRVSFSKS 176
L + + +S
Sbjct: 59 PALIRGRRVYIQYSNH 74
>gnl|CDD|222341 pfam13721, SecD-TM1, SecD export protein N-terminal TM region.
This domain appears to be the fist transmembrane region
of the SecD export protein. SecD is directly involved in
protein secretion and important for the release of
proteins that have been translocated across the
cytoplasmic membrane.
Length = 101
Score = 32.1 bits (74), Expect = 0.043
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 95 NIYPPSPTLHLSNIPASVTEDEL---KEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEA 151
N+Y P + +S V+ D L ++A E G K + + L++ S ++
Sbjct: 26 NLYGEDPAVQISGTRGGVSVDTLDRVEQALDEAGIAYKSIEL---ENGSLLVRFSSTDQQ 82
Query: 152 ITA 154
+ A
Sbjct: 83 LKA 85
>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 = 31.8 bits (73), Expect = 0.043
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK-----DRKMALLQLDSIEEAITALIQ 157
L + + SVTE +L+E F+ G TV + K DR A + L + E +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFG-TVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 158 MHNHQLSEQSHLRVSFSK 175
N + S L++ +K
Sbjct: 61 TLNGTKWKGSVLKIEEAK 78
>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 = 31.5 bits (72), Expect = 0.051
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMH 40
YGDV V + KK SA+++ A A A+ +
Sbjct: 28 YGDVSDVVVSSKKKGSAIVEFASKKAAEAAVEN 60
>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 = 31.5 bits (72), Expect = 0.052
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFKFFP----KDRKMALLQLDSIEEA 151
N+PAS+TE ELKE F++ G + K K R++A + + EEA
Sbjct: 6 KNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEA 55
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or
U1A). This subgroup corresponds to the RRM2 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 that
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).
U1A also binds to a flavivirus NS5 protein and plays an
important role in virus replication. It 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 it
may be free for binding 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 = 80
Score = 31.6 bits (71), Expect = 0.054
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITALI 156
PP+ L L+N+P E L F + GF K + P +A ++ D+ +A A
Sbjct: 3 PPNHILFLTNLPEETNELMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFDNEVQAGAARE 60
Query: 157 QMHNHQLSEQSHLRVSFSK 175
+ ++++ + +++SF+K
Sbjct: 61 ALQGFKITQSNAMKISFAK 79
>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 = 31.4 bits (71), Expect = 0.062
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 8/64 (12%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD------RKMALLQLDSIEEAITALI 156
L+++N+P +TEDEL++ F G V+ +D R +A ++ D EEA A+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQ--CNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 157 QMHN 160
++
Sbjct: 61 SLNG 64
>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 = 31.2 bits (71), Expect = 0.065
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK-----DRKMALLQLDSIEEA 151
P+ T+ L +P SVTE++++ A G K + + R A ++ S+EEA
Sbjct: 1 PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEA 58
>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 = 30.6 bits (69), Expect = 0.089
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L + N+P +TE+E+++ F + G G F KD+ ++L++ A A ++ N
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYG--KAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMP 61
Query: 163 LSEQSHLRVSF 173
L + LRV F
Sbjct: 62 LRGK-QLRVRF 71
>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 = 30.7 bits (70), Expect = 0.091
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKF-FPKD---RKMALLQLDSIEEAITALIQMHN 160
N+P + ED+L++ F G T+ + + KD RK + + EEA AL +N
Sbjct: 7 NLPKGIKEDKLRKLFEAFG-TITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNN 63
>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 = 30.5 bits (69), Expect = 0.097
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
S +++ N+P S +E+EL+E + G + K K++ +A + SI AI + +
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFG-PIDQIKIV-KEKNIAFVHFLSIANAIKVVTTL 59
>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 = 30.3 bits (68), Expect = 0.13
Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S L ++N+ S +ED L+E F EK +++ + + + A ++ +S E+A AL +
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVF-EKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCN 59
Query: 160 NHQLSEQSHLRVSF 173
N ++ +S +R+ F
Sbjct: 60 NTEIEGRS-IRLEF 72
>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 = 29.9 bits (68), Expect = 0.15
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGF---KFFPKDRKMALLQLDSIEEAITAL 155
N+P TE +LK+ F+ GF + K K + A +Q S +A A+
Sbjct: 6 NLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAI 57
>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 = 30.2 bits (69), Expect = 0.15
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 102 TLHLSNIPASVTEDELKEA----FTEKG--FTVKGFKFFPKDRKMALLQLDSIEEAITAL 155
TL+++N+ + +DELK + F++ G + K K R A + +E A AL
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKT-LKMRGQAFVVFKDVESATNAL 59
Query: 156 IQMHNHQLSEQSHLRVSFSK 175
+ ++ +R+ ++K
Sbjct: 60 RALQGFPFYDKP-MRIQYAK 78
Score = 25.6 bits (57), Expect = 6.5
