RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10125
(312 letters)
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 117 bits (295), Expect = 2e-33
Identities = 43/62 (69%), Positives = 49/62 (79%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
TK ++ED F YGP+++VWVARNPPGF FVEFED RDAEDAVR DGR I G RVRVE+S
Sbjct: 12 TKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELS 71
Query: 111 NP 112
Sbjct: 72 RG 73
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 90.8 bits (225), Expect = 3e-23
Identities = 45/69 (65%), Positives = 53/69 (76%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T + K ++E AFSYYGP++ VW+ARNPPGF FVEFED RDAEDAVRG DG+ I G RVRV
Sbjct: 9 TGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 68
Query: 108 EMSNPQKMR 116
E+S R
Sbjct: 69 ELSTGMPRR 77
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 89.7 bits (222), Expect = 7e-23
Identities = 43/66 (65%), Positives = 52/66 (78%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+ K ++E AF YYGP+++VWVARNPPGF FVEFED RDA DAVR DGR + G RVRVE
Sbjct: 15 NGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE 74
Query: 109 MSNPQK 114
+SN +K
Sbjct: 75 LSNGEK 80
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 75.3 bits (186), Expect = 1e-17
Identities = 24/75 (32%), Positives = 45/75 (60%), Gaps = 7/75 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAV 92
++V + +T+E++ + FS +G +++V + R+ GF FVEFE DAE A+
Sbjct: 1 TLFVGNL--PPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58
Query: 93 RGFDGREINGRRVRV 107
+G+E++GR ++V
Sbjct: 59 EALNGKELDGRPLKV 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 73.8 bits (182), Expect = 5e-17
Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 4/60 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
T+ED++D FS +GPI+++ + R+ GF FVEFED DAE A+ +G+E+ GR +R
Sbjct: 11 TEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 72.0 bits (177), Expect = 2e-16
Identities = 35/60 (58%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 52 KEDIEDAFSYYGPIKNV--WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
+ DIED F YGPIK + R P F FVEFED RDAEDAVRG DG + +G R+RVE
Sbjct: 13 ERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 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 = 72.0 bits (177), Expect = 2e-16
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 6/74 (8%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRG 94
++V + +T+ED+ + FS +G I++V + R+ GF FVEFE DAE A+
Sbjct: 1 LFVGNL--PPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEA 58
Query: 95 FDGREINGRRVRVE 108
+G+E++GR+++V
Sbjct: 59 LNGKELDGRKLKVS 72
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 69.8 bits (171), Expect = 2e-15
Identities = 30/58 (51%), Positives = 43/58 (74%), Gaps = 2/58 (3%)
Query: 54 DIEDAFSYYGPIKNV--WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
++ED F YGPI ++ + PPG+ F+EFED RDAEDA+RG DG + +G+R+RVE+
Sbjct: 15 EVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGYDFDGQRLRVEL 72
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 26/69 (37%), Positives = 45/69 (65%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
ST +T++++E FS +G ++ V + ++P GFGFV FE DA+ A+R +G+E+
Sbjct: 10 STRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELE 69
Query: 102 GRRVRVEMS 110
GR ++VE +
Sbjct: 70 GRVIKVEKA 78
>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 = 65.9 bits (161), Expect = 5e-14
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
S TKE++E F +G +K+V + N P G +VE+E+ A AV DG EI +
Sbjct: 13 SVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEKT 72
Query: 105 VRVEMSNP 112
+ V +SNP
Sbjct: 73 ISVAISNP 80
>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 = 63.9 bits (156), Expect = 2e-13
Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T +D+ F YG + +V++ R+ GF FV F D+RDAEDA+ DG+E++GR +
Sbjct: 11 TPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGREL 70
Query: 106 RV 107
RV
Sbjct: 71 RV 72
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 62.1 bits (151), Expect = 1e-12
Identities = 32/57 (56%), Positives = 40/57 (70%), Gaps = 1/57 (1%)
Query: 53 EDIEDAFSYYGPIKNVWVA-RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+DIED F YG I+++ + R P F FVEFED RDAEDAV G DG + +G R+RVE
Sbjct: 14 KDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE 70
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 61.2 bits (149), Expect = 2e-12
Identities = 28/60 (46%), Positives = 38/60 (63%), Gaps = 3/60 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
+ D+E F YG I+ + + GFGFVEFED RDA+DAV +G+E+ G RV VE +
Sbjct: 12 RERDVERFFKGYGRIREINLKN---GFGFVEFEDPRDADDAVYELNGKELCGERVIVEHA 68
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 65.4 bits (158), Expect = 4e-12
Identities = 45/237 (18%), Positives = 84/237 (35%), Gaps = 18/237 (7%)
Query: 1 MWNKMSHFKLKLLLCFSSLCQEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFS 60
M + + L + +E ++V + T+ED+ + F
Sbjct: 80 MEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNL--PYDVTEEDLRELFK 137
Query: 61 YYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQKM 115
+GP+K V + R+ GF FVEFE AE A+ +G+E+ GR +RV+ + P
Sbjct: 138 KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPAS- 196
Query: 116 RGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKI 175
+ RS + D + +RG+ + G R
Sbjct: 197 QPRSELSNNLDASFAKK-LSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR------ 249
Query: 176 NGRRVRVEMSNPQKMRGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYAR 232
G VR + + + + G+ + ++ + R K G R +++
Sbjct: 250 -GDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKK--KILGRGPRKAFSQ 303