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 2/58 (3%)
Query: 2 FSLTGVYGDVLRVKILYNKKD--SALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
++L +G VL + K A + + A A+ + + K MR+ +K
Sbjct: 21 YALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQYAK 78
>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 = 30.0 bits (67), Expect = 0.16
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L + N+ +VTE+ L++AF + G + K + A + D + A+ A+ +M+ +
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFG----KLERVKKLKDYAFIHFDERDGAVKAMEEMNGKE 59
Query: 163 LSEQSHLRVSFSK 175
L E ++ + F+K
Sbjct: 60 L-EGENIEIVFAK 71
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
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),
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 = 96
Score = 30.5 bits (69), Expect = 0.16
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 8 YGDVLRVKILYNKKDS--ALIQMAESHQAHLAMMHMD 42
+G VL++ I + K + ALIQ A++ A A + +D
Sbjct: 27 FGTVLKI-ITFTKNNQFQALIQFADAVSAQAAKLSLD 62
>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 = 29.8 bits (67), Expect = 0.16
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S +L + N+P VTE L+ F G V+G + + + I +A A+ ++
Sbjct: 1 SRSLFVINVPRDVTESTLRRLFEVYG-DVRGVQTERISEGIVTVHFYDIRDAKRAVRELC 59
Query: 160 NHQLSEQS 167
+ +Q+
Sbjct: 60 GRHMQQQA 67
>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 = 29.8 bits (67), Expect = 0.16
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFF-----PKDRKMALLQLDSIEEAITALIQMHNH 161
NIP TE++LK+ F+E G V F+ K + + E A++A+ ++ +
Sbjct: 5 NIPYEATEEQLKDIFSEVG-PVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGY 63
Query: 162 QLSEQSHLRVSFS 174
+L+ + LRV +
Sbjct: 64 ELNGRQ-LRVDNA 75
>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 = 29.8 bits (68), Expect = 0.18
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKF-FPKDRKM---ALLQLDSIEEAITALIQ 157
+ L +P S TE+++++ F+ G + D + A ++ S E+A AL +
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 158 MHNH 161
+N
Sbjct: 61 HNNK 64
>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 = 29.8 bits (68), Expect = 0.18
Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 28/87 (32%)
Query: 93 FQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPKDRKM 140
F N+Y + N+ + +++LKE F + G KGF F
Sbjct: 1 FTNVY-------VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGF------- 46
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQS 167
+ ++ E A A+ +++ +++ +
Sbjct: 47 --VNFENHEAAQKAVEELNGKEVNGKK 71
>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 = 29.7 bits (67), Expect = 0.20
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 104 HLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALIQMH 159
+SNIP + +LK+ F EK V + F + R +++ E AL M+
Sbjct: 3 FISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMN 62
Query: 160 NHQLS 164
++L
Sbjct: 63 RYELK 67
>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 = 30.1 bits (68), Expect = 0.20
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 12/88 (13%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGF-KFFPKDRKMALLQLDSI---------EEAI 152
L++SN+P T+ EL+ FT+ G F D + DSI EEA+
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 153 TALIQMHNHQLSEQSHLRVSFSKSNIQD 180
AL ++ L E++ + V S S + D
Sbjct: 63 EAL-ALNGRCLGERA-IEVQPSSSRVLD 88
>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 = 29.7 bits (67), Expect = 0.20
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG 125
P S L + N+P +TEDELKE F E G
Sbjct: 1 PDSHQLFVGNLPHDITEDELKEFFKEFG 28
>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 = 29.6 bits (67), Expect = 0.23
Identities = 9/52 (17%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 4 LTGVYGDVLRVKILYNKKDS--ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
L G + K++ + A ++ + A A+ M+ + G++++V
Sbjct: 18 LFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGRLILGQEIKV 69
>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 = 29.1 bits (66), Expect = 0.25
Identities = 12/51 (23%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR-KMALLQLDSIEEAITAL 155
N+P TE+++++ F + G ++ K + +A+++ ++ +EA+ AL
Sbjct: 6 KNLPKDTTENKIRQFFKDCG-EIREVKIVESEGGLVAVIEFETEDEALAAL 55
>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 = 29.5 bits (66), Expect = 0.25
Identities = 18/54 (33%), Positives = 25/54 (46%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAI 152
PS LHL N+P TE+EL E G V +R A ++ + +AI
Sbjct: 1 PSKVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAI 54
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). 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 to bind 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 and its nuclear
transport 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 = 80
Score = 29.2 bits (65), Expect = 0.30
Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITAL 155
PP+ L L+N+P E L F + GF K + P +A ++ ++ +A A
Sbjct: 2 NPPNYILFLNNLPEETNEMMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFENEAQAGAAR 59
Query: 156 IQMHNHQLSEQSHLRVSFSK 175
+ +++ ++++++K
Sbjct: 60 DALQGFKITPSHAMKITYAK 79
>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 = 30.8 bits (69), Expect = 0.33
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 9/80 (11%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKM 140
+ +PG ++ ++ L+++N+P ++T+D+L F + G V+ K R +
Sbjct: 183 YARPGGESIKDT-----NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGV 237
Query: 141 ALLQLDSIEEAITALIQMHN 160
A ++ + EEA A+ ++N
Sbjct: 238 AFVRFNKREEAQEAISALNN 257
>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 = 28.7 bits (65), Expect = 0.38
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALIQMHN 160
N+P VTED L+E F KG V K R+ + S E+A A+ +
Sbjct: 7 NLPKYVTEDRLREHFESKG-EVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63
>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 = 28.9 bits (64), Expect = 0.39
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 3 SLTGVYGDVLRVKILYNKKDSA-----LIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+L G YG VL K++ N + ++ M+ S + + H+ + + G+Q+ V
Sbjct: 18 NLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHLHRTELHGQQISV 73
>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 = 28.7 bits (64), Expect = 0.41
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP----KDRKMALLQLDSIEEAITALIQM 158
L++ N+ VTED LK+ F G V+ K P K ++ +A AL Q
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGG-PVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIAL-QT 58
Query: 159 HNHQLSEQSHLRVSFS 174
N + E + +RV+++
Sbjct: 59 LNGRQIENNEIRVNWA 74
>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 = 28.8 bits (65), Expect = 0.48
Identities = 20/91 (21%), Positives = 31/91 (34%), Gaps = 23/91 (25%)
Query: 102 TLHLSNIPASVTEDELKEAFTE---------------------KGFTVKGFKFFPKDRKM 140
T+ + N+P + + +LK+ F + K +K KD
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQSHLRV 171
A + E A AL N E H+RV
Sbjct: 62 AYVVFKEEESAEKAL--KLNGTEFEGHHIRV 90
>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 = 28.3 bits (64), Expect = 0.60
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 10/81 (12%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG--FTVKGFKFFPKDRKMALL-------QLDSIEEAI 152
TL + N+ TE+ LK+ F + G +V K LL + S E A
Sbjct: 2 TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 153 TALIQMHNHQLSEQS-HLRVS 172
AL ++ L + L++S
Sbjct: 62 KALKRLQGTVLDGHALELKLS 82
>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 = 28.4 bits (64), Expect = 0.61
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFK 132
S +P VTED L E F G +K K
Sbjct: 4 SGLPDDVTEDSLAELFGGIG-IIKRDK 29
>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 = 28.1 bits (63), Expect = 0.63
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKG 130
L++ N+ + V E +L++ F E V
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSS 28
>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 = 28.3 bits (64), Expect = 0.64
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITALI 156
LH+ + +V +D LKE F+ G TVK P DR+ A ++ +S E+A A+
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYG-TVKDVD-LPIDREVNLPRGYAYVEFESPEDAEKAIK 58
Query: 157 QMHNHQL 163
M Q+
Sbjct: 59 HMDGGQI 65
Score = 25.6 bits (57), Expect = 5.5
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 6 GVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V V + +++ + A ++ A A+ HMD ++ G+++ V
Sbjct: 20 SNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72
>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 = 28.0 bits (63), Expect = 0.70
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD------RKMALLQLDSIEEAITALI 156
L + N+ T D+L+ F + G G + P+D R A ++ +A A+
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEV--GDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58
Query: 157 QMHNHQLSEQSHLRV 171
M +L + LRV
Sbjct: 59 AMDGKEL-DGRELRV 72
>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 = 28.0 bits (63), Expect = 0.71
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAITAL 155
T+ +SN+ SV EDEL++ F++ G + + K+ K A ++ ++ E AL
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCG-EITDVR-LVKNYKGKSKGYAYVEFENEESVQEAL 57
>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 = 28.0 bits (63), Expect = 0.74
Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G++ V++ + K IQ A++ A A+ ++ + G+ ++V
Sbjct: 22 FGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72
Score = 26.5 bits (59), Expect = 3.1
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 19/67 (28%)
Query: 103 LHLSNIPASVTEDELKEAF--------------TEKGFTVKGFKFF----PKDRKMALLQ 144
L++ N+ ++TED+L+ F E G + KG+ F +D K AL Q
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRS-KGYGFIQFADAEDAKKALEQ 59
Query: 145 LDSIEEA 151
L+ E A
Sbjct: 60 LNGFELA 66
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 28.4 bits (63), Expect = 0.79
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVK 129
YP S L + N+P + E ELKE F G V+
Sbjct: 2 YPDSHQLFVGNLPHDIDESELKEFFMSFGNVVE 34
>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 = 28.1 bits (62), Expect = 0.79
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHN 160
LH+ NI +S T EL+ F E G ++ KD A + ++ E+A+ A+ + N
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIEC--DIVKD--YAFVHMERAEDAVEAIRGLDN 56
Score = 25.8 bits (56), Expect = 5.2
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V+ I+ KD A + M + A A+ +D GK+M V
Sbjct: 24 YGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV 66
>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 = 28.0 bits (63), Expect = 0.81