>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 = 59.8 bits (146), Expect = 4e-12
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
FS +G ++ + + + PGF FVEF AE AV+ +G GR +RV+ S
Sbjct: 5 FSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 58.2 bits (141), Expect = 3e-11
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+EDIE F +GP+ + + F FVEFED DA A+ G I+G + VE
Sbjct: 13 REEDIEKLFEPFGPLVRCDIRKT---FAFVEFEDSEDATKALEALHGSRIDGSVLTVE 67
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGR 103
+ T+ED++D F +G + + V + GFGFVE E +A A+ +G + GR
Sbjct: 10 NVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGR 69
Query: 104 RVRVEMSNP 112
+ V + P
Sbjct: 70 TLTVNEARP 78
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 5/67 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
+T+E + + FS GP+ + + + P G+GF EFED A A+R +G E NGR
Sbjct: 9 DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGR 68
Query: 104 RVRVEMS 110
+RV+ +
Sbjct: 69 ALRVDFA 75
>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 = 57.6 bits (140), Expect = 5e-11
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
+T E +E+ FS GPIK +V ++ GFG+V F DA+ A+ + GR
Sbjct: 10 DTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGR 69
Query: 104 RVRVE 108
++ VE
Sbjct: 70 KIHVE 74
>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 = 57.2 bits (139), Expect = 5e-11
Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
K+ +++ FS YG +K+V + + G+ +VEFE DAE A++ DG +I+G+ V
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70
Query: 106 RVE 108
VE
Sbjct: 71 TVE 73
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 57.2 bits (139), Expect = 5e-11
Identities = 24/55 (43%), Positives = 38/55 (69%), Gaps = 3/55 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
+KED+E+ FS YG I + + + G+GFV+F++ DA AV G +GREI G+++
Sbjct: 14 SKEDLEEIFSKYGKILGISLHK---GYGFVQFDNEEDARAAVAGENGREIAGQKL 65
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 56.4 bits (137), Expect = 1e-10
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARN---PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
S T+ED+ + FS YG ++ V + RN P GF FVEF DAE A++ +G ++GR +
Sbjct: 9 SVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68
Query: 106 R 106
R
Sbjct: 69 R 69
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 56.9 bits (138), Expect = 1e-10
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 10/73 (13%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ + F YGPIK + + R+ P G+ F+EFE RD + A + DG++I+GRRV
Sbjct: 14 TESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGRRV 73
Query: 106 RVEMSNPQKMRGR 118
V++ RGR
Sbjct: 74 LVDVE-----RGR 81
>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 = 55.7 bits (135), Expect = 2e-10
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
++ + AF +G IK++ + + GF FVEFE+ DA A+ + E+ GR +
Sbjct: 11 DEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTI 70
Query: 106 RV 107
RV
Sbjct: 71 RV 72
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 55.8 bits (135), Expect = 3e-10
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 53 EDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+D+ F YGPI +V++ R P GF +V+FED RDAEDA+ D GR + +
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEI 74
Query: 108 E 108
+
Sbjct: 75 Q 75
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 55.6 bits (134), Expect = 3e-10
Identities = 24/64 (37%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+ ++ +E FS YG I V V ++ GFGFV FE+ DA+DA+ +G+ ++GR+
Sbjct: 12 TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQ 71
Query: 105 VRVE 108
+RV+
Sbjct: 72 IRVD 75
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 54.8 bits (132), Expect = 4e-10
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 5/70 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
S T+ED+ D FS PIK+ V +P G+GFV F DA++A+ ++++GR
Sbjct: 10 SVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGR 69
Query: 104 RVRVEMSNPQ 113
+R++++ +
Sbjct: 70 ILRLDIAERR 79
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 54.6 bits (131), Expect = 7e-10
Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
+ + ED+ F YGPI +V+V R P GF +V+FED RDAEDA+ D + I
Sbjct: 9 ADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWIC 68
Query: 102 GRRVRVEMS 110
GR++ ++ +
Sbjct: 69 GRQIEIQFA 77
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 53.8 bits (129), Expect = 1e-09
Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 3/60 (5%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++ ++D+E F YG I+++ + R GFGFVEF+D RDA+DAV DG+E+ RV +E
Sbjct: 10 AAREKDVERFFKGYGRIRDIDLKR---GFGFVEFDDPRDADDAVYELDGKELCNERVTIE 66
>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 = 53.3 bits (129), Expect = 1e-09
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
E +++ F YG I + V ++ G FGFV FE+ A+ AV +G+E+NG+++
Sbjct: 14 DDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLY 73
Query: 107 V 107
V
Sbjct: 74 V 74
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 53.4 bits (129), Expect = 2e-09
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRR 104
T+ D++ FS +G + V + R P GF FV+F + DAE A++G +G++I GR
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69
Query: 105 VRV 107
V V
Sbjct: 70 VAV 72
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 53.0 bits (128), Expect = 3e-09
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S +T+E + + FS YG I+ + + R G+ FVE+E RDA A R I+
Sbjct: 12 SLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVID 71
Query: 102 GRRVRVEMSNPQKMRG 117
G + V+ + + G
Sbjct: 72 GSEIFVDFERERTLPG 87
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 54.4 bits (131), Expect = 3e-09