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 21/71 (29%)
Query: 103 LHLSNIPASVTEDELKEAF------------TEKGFTVKGFKFFPKDRKMALLQLDSIEE 150
L++ N+ S+ ++ L+E F T++ KGF F + S EE
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGF---------VCFSSPEE 54
Query: 151 AITALIQMHNH 161
A A+ +M+
Sbjct: 55 ATKAVTEMNGR 65
>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 = 29.8 bits (67), Expect = 0.83
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 91 KNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKG 125
K F N+Y + N+ SV ED+L+E F + G
Sbjct: 176 KKFTNLY-------VKNLDPSVNEDKLRELFAKFG 203
Score = 28.2 bits (63), Expect = 2.7
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 21/71 (29%)
Query: 101 PTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPKDRKMALLQLDSI 148
L++ N+ +VT+++L+E F+E G +GF F + +
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGF---------VCFSNP 336
Query: 149 EEAITALIQMH 159
EEA A+ +MH
Sbjct: 337 EEANRAVTEMH 347
>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 = 28.0 bits (63), Expect = 0.85
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 6 GVYGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
GV DV +K +K K A ++ A A ++ GK+ V
Sbjct: 23 GVV-DVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVV 74
>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 = 28.1 bits (63), Expect = 0.88
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 102 TLHLSNIPASVTEDELKE----AFTEKGFTVKGFKFFPKDR--KMALLQLDSIEEAITAL 155
L +SN+ ++ EL++ F G V P+ +A +++ ++++A A+
Sbjct: 6 DLQVSNLDYRLSRKELQQTLTNQFKRHG-KVLSVSLRPQTDGSLVASVRVPNLQDAQYAI 64
Query: 156 IQMH 159
Q+H
Sbjct: 65 SQLH 68
>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 = 28.0 bits (63), Expect = 0.89
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 103 LHLSNIPASVTEDELKEAF 121
L++ N+ VTE+ L + F
Sbjct: 4 LYVGNLNPKVTEEVLCQEF 22
>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 = 27.9 bits (63), Expect = 0.94
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG 125
T+ + N+P TE+ELKE F++ G
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFG 25
>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 = 27.8 bits (62), Expect = 1.00
Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP----KDRKMALLQLDSIEEAITALIQ 157
L +S +P SVT++EL++ F + G VK + K + +A ++ ++ A A+++
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHG-VVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62
Query: 158 MHNHQLSEQSHLRVSFS 174
M ++ E++ + V+ S
Sbjct: 63 MDGTEIKEKT-ISVAIS 78
Score = 25.5 bits (56), Expect = 6.4
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS 56
+G V V+++ N+ K A ++ A A++ MD + K + V IS
Sbjct: 26 HGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEKTISVAIS 78
>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 = 27.8 bits (62), Expect = 1.0
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-------MALLQLDSIEEAITAL 155
L + N+P +V E+ + E F G V+ K PK + + + S ++A A+
Sbjct: 2 LWVGNLPENVREERISEHFKRYG-RVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAV 60
Query: 156 IQMHNHQL 163
+M + L
Sbjct: 61 NKMGDRDL 68
>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 = 27.6 bits (62), Expect = 1.2
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKMALLQLDSIEEAITALIQ 157
L +S + TE EL+ F++ G + + R + +S+E+A A+
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 158 MHNHQL 163
++ +L
Sbjct: 63 LNGKEL 68
Score = 25.6 bits (57), Expect = 5.6
Identities = 9/55 (16%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 8 YGDVLRVKILYNK--KDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
+G V V ++ + +S + A A+ ++ + G+ ++V +K
Sbjct: 25 FGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79
>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 = 27.6 bits (62), Expect = 1.5
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 24/76 (31%)
Query: 105 LSNIPASVTEDELKEAFTE--------------KGFTVKGFKFFPKDRKMALLQLDSIEE 150
++ + E+++ + F E GF VKG+ AL++ ++ +E
Sbjct: 11 VTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGF-VKGY---------ALIEYETKKE 60
Query: 151 AITALIQMHNHQLSEQ 166
A A+ ++ +L Q
Sbjct: 61 AQAAIEGLNGKELLGQ 76
>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 = 27.2 bits (60), Expect = 1.6
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L + N+PA +TEDE K+ F + G G F K + ++L+S A A ++ +
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYG--EPGEVFINKGKGFGFIKLESRALAEIAKAELDDTP 61
Query: 163 LSEQSHLRVSF 173
+ + LRV F
Sbjct: 62 MRGR-QLRVRF 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 = 27.5 bits (62), Expect = 1.6
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGF-----KFFPKDRKMALLQLDSIEEAI 152
P+ TL L + TE+++ +A + +K K R A ++ S+E+A
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60
Query: 153 TAL 155
+
Sbjct: 61 QWM 63
>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 = 27.2 bits (61), Expect = 1.6
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 101 PTLHLSNIPASVTEDELKEAFTEKGFTVK 129
L +SN+ VTE++L+E F + VK
Sbjct: 1 TRLRVSNLHYDVTEEDLEELF-GRVGEVK 28
>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 = 27.2 bits (61), Expect = 1.7
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S TL + NI ++V ++EL+ F + G ++ K R ++ I A A +