Identities = 32/103 (31%), Positives = 43/103 (41%), Gaps = 4/103 (3%)
Query: 146 CYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNGRS---GGDR 202
CY CGG GH +R+C + G+ + C G + P G RS G
Sbjct: 3 CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECP-SAPGGRGERSCYNCGKT 61
Query: 203 GYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRR 245
G+ P + CY CG GH +R+C +R GG RR
Sbjct: 62 GHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARR 104
Score = 52.5 bits (126), Expect = 1e-08
Identities = 31/101 (30%), Positives = 38/101 (37%), Gaps = 1/101 (0%)
Query: 146 CYECGGRGHYARDCRSRRSGGSGRP-ELCKINGRRVRVEMSNPQKMRGRSNGRSGGDRGY 204
CY+CG GH +R+C S G R C G R P RS G
Sbjct: 30 CYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHI 89
Query: 205 RGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRR 245
R + CY CGG GH +RDC + GG +
Sbjct: 90 SRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDK 130
Score = 45.6 bits (108), Expect = 4e-06
Identities = 31/103 (30%), Positives = 40/103 (38%), Gaps = 27/103 (26%)
Query: 137 GRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPE--LCKINGRRVRVEMSNPQKMRGRS 194
P + CY CG GH +R+C +R GG+ R C G R + N K
Sbjct: 71 APPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISR-DCPNAGK----- 124
Query: 195 NGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSR 237
R GGD+ CY CG GH +RDC +
Sbjct: 125 --RPGGDK-----------------TCYNCGQTGHLSRDCPDK 148
Score = 29.8 bits (67), Expect = 0.98
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 221 CYECGGRGHYARDCRSRRSGGGGRRRS 247
CY CGG GH +R+C + G + R
Sbjct: 3 CYRCGGVGHQSRECPNSAPAGAAKARP 29
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 53.1 bits (127), Expect = 3e-09
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S +T+ D+ + FS YGPI +V + +R GF FV FE+ DA++A +G E++
Sbjct: 18 SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 77
Query: 102 GRRVRVEMS 110
GRR+RV+ S
Sbjct: 78 GRRIRVDFS 86
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 52.5 bits (127), Expect = 3e-09
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 7/76 (9%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVR 93
+YV + S +T+E I + FS G IK + + + P GF FVE+ R DAE+AV+
Sbjct: 1 LYVGNL--SFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58
Query: 94 GFDGREINGRRVRVEM 109
+G +++ R +RV+
Sbjct: 59 YLNGTKLDDRIIRVDW 74
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 50.8 bits (122), Expect = 1e-08
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGFDGREING 102
T+E++ F GPI++ + R G+GFV++ D DA+ A+ +G EI
Sbjct: 10 QDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRN 69
Query: 103 RRVRV 107
+R++V
Sbjct: 70 KRLKV 74
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDG 97
V+YV + ST T+E + + FS YG ++ V + + FV FE+R DA A+ +G
Sbjct: 3 VLYVRNLPLST--TEEQLRELFSEYGEVERV---KKIKDYAFVHFEERDDAVKAMEEMNG 57
Query: 98 REINGRRVRVEMSNP 112
+E+ G + V ++ P
Sbjct: 58 KELEGSPIEVSLAKP 72
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 51.0 bits (123), Expect = 1e-08
Identities = 18/59 (30%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPP-GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
KED+ + S +GP++++ V +N P G +V+F+ A+ ++ +GR +GR++ E
Sbjct: 25 KEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITAEY 83
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWV----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
T+ED+E+ F G +K V + + G V FE R DAE A++ F+G ++G+ ++
Sbjct: 13 TEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQ 72
Query: 107 VEM 109
VE+
Sbjct: 73 VEL 75
>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 = 51.1 bits (123), Expect = 1e-08
Identities = 18/63 (28%), Positives = 39/63 (61%), Gaps = 5/63 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+ +ED+ D F+ +G IKN+ + + G+ +E+E +++A+ A+ G +G+E+ G+
Sbjct: 18 AQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQT 77
Query: 105 VRV 107
+ V
Sbjct: 78 ISV 80
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 50.4 bits (121), Expect = 2e-08
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
E + AF+ +G I + V ++ G+GFV F + DAE+A++ +G+ + GR +
Sbjct: 12 DTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71
Query: 106 R 106
R
Sbjct: 72 R 72
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++T E++ F YG + V +N +GFV E+ DAEDA++ +G E G+R+ VE
Sbjct: 10 ATTSEELRALFEKYGTVTECDVVKN---YGFVHMEEEEDAEDAIKALNGYEFMGKRINVE 66
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 49.8 bits (119), Expect = 2e-08
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
S + +D+ F YG IK + N F+EF D R AE A++ + EI G+R+++
Sbjct: 11 PSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSEIAGKRIKL 70
Query: 108 E 108
E
Sbjct: 71 E 71
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 49.5 bits (119), Expect = 3e-08
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFG---FVEFEDRRDAEDAVRGFDGREINGRRV 105
+ +++ FS +G +K++ R P FVEF D R AE A+ +GR G R+
Sbjct: 12 PISDQELRSLFSQFGEVKDI---RETPLRPSQKFVEFYDIRAAEAALDALNGRPFLGGRL 68
Query: 106 RVE 108
+V+
Sbjct: 69 KVK 71
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 50.0 bits (120), Expect = 3e-08
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T ED+E FS +G IK+ V R+ + F+EFE + D E+A D I+ RR+
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75
Query: 106 RVEMS 110
V+ S
Sbjct: 76 HVDFS 80
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 50.0 bits (119), Expect = 3e-08
Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
++ ED+ F YGPI +V+V R P GF +++FED RDAEDA+ + + + GR
Sbjct: 11 ATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGR 70
Query: 104 RVRVEMS 110
++ ++ +
Sbjct: 71 QIEIQFA 77
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 49.1 bits (117), Expect = 5e-08
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
+++E++ F YG + + V R F FV A+ A+ +GRE++GR++ VE
Sbjct: 12 TSQEELRALFEAYGAVLSCAVMRQ---FAFVHLRGEAAADRAIEELNGRELHGRKLVVEH 68
Query: 110 S 110
S
Sbjct: 69 S 69
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 49.6 bits (119), Expect = 5e-08
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 59 FSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQK 114
FS G +A P GF FVE+ DAE+A + +G + G +RV NP +
Sbjct: 24 FSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNPGR 83
Query: 115 MRGRS 119
G S
Sbjct: 84 -PGAS 87
>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 = 49.1 bits (118), Expect = 6e-08
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S + ++D+ + F +GPI V++A++ GF FV F R DAE A+ +G +
Sbjct: 8 SEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYD 67
Query: 102 GRRVRVEMS 110
+ VE +
Sbjct: 68 NLILSVEWA 76
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 48.7 bits (117), Expect = 9e-08
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 52 KEDIEDAFSYYGPIKNVWVAR------NPPGFG--FVEFEDRRDAEDAVRGFDGREINGR 103
ED+++ YG + +V + R + PG G FVEF D DA+ A GR+ +GR
Sbjct: 25 LEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGR 84
Query: 104 RVRVE 108
V
Sbjct: 85 TVVAS 89
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 48.4 bits (116), Expect = 1e-07
Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S +T+ D+ + FS YGPI+ V V GFGFV FE DA++A +G EI+
Sbjct: 8 SLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEID 67
Query: 102 GRRVRVEMS 110
GRR+RV+ S
Sbjct: 68 GRRIRVDYS 76
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 48.4 bits (116), Expect = 1e-07
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFG------FVEFEDRRDAEDAVRGFDGREINGRRV 105
K++IE+ YG + NV V FVEF D +A AVR +GR GR+V
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGRKV 79
Query: 106 RVEMSN 111
+
Sbjct: 80 TARFYD 85
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 48.0 bits (115), Expect = 1e-07
Identities = 21/39 (53%), Positives = 24/39 (61%)
Query: 70 VARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
V R+ G G VEF + D E A+R DG E GRRVRVE
Sbjct: 32 VDRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRVE 70
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+E ++D FS GP+ + + + P G+GF E++D+ A A+R +G E+NGR+
Sbjct: 10 ATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQ 69
Query: 105 VRVE 108
+RV+
Sbjct: 70 LRVD 73
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 48.1 bits (115), Expect = 1e-07
Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 44 VLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGR 98
++C S T++D+ +AF+ +G I+++WV ++ G +V+F A A+ +G+
Sbjct: 8 IVCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGK 67
Query: 99 EINGR 103
+ G
Sbjct: 68 CLGGD 72
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 47.6 bits (113), Expect = 1e-07
Identities = 25/57 (43%), Positives = 37/57 (64%), Gaps = 3/57 (5%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++DI+ F YG + + + G+GFVEFED RDA+DAV +G+++ G RV VE
Sbjct: 13 EKDIQRFFGGYGKLLEIDLKN---GYGFVEFEDSRDADDAVYELNGKDLCGERVIVE 66
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 47.7 bits (114), Expect = 2e-07
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNV-WVARNPPG--FGFVEFEDRRDAEDAVRGF 95
I+V + S TKE++ + FS +G I V + R F F++FE + A AV
Sbjct: 6 IFVGQL--SPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63
Query: 96 DGREINGRRVRVE 108
+ + + + V+
Sbjct: 64 NHSMLKNKTMHVQ 76
>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 = 47.0 bits (112), Expect = 2e-07
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ I + FS YG +K V + N F FVEFE A A G+ +N + V
Sbjct: 13 ESAIREIFSPYGAVKEVKMISN---FAFVEFESLESAIRAKDSVHGKVLNNNPLYV 65
>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 = 47.2 bits (113), Expect = 3e-07
Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 47 STSSTKEDIEDAFSYYG--PIKNVWVARNPP-----GFGFVEFEDRRDAE---DAVRGFD 96
+T+EDI A S PIK+V + R+ GF FVEF DA DA+ D
Sbjct: 11 DLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLD 70
Query: 97 GREINGRRVRVEMS 110
I+GR VRV +
Sbjct: 71 PFVIDGRVVRVSYA 84
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 47.0 bits (112), Expect = 3e-07
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S S E ++ F +G + V GFG+V+FE DA+ A+ DG+E++
Sbjct: 8 SWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELD 67
Query: 102 GRRVRVEMS 110
GR + V+ S
Sbjct: 68 GRPINVDFS 76
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 46.9 bits (111), Expect = 3e-07
Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S +T+ D+ + FS YGP+ V V + GF FV FE D+++A+ +G E++
Sbjct: 8 SLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELD 67
Query: 102 GRRVRVEMS 110
GRR+RV+ S
Sbjct: 68 GRRIRVDYS 76
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 46.5 bits (111), Expect = 3e-07
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 44 VLCSTSSTKEDI-EDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
++C+ S + I ED F +G + +V++ +G+ ++ DR AE A+ G+E+NG
Sbjct: 4 IVCNPSPPPDYILEDVFCRFGGLIDVYLVPGK-NYGYAKYADRESAERAITTLHGKEVNG 62
Query: 103 RRVRV 107
+++V
Sbjct: 63 VKLKV 67
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 48.5 bits (115), Expect = 3e-07
Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 5/90 (5%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S + + DAF+++G + + V + GFGFV F D A A+ DG+E+N
Sbjct: 43 SWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN 102
Query: 102 GRRVRVEMSNPQKMRGRSNGRSGGDRGYRG 131
GR +RV +N + R+ G GG G G
Sbjct: 103 GRHIRVNPANDRPSAPRAYGGGGGYSGGGG 132