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFG-DIRTLYTACKHRGFIMVSYYDIRAARRAKRALQ 59
Query: 160 NHQLSEQSHLRVSFS 174
+L + L + FS
Sbjct: 60 GTELGGRK-LDIHFS 73
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 29.1 bits (65), Expect = 1.7
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 9 GDVLRVKILYNK---KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS 56
G V+ VK+ K KD+ ++ E +A L M H D+L + ++ + +S
Sbjct: 936 GTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVS 986
>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 = 26.9 bits (60), Expect = 1.8
Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 22/74 (29%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPKDRKMALLQLDSIE 149
TL + N+ S +D+L+E F E G V KGF ++ + E
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGF---------GHVEFATEE 51
Query: 150 EAITALIQMHNHQL 163
A AL + +L
Sbjct: 52 GAQKAL-EKSGEEL 64
>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 = 27.0 bits (60), Expect = 1.9
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 20/70 (28%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTV-----------KGFKFFPKDRKMALLQLDSIEEA 151
LH+SNIP + +L++ F + G + KGF F + + +A
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGF---------VTFANSADA 53
Query: 152 ITALIQMHNH 161
A ++H
Sbjct: 54 DRAREKLHGT 63
>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 = 26.4 bits (59), Expect = 2.1
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 14/66 (21%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFT-----VKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
L + N+P + T +EL+ F + G VK + F + ++ E+A A+
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGF---------VHMEEEEDAEDAIKA 52
Query: 158 MHNHQL 163
++ ++
Sbjct: 53 LNGYEF 58
>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 = 27.1 bits (61), Expect = 2.3
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGF 126
+++S +P +T +E E F++ G
Sbjct: 4 VYVSGLPLDITVEEFVEVFSKCGI 27
>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 = 26.8 bits (59), Expect = 2.3
Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKMALLQLDSIEEAITALIQM 158
L++S +P ++T+ EL++ F++ G + + R + ++ D EA A+ +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 159 HN 160
+
Sbjct: 63 NG 64
>gnl|CDD|180280 PRK05835, PRK05835, fructose-bisphosphate aldolase; Provisional.
Length = 307
Score = 28.0 bits (62), Expect = 3.2
Identities = 30/126 (23%), Positives = 57/126 (45%), Gaps = 21/126 (16%)
Query: 53 VMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIP--- 109
V+++ +A Q KE Q D T+ +FK +F+ + L+NIP
Sbjct: 153 VLVNPKEAEQFVKESQVDYLAPAIGTSHGAFKFKGEPKLDFERL---QEVKRLTNIPLVL 209
Query: 110 --ASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQS 167
AS D++++++ + G +KG K P LQ E++ I ++++ +
Sbjct: 210 HGASAIPDDVRKSYLDAGGDLKGSKGVP----FEFLQ-----ESVKGGI----NKVNTDT 256
Query: 168 HLRVSF 173
LR++F
Sbjct: 257 DLRIAF 262
>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 = 26.1 bits (58), Expect = 3.2
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 17/61 (27%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTV-------------KGFKF----FPKDRKMALLQL 145
L + N+P + TE+EL+E F G KGF F FP+ A +L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 146 D 146
D
Sbjct: 62 D 62
>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 = 26.2 bits (58), Expect = 3.2
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L++ P +E ++E F+ G VK K A ++ +S+E AI A +H
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYG-AVKEVKMI---SNFAFVEFESLESAIRAKDSVHGKV 57
Query: 163 LSEQ 166
L+
Sbjct: 58 LNNN 61
>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 = 26.5 bits (59), Expect = 3.3
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALIQM 158
L++S +P ++T+ EL+ F+ G + R + ++ D EA A+ +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 159 HNHQLS 164
+
Sbjct: 63 NGTIPP 68
>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 = 26.4 bits (59), Expect = 3.3
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLD---------SIEEAITALI 156
N+ + ED+L+ F++ G V+ + PK + +L+ A AL
Sbjct: 6 RNLDFKLDEDDLRGIFSKFG-EVESIR-IPKKQDEKQGRLNNGFAFVTFKDASSAENAL- 62
Query: 157 QMHNHQL 163
Q++ +L
Sbjct: 63 QLNGTEL 69
>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 = 26.0 bits (58), Expect = 3.5
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 29/86 (33%)
Query: 103 LHLSNIPASVTEDELKEAF----------------TEKGFTVKGFKFFPKDRKMALLQLD 146
L++ + V E L AF T+K +GF F ++ +
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKH---RGFAF---------VEFE 48
Query: 147 SIEEAITALIQMHNHQLSEQSHLRVS 172
E+A A+ M+ +L ++ +RV+
Sbjct: 49 EPEDAAAAIDNMNESELFGRT-IRVN 73
>gnl|CDD|241223 cd12779, RRM1_ROD1, RNA recognition motif 1 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM1 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 that 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 = 90
Score = 26.6 bits (58), Expect = 3.7
Identities = 24/72 (33%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
PS LHL IP VTE E+ G K + A L++ S E A+T M
Sbjct: 4 PSRVLHLRKIPNDVTEAEIISLGLPFGKVTNLLML--KGKSQAFLEMASEEAAVT----M 57
Query: 159 HNHQLSEQSHLR 170
N+ HLR
Sbjct: 58 VNYYTPITPHLR 69
>gnl|CDD|178439 PLN02847, PLN02847, triacylglycerol lipase.
Length = 633
Score = 27.9 bits (62), Expect = 3.8
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 94 QNIYPPSPTLHLSNIPASVTEDELKEAFTE 123
Q YPP +H+ ++P S +E++ E TE
Sbjct: 555 QQFYPPGRIMHIVSMPPSDSENDDDEVATE 584
>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM2 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila 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).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 80
Score = 26.2 bits (57), Expect = 3.8
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITALI 156
PP+ L L+N+P E L F + GF K + P +A ++ ++ ++ A
Sbjct: 3 PPNQILFLTNLPEETNEMMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFENEVQSAAAKE 60
Query: 157 QMHNHQLSEQSHLRVSFSK 175
+ +++ ++++F+K
Sbjct: 61 ALQGFKITPTHAMKITFAK 79
>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 = 26.1 bits (57), Expect = 3.9
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD---RKMALLQLDSIEEAITALIQM 158
T+ ++N+ V +LKE F+ G V+ KD R + + + EA+ A I M
Sbjct: 2 TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQA-ISM 60
Query: 159 HNHQL 163
N QL
Sbjct: 61 FNGQL 65
>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 = 26.5 bits (59), Expect = 4.0
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG 125
TL + N+P TE+ LK F+ G
Sbjct: 2 TLFVLNVPPYCTEESLKRLFSRCG 25
>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 = 26.0 bits (58), Expect = 4.2
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK 139
T+ ++N+ ED+L+E F G + + KD++
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISR--VYLAKDKE 36
>gnl|CDD|240716 cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate
methenyltetrahydrofolate synthetase domain-containing
proteins. This subfamily corresponds to
methenyltetrahydrofolate synthetase domain (MTHFSD), a
putative RNA-binding protein found in various vertebrate
species. It contains an N-terminal
5-formyltetrahydrofolate cyclo-ligase domain and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The biological role of MTHFSD remains unclear. .
Length = 74
Score = 25.8 bits (57), Expect = 4.2
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 16/59 (27%)
Query: 102 TLHLSNIPASVTEDELKEAFTE----------KGFTVKGFKFFPK------DRKMALLQ 144
T+ + NI ++ +LK A E +G K F FP D +A LQ
Sbjct: 1 TVKVGNISRNLRVSDLKSALRERGVKPLRITWQGARGKAFLHFPDKDAADADSALASLQ 59
>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 = 25.9 bits (57), Expect = 4.4
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKF-----FPKDRKMALLQLDSIEEAITALI 156
+++ ++P E ELK+ F++ G TVK + + +Q + E A A
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFG-TVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK 59
Query: 157 QMHNHQLSEQ 166
M+N+ L +
Sbjct: 60 SMNNYLLMGK 69
>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 = 26.0 bits (57), Expect = 4.5
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDS 147
L + N+P +TE++ K+ F + G + F +DR ++L+S
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSE--VFINRDRGFGFIRLES 46
>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 = 25.7 bits (57), Expect = 4.6
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKG---FKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
N+P SVT +LK+ F E G ++ + + + +S E+A A+ + +
Sbjct: 4 RNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYD 63
Query: 163 LS 164
L
Sbjct: 64 LE 65
>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 = 25.7 bits (57), Expect = 4.6
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 102 TLHLSNIPASVTEDELKEAF 121
L +SN+ SVTED++ E F
Sbjct: 2 RLVVSNLHPSVTEDDIVELF 21
>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 = 27.6 bits (61), Expect = 5.0
Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 22/88 (25%)
Query: 90 SKNFQNIYPPSPTLHLSNIPASVTEDELK---EAFTE----------KGFTVKGFKFFPK 136
+ + P L++ N+ ++TE EL+ E F + + KGF F
Sbjct: 176 ATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGF--- 232
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQLS 164
+Q EEA AL M+ +L+
Sbjct: 233 ------IQFHDAEEAKEALEVMNGFELA 254
>gnl|CDD|238399 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate.