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 46.5 bits (110), Expect = 4e-07
Identities = 27/62 (43%), Positives = 38/62 (61%), Gaps = 3/62 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S + + D+E F YG I V + G+GFVEF+D RDA+DAV +G+++ G RV
Sbjct: 8 SYQARERDVERFFKGYGKILEVDLKN---GYGFVEFDDLRDADDAVYELNGKDLCGERVI 64
Query: 107 VE 108
VE
Sbjct: 65 VE 66
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 45.9 bits (109), Expect = 5e-07
Identities = 27/59 (45%), Positives = 37/59 (62%), Gaps = 2/59 (3%)
Query: 52 KEDIEDAFSYYGPIKNVWVA--RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++D+ED F YG I+++ + R F FV FED RDAEDAV G +G + R+RVE
Sbjct: 13 EKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVE 71
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 46.0 bits (109), Expect = 6e-07
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 50 STKEDIEDAFSYYGPIKNVWVA----RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
+TK+D+ FS YG +K+V V ++ GF FVEF ++A +A+ + GRR+
Sbjct: 12 ATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRL 71
Query: 106 RVEMS 110
++ +
Sbjct: 72 VLQYA 76
>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 = 45.9 bits (109), Expect = 7e-07
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 52 KEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+++++ FS +G +KNV VAR N +GF++F + A A + + + G+ ++
Sbjct: 13 EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72
Query: 107 V 107
V
Sbjct: 73 V 73
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 45.6 bits (108), Expect = 7e-07
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP---GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ E + F YG +K + R P FVEF D RDA A+R +G+EI+G+ V +
Sbjct: 14 SSETLRSIFQVYGDVKEL---RETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVVI 70
Query: 108 E 108
E
Sbjct: 71 E 71
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 45.9 bits (109), Expect = 9e-07
Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 15/85 (17%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIK--------NVWVARN-----PPGFGFVEFEDR 85
++VS + ++T++D+ + F G IK +W+ ++ P G V ++D
Sbjct: 1 VFVSNL--PPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDP 58
Query: 86 RDAEDAVRGFDGREINGRRVRVEMS 110
A A+ F+ ++ G ++V ++
Sbjct: 59 HAASAAIEWFNNKDFMGNTIKVSLA 83
>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 = 45.4 bits (108), Expect = 9e-07
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREING 102
S S+ ++D+E+ F G + +V +A++ GFG VEF A+ A+ G E+ G
Sbjct: 8 SWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLG 66
Query: 103 RRVRVEMSNP 112
R +RV+++
Sbjct: 67 REIRVDLATE 76
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 49.7 bits (118), Expect = 1e-06
Identities = 27/96 (28%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 17 SSLCQEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP- 75
S++ Q I D V A+ IYV+ V S + DI+ F +G I +AR P
Sbjct: 185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLS--ETDIKSVFEAFGEIVKCQLARAPTG 242
Query: 76 ----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GF+E+ + + +A+ + ++ G+ +RV
Sbjct: 243 RGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278
Score = 39.7 bits (92), Expect = 0.002
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 8/70 (11%)
Query: 52 KED-IEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
+ED I AF +GPIK++ ++ +P GF FVE+E A+ A+ +G+ + GR +
Sbjct: 120 REDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNI 179
Query: 106 RVEMSNPQKM 115
+V P M
Sbjct: 180 KVGR--PSNM 187
Score = 30.4 bits (68), Expect = 1.4
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 79 FVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
FVEF D + + A DGR GR V E
Sbjct: 569 FVEFSDSMEVDRAKAALDGRFFGGRTVVAEA 599
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 45.3 bits (108), Expect = 1e-06
Identities = 23/74 (31%), Positives = 45/74 (60%), Gaps = 7/74 (9%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVR 93
IYV+ V +++DI+ F +G IK+ +A +P G+GF+E+E+ + A+DA+
Sbjct: 3 IYVASV--HPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 94 GFDGREINGRRVRV 107
+ ++ G+++RV
Sbjct: 61 SMNLFDLGGQQLRV 74
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 45.3 bits (108), Expect = 1e-06
Identities = 18/63 (28%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
+TK+++ + FS +G +K+V + + GF FVEF +++A++A+ + GR +
Sbjct: 12 ATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHL 71
Query: 106 RVE 108
+E
Sbjct: 72 VLE 74
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 45.0 bits (106), Expect = 1e-06
Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
K D+E FS YG I V + GF FV++ + R+A AV G DGR I G+ + + ++
Sbjct: 15 KKSDVEAIFSKYGKIVGCSVHK---GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 71
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammals, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 45.2 bits (108), Expect = 1e-06
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ + + FS GP+ ++ V R+ G+ +V F++ DAE A+ + I G+ +
Sbjct: 12 TEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPI 71
Query: 106 RV 107
R+
Sbjct: 72 RI 73
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 11/72 (15%)
Query: 50 STKED-IEDAFSYYGPIKNVWVARNPP----------GFGFVEFEDRRDAEDAVRGFDGR 98
T E+ ++ F G +++V +A+ G+GFVEF+ + A+ A++ G
Sbjct: 11 KTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGT 70
Query: 99 EINGRRVRVEMS 110
++G + +++S
Sbjct: 71 VLDGHALELKLS 82
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 44.4 bits (105), Expect = 2e-06
Identities = 27/57 (47%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREI--NGRRVRVE 108
+IE F YG + V + GF FV ED RDAEDA+RG D E RR+RVE
Sbjct: 16 EIERLFGKYGRVDRVDMK---SGFAFVYMEDERDAEDAIRGLDNFEFGRQRRRLRVE 69
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 44.6 bits (106), Expect = 3e-06
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 55 IEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
I AF+ G + +V + RN G+GFVEF AE A++ +G+ I
Sbjct: 16 IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNT 69
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 44.2 bits (105), Expect = 3e-06
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVR 93
I+V V +T E++++ F G I + + P GF ++EF D+ E+A+
Sbjct: 2 IFVGNV--DYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL- 58
Query: 94 GFDGREINGRRVRV 107
+ E GR+++V
Sbjct: 59 LLNESEFRGRQIKV 72
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 44.0 bits (104), Expect = 3e-06
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
+KED+ FS YG + + + +GFV+F+ +A+ G+ I GR++ +E+S
Sbjct: 13 SKEDLFRIFSTYGELAQIVLKNA---YGFVQFDSPESCANAINCEQGKMIRGRKLHLEVS 69
Query: 111 NP 112
P
Sbjct: 70 KP 71
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 44.2 bits (105), Expect = 3e-06
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
S T D+ FS YG + V + R G F+ F DR DA V+ + +E+ GR
Sbjct: 12 SLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGR 71
Query: 104 RVRVEMS 110
++ ++
Sbjct: 72 TLKCSIA 78
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 44.2 bits (105), Expect = 4e-06
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ DI FS YG I ++ + R+ GF F+ +ED+R AV +G ++ GR +
Sbjct: 22 TEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTI 81
Query: 106 RVE 108
RV+
Sbjct: 82 RVD 84
>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 = 43.7 bits (103), Expect = 4e-06
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S S++++ +++ F I+ P G+ FVEFE DA++A+ + EI GR +R
Sbjct: 10 SYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSIR 69
Query: 107 VEM 109
+E
Sbjct: 70 LEF 72
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 43.4 bits (103), Expect = 4e-06
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAVRGFDGREINGRR 104
+ T++ + + FS GPIK+ + R + FVE+ D R A A++ +GR I G+
Sbjct: 7 DRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGRLILGQE 66
Query: 105 VRV 107
++V
Sbjct: 67 IKV 69
>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 = 43.4 bits (103), Expect = 5e-06
Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++D+ F +G I+ V + R+P G+GF++F D DA+ A+ +G E+ GR +
Sbjct: 11 TEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPI 70
Query: 106 RV 107
+V
Sbjct: 71 KV 72
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 43.3 bits (103), Expect = 5e-06
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRR 104
S + + D FS +G I + VA + G+GFV FE A A+ +G +N ++
Sbjct: 13 SIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKK 72
Query: 105 VRV 107
V V
Sbjct: 73 VFV 75
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.5 bits (103), Expect = 5e-06
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 11/63 (17%)
Query: 49 SSTKEDIEDAFSYYGPIKNVW-----VARNPPGFGFVEFEDRRDAEDAVRGF---DGREI 100
+ T+ED+E FS YGP+ V + + P GF FV + E AV+ F DG
Sbjct: 13 TCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY---MIPEHAVKAFAELDGTVF 69
Query: 101 NGR 103
GR
Sbjct: 70 QGR 72
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 43.5 bits (103), Expect = 5e-06
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T E+ F GP+KN + R+ GFGFV+++ DA+ A+R +G ++ +R+
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72
Query: 106 RVEMSNPQ 113
+V + P
Sbjct: 73 KVAYARPG 80
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 42.9 bits (101), Expect = 6e-06
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+T+++I F YG + + +N +GFV +D+ A++A+R +++G +
Sbjct: 9 PPEATEQEIRSLFEQYGKVLECDIIKN---YGFVHMDDKTAADEAIRNLHHYKLHGVAIN 65
Query: 107 VE 108
VE
Sbjct: 66 VE 67
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 42.7 bits (100), Expect = 9e-06
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+T+ T+E +E +FS +G ++ V + + FV FE+R A A+ +G+EI G +
Sbjct: 10 ATTVTEEILEKSFSEFGKLERV---KKLKDYAFVHFEERDAAVRAMDEMNGKEIEGEEIE 66
Query: 107 VEMSNP 112
+ ++ P
Sbjct: 67 IVLAKP 72
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 42.7 bits (101), Expect = 9e-06
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNV-WVAR----NPPGFGFVEFEDRRDAEDAVRGFDGREI 100
S + ++ I +AF YG I +V P GFG+VEF + A+ A+ G ++
Sbjct: 6 LSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDL 65
Query: 101 NGRRVRVE 108
GR VR++
Sbjct: 66 LGRPVRLD 73
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T+E+++ FS +G I+ V V ++ G+ FV F+ A A+ +G ING+ V+
Sbjct: 13 TEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTSINGQTVKC 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 = 42.6 bits (101), Expect = 1e-05
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 11/79 (13%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP--------GFGFVEFEDRRDAED 90
IYV + ++D+ FS +G ++++ + + GF FV F+D AE+
Sbjct: 3 IYVRNL--DFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 91 AVRGFDGREINGRRVRVEM 109
A++ +G E+ GR++ V +
Sbjct: 61 ALQ-LNGTELGGRKISVSL 78
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 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 = 91
Score = 43.0 bits (102), Expect = 1e-05
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 52 KEDIEDAFSYYGPIKNVWV-ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++D+ + +G +K V V R+P G V+F++ +A+ + +GR GR++ E
Sbjct: 26 RDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAE 83
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 42.2 bits (100), Expect = 1e-05