Length = 322
Score = 27.1 bits (61), Expect = 5.3
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 17/55 (30%)
Query: 115 DELKEAFTEKGFTVKGFKFFPKDRK-----------------MALLQLDSIEEAI 152
DEL+E E G + F+++ RK M LL LD+I EAI
Sbjct: 261 DELEERIKEHGLDPESFEWYLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIREAI 315
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which 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 heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 25.8 bits (56), Expect = 5.3
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEA 151
SP +H+ + SV E +L EA + G + P R+ AL++ + +E A
Sbjct: 3 SPVVHVRGLCESVVEADLVEALEKFG-PICYVMMMPFKRQ-ALVEFEMVESA 52
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It 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. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 26.2 bits (58), Expect = 5.5
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKF 133
TL L N+P TE L++ F G ++ F
Sbjct: 2 TLFLVNLPVDTTERHLRKLFGSGGGIIESVVF 33
>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 = 27.3 bits (60), Expect = 5.5
Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L++ N+ + TE+ ++++F+E F + K R A + + E+A+ A+ +++ +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSE--FKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKE 293
Query: 163 LSEQSHLRVSFSK 175
L E S + V+ +K
Sbjct: 294 L-EGSEIEVTLAK 305
>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 = 25.8 bits (57), Expect = 5.7
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGF--------TVKGFKFFP-KDRKMALLQLDSIEEAI 152
+++SN+ S +E++L+E + TV+GF+ + +A + S E+A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 153 TALIQMHNHQLSEQ 166
+ ++ +
Sbjct: 61 KVVKDLNGKVFKNR 74
>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 = 25.4 bits (56), Expect = 6.0
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVK----GFKFFPKDRKMALLQLDSIEEAITALIQ 157
L + N+P T ++L F G K K + A ++ D EA+T ++
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFD-TAEAMTKALK 60
Query: 158 MHNHQLSE 165
+H+ L
Sbjct: 61 LHHTLLKG 68
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 25.4 bits (56), Expect = 6.2
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 11/69 (15%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD-------RKMALLQLDSIEEAITA 154
T +L N+P VTE+++KE F +G V + P++ R + + + + A
Sbjct: 3 TAYLGNLPYDVTEEDIKEFF--RGLNVSSVR-LPREPGDPGRLRGFGYAEFEDRDSLLQA 59
Query: 155 LIQMHNHQL 163
L +++ L
Sbjct: 60 L-SLNDESL 67
>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 = 25.4 bits (56), Expect = 6.5
Identities = 12/71 (16%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFF----PKDRKMALLQLDSIEEAITAL 155
+ + + +P +VTE +L++ F++ G + + + R + +S E+++ +
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQV 60
Query: 156 IQMHNHQLSEQ 166
+ H H ++ +
Sbjct: 61 VNEHFHDINGK 71
>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 = 25.4 bits (56), Expect = 6.6
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG 125
TL + N+ ++TE+EL+ AF G
Sbjct: 4 TLFVGNLEITITEEELRRAFERYG 27
>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 = 25.6 bits (57), Expect = 6.9
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 9/67 (13%)
Query: 105 LSNIPASVTEDELKEAFTEKGFTVKGFKFF--PKDRKM------ALLQLDSIEEAITALI 156
+ NIP T++ L + E G + F P D K A + + E A
Sbjct: 3 IRNIPNKYTQEMLLQLLDEHGKGGA-YDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYK 61
Query: 157 QMHNHQL 163
+ +
Sbjct: 62 AFNGKKW 68
>gnl|CDD|225852 COG3315, COG3315, O-Methyltransferase involved in polyketide
biosynthesis [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 297
Score = 26.5 bits (59), Expect = 7.4
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGF 126
+P H + + ED+ +A GF
Sbjct: 140 TPPAHRRLVAVDLREDDWPQALAAAGF 166
>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 = 25.2 bits (56), Expect = 7.5
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 107 NIPASVTEDELKEAFTEKG 125
N+P + E+EL++ F + G
Sbjct: 6 NLPFDIEEEELRKHFEDCG 24
>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 = 25.1 bits (55), Expect = 7.6
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVK-GFKFFPKDRKMALLQLDSIEEAITALIQMHN 160
TL + N+ + T +L+EAF G + K + A +Q I + A+ +M
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63
Query: 161 HQL 163
L
Sbjct: 64 EYL 66
>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 = 25.2 bits (56), Expect = 8.1
Identities = 9/51 (17%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G V R+++ +K K A ++ A + M+ +F + ++
Sbjct: 23 FGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73
>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 = 25.6 bits (57), Expect = 8.4
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDR 138
N+P SV E +LKE F + V K +
Sbjct: 7 NLPKSVDEKKLKELFLK---AVSERAGKKKPK 35
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 26.7 bits (60), Expect = 8.8
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 17/55 (30%)
Query: 115 DELKEAFTEKGFTVKGFKFFPK----------------DR-KMALLQLDSIEEAI 152
D L E+ EKG + F+F+ + +R M LL L++I EA+
Sbjct: 372 DMLVESIKEKGLNPESFEFYLEAFKYGMPPHGGFGLGLERLTMKLLGLENIREAV 426
>gnl|CDD|222247 pfam13590, DUF4136, Domain of unknown function (DUF4136). This
domain is found in bacterial lipoproteins. The function
is not known.