Identities = 15/63 (23%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T +D+ F+ +G + + V + FGFV +++ A+ A++ +G ++ G+R+
Sbjct: 11 TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
Query: 106 RVE 108
+V+
Sbjct: 71 KVQ 73
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 42.6 bits (101), Expect = 1e-05
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 14/72 (19%)
Query: 47 STSSTKEDIEDAFSYYGPIKNV---W--------VARNPPGFGFVEFEDRRDAEDAVRGF 95
+ T+E + F +GP+ +V W RN GFV F +R DAE A+
Sbjct: 10 NPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC---GFVAFMNRADAERALDEL 66
Query: 96 DGREINGRRVRV 107
DG+++ G +++
Sbjct: 67 DGKDVMGYELKL 78
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T+E+ ++ FS YG + V++ + GFGF+ + R +AE A DG GR++RV
Sbjct: 11 NDITEEEFKELFSKYGEVSEVFLNKEK-GFGFIRLDTRTNAEKAKAELDGIMRKGRQLRV 69
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 48 TSSTK-EDIEDAFSYYGPI---KNVWVARNPPG--FGFVEFEDRRDAEDAVRGFDGREIN 101
+S+TK D++ FS YG + K V AR+P FGFV +A ++ E++
Sbjct: 8 SSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELH 67
Query: 102 GRRVRVE 108
GR + VE
Sbjct: 68 GRVISVE 74
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 41.9 bits (99), Expect = 1e-05
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
T++++ F +G I V + PPG GFV+F R AE A++ G I G R+R
Sbjct: 14 TEDELRSLFGPFGEIVYVKI---PPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIR 68
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 41.9 bits (99), Expect = 2e-05
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
+ T+ED+ FS +G + +V++ + F FV F D A+ + I G V
Sbjct: 8 LTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCG--EDHIIKGVSV 65
Query: 106 RVE 108
V
Sbjct: 66 HVS 68
>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 = 41.9 bits (99), Expect = 2e-05
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVA-----RNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
++T+E++ + F +G I V + + GF FV F A A DG GR
Sbjct: 10 TTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGR 69
Query: 104 RVRV 107
+ V
Sbjct: 70 LLHV 73
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVR-----GFDGRE 99
+T+E++++ FS +G +K + ++ G FV+F+ + A+ + G
Sbjct: 12 ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLS 71
Query: 100 INGRRVRVEMS 110
++GRR+ V ++
Sbjct: 72 LDGRRLIVTLA 82
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 41.9 bits (99), Expect = 2e-05
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 51 TKEDIEDAFSYYGPIKNVWV--------ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
T+ + FS YG IK P G+ FV FE + +AE A++ +G+ G
Sbjct: 12 TEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALG 71
Query: 103 RRVRV 107
+++ V
Sbjct: 72 KKLVV 76
>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 = 45.4 bits (107), Expect = 2e-05
Identities = 49/189 (25%), Positives = 76/189 (40%), Gaps = 26/189 (13%)
Query: 22 EAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVE 81
E E+++ VM + ++YV ++ T++T+E IE +FS + P K V + + FV
Sbjct: 222 EEEVDEDVMAKVK---ILYVRNLM--TTTTEEIIEKSFSEFKPGK-VERVKKIRDYAFVH 275
Query: 82 FEDRRDAEDAVRGFDGREINGRRVRVEMSNP--QKMRGRSNGRSGGDRGYRGSVRARGRP 139
FEDR DA A+ +G+E+ G + V ++ P +K R +GG R + R
Sbjct: 276 FEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLG- 334
Query: 140 FNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNG--R 197
D SR M P + RGR R
Sbjct: 335 ---------------QVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSR 379
Query: 198 SGGDRGYRG 206
+ G RGY
Sbjct: 380 AAGGRGYPP 388
>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 = 41.5 bits (97), Expect = 2e-05
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S+S T +++ F YGP+ + ++ + FV E DA +A+RG D E G+R+
Sbjct: 9 SSSCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEAIRGLDNTEFQGKRMH 65
Query: 107 VE 108
V+
Sbjct: 66 VQ 67
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 41.9 bits (99), Expect = 2e-05
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 13/66 (19%)
Query: 55 IEDAFSYYG-PIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
I+ AF+ G + +V + RN P G+ FVEF D AE + +G+ I G
Sbjct: 16 IKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPG------ 69
Query: 109 MSNPQK 114
SNP K
Sbjct: 70 -SNPPK 74
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 41.6 bits (97), Expect = 3e-05
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S T EDI+ AF+ +G I + V ++ G+GFV F ++ DAE+A+ G+ +
Sbjct: 10 SPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLG 69
Query: 102 GRRVR 106
GR++R
Sbjct: 70 GRQIR 74
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 41.4 bits (97), Expect = 3e-05
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S + T +++ F +G + + + FV E +A A+ +G+E+ GRR+
Sbjct: 9 SATCTSDELRGLFEEFGRVVECDKVK---DYAFVHMEREEEALAAIEALNGKEVKGRRIN 65
Query: 107 VEM 109
VE+
Sbjct: 66 VEL 68
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 41.3 bits (97), Expect = 3e-05
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 47 STSSTKEDIEDAFSYYGPIKNV-WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
TS D++ F GP++ V ++R F+ FE+ A+ A+ +G ++G +
Sbjct: 8 PTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGASVDGNCI 67
Query: 106 RVE 108
+V+
Sbjct: 68 KVQ 70
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 41.3 bits (97), Expect = 3e-05
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
S ++T++D++ FS +G +++ + + GFGFV FE D D V EIN
Sbjct: 8 SANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFES-EDVVDKVCEIHFHEIN 66
Query: 102 GRRVRV 107
+ V
Sbjct: 67 NKMVEC 72
>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 = 40.8 bits (96), Expect = 4e-05