Length = 151
Score = 26.0 bits (58), Expect = 8.8
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 129 KGFKFFPKDRKMAL---LQLDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
K + F P A L IE+A+ A + +E + L V++
Sbjct: 18 KTYAFAPPASDPAQISDLDEKRIEDAVDAELAAKGFTRAESADLLVNYH 66
>gnl|CDD|240596 cd12935, LEM_like, LEM-like domain of lamina-associated polypeptide
2 (LAP2) and similar proteins. LAP2, also termed
thymopoietin (TP), or thymopoietin-related peptide
(TPRP), is composed of isoform alpha and isoforms
beta/gamma and may be involved in chromatin organization
and postmitotic reassembly. Some of the LAP2 isoforms
are inner nuclear membrane proteins that can bind to
nuclear lamins and chromatin, while others are
nonmembrane nuclear polypeptides. All LAP2 isoforms
contain an N-terminal lamina-associated
polypeptide-Emerin-MAN1 (LEM)-domain that is connected
to a highly divergent LEM-like domain by an unstructured
linker. Both LEM and LEM-like domains share the same
structural fold, mainly composed of two large parallel
alpha helices. However, their biochemical nature of the
solvent-accessible residues is completely different,
which indicates the two domains may target different
protein surfaces. The LEM domain is responsible for the
interaction with the nonspecific DNA binding protein
barrier-to-autointegration factor (BAF), and the
LEM-like domain is involved in chromosome binding. The
family also includes the yeast helix-extension-helix
domain-containing proteins, Heh1p (formerly called
Src1p) and Heh2p, and their uncharacterized homologs
found mainly in fungi and several in bacteria. Heh1p and
Heh2p are inner nuclear membrane proteins that might
interact with nuclear pore complexes (NPCs). Heh1p is
involved in mitosis. It functions at the interface
between subtelomeric gene expression and transcription
export (TREX)-dependent messenger RNA export through
NPCs. The function of Heh2p remains ill-defined. Both
Heh1p and Heh2p contain a LEM-like domain (also termed
HeH domain), but lack a LEM domain.
Length = 36
Score = 23.9 bits (53), Expect = 8.9
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 109 PASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQL 145
P+S+T EL+ TE G ++ +K L++L
Sbjct: 1 PSSLTVAELRSILTE-----HGVEYPSNAKKAELVKL 32
>gnl|CDD|219056 pfam06485, DUF1092, Protein of unknown function (DUF1092). This
family consists of several hypothetical proteins of
unknown function all from photosynthetic organisms
including plants and cyanobacteria.
Length = 270
Score = 26.4 bits (59), Expect = 9.0
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 42 DKLRVFGKQMRVMISK 57
D++R F QM MI +
Sbjct: 63 DRIRFFRSQMLTMIQR 78
>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 = 25.0 bits (55), Expect = 9.3
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 17/61 (27%)
Query: 103 LHLSNIPASVTEDELKEAFTEKG-------------FTVKGFKF----FPKDRKMALLQL 145
L + N+P S ED+L++ F++ G KGF + P+D A +L
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 146 D 146
D
Sbjct: 65 D 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 = 25.3 bits (55), Expect = 9.7
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVK 129
P S L + N+P V + ELKE F + G V+
Sbjct: 1 PDSHQLFVGNLPHDVDKSELKEFFQQYGNVVE 32
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 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 = 93
Score = 25.3 bits (56), Expect = 9.8
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 13/67 (19%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG------FTVKGFK----FFPKDRKMALLQLDS---I 148
T++ +P VT+++L+E F + F + K + AL+ LD+ +
Sbjct: 4 TVYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEETL 63
Query: 149 EEAITAL 155
+E I +L
Sbjct: 64 DEIIESL 70
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
0.319 0.132 0.372
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,173,866
Number of extensions: 823478
Number of successful extensions: 1200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1172
Number of HSP's successfully gapped: 179
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)