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVA-----RNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S ++D+E FS +G + V VA GF +V F D DA A + DG+
Sbjct: 11 PYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQ 70
Query: 102 GRRVRV 107
GR + +
Sbjct: 71 GRLIHI 76
>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 = 40.6 bits (95), Expect = 4e-05
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVA--RNPPG--FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
T++ ++ F GP++NV + +N G +GFVE+ DAE A++ +GR+I +R
Sbjct: 11 TEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLNGRQIENNEIR 70
Query: 107 V 107
V
Sbjct: 71 V 71
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 40.8 bits (96), Expect = 5e-05
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 51 TKEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGF 95
T E ++ FS YG + V + R + GF F+EFE +A+ A +
Sbjct: 12 THEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
>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 = 40.3 bits (95), Expect = 5e-05
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
S T++DI + FS G +K + R PG V + + DA A+ ++ RE++G+ ++
Sbjct: 10 PSVTEDDIVELFSAIGALKRARLVR--PGVAEVVYVRKDDALTAIDKYNNRELDGQPMKC 67
Query: 108 EM 109
++
Sbjct: 68 KL 69
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 40.4 bits (94), Expect = 6e-05
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S T +DI+ AF+ +G I + V ++ G+GFV F ++ DAE+A++ G+ +
Sbjct: 10 SPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 69
Query: 102 GRRVR 106
GR++R
Sbjct: 70 GRQIR 74
>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 = 40.2 bits (95), Expect = 6e-05
Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+E++ F G ++ V + R+ GFG+V F+ + A++ +G ++ GR+
Sbjct: 11 IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-LNGIKLKGRK 69
Query: 105 VRVE 108
+RV+
Sbjct: 70 IRVK 73
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 40.2 bits (95), Expect = 6e-05
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 49 SSTKEDIEDAFS-YYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
S+T+EDI D FS P + + + P G +VEF DA A+R ++ GR
Sbjct: 10 SATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALR-KHNNKMGGR 68
Query: 104 RVRV 107
+ V
Sbjct: 69 YIEV 72
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 40.0 bits (94), Expect = 7e-05
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 72 RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ P G VEF D + A+ DG E+NGR++++
Sbjct: 34 KQRPNEGVVEFATYSDMKRAIEKLDGTELNGRKIKL 69
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM3 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 83
Score = 40.4 bits (94), Expect = 7e-05
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGP--IKNVWVARNPPGFGFVEFEDRRDAEDAVRGF 95
++YV ++ ST T+E IE F+ P ++ V R+ + FV F +R DA DA+
Sbjct: 10 ILYVRNLMLST--TEETIEKEFNSIKPGAVERVKKIRD---YAFVHFSNREDAVDAMNAL 64
Query: 96 DGREINGRRVRVEMSNP 112
+G+ I+G + V ++ P
Sbjct: 65 NGKVIDGSPIEVTLAKP 81
>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 = 40.4 bits (95), Expect = 7e-05
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 14/83 (16%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIK--------NVWVARN----PPGFGFVEFEDRR 86
IY+S + T++ + + F G IK + + + P G V ++D
Sbjct: 1 IYISGL--PDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPS 58
Query: 87 DAEDAVRGFDGREINGRRVRVEM 109
A+ A+ F+G E G +++V +
Sbjct: 59 AAQAAIEWFNGYEFRGNKIKVSL 81
>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 = 40.1 bits (94), Expect = 8e-05
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 14/85 (16%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----------ARNPPGFGFVEFEDRRD 87
+Y+S + S SS++ED+E+ + P+ +V + P G + EF
Sbjct: 2 VYISNL--SYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQ 58
Query: 88 AEDAVRGFDGREINGRRVRVEMSNP 112
AE V+ +G+ R++ V++ P
Sbjct: 59 AEKVVKDLNGKVFKNRKLFVKLHVP 83
>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 = 39.9 bits (94), Expect = 8e-05
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 48 TSSTKEDIEDAFS-YYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREING 102
S T+ ++++ FS + G I +V + R G F+ ++ +A+ A F+ IN
Sbjct: 10 ASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINT 69
Query: 103 RRVRVEMS 110
++ VE +
Sbjct: 70 SKISVEFA 77
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 43.6 bits (103), Expect = 8e-05
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
T E + + FS G I + V + GFGFV F + +A AV GR + G+
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354
Score = 39.4 bits (92), Expect = 0.002
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRGFDGREING 102
S ++ + + F+ +G I + V ++ GF FV FE DA AV +G++I
Sbjct: 189 SVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 36.3 bits (84), Expect = 0.016
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 57 DAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSN 111
D F +GP+ +V V R+ G+G+V F++ DAE A+ + + + G+ +R+ S
Sbjct: 19 DLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ 78
Query: 112 PQKMRGRSNGRSG 124
R S RSG
Sbjct: 79 ----RDPSLRRSG 87
Score = 36.3 bits (84), Expect = 0.021
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 57 DAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
D FS +G I + VA + G+GFV FE A+ A++ +G +N + V V
Sbjct: 107 DTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK 166
Query: 113 QKMR 116
+ R
Sbjct: 167 KHER 170
>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 = 40.1 bits (94), Expect = 8e-05
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 54 DIEDAFSYYGPIKNVWV---ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
D+ F +GPI +V + R GFGFV F + DA+ A G + GR++ V
Sbjct: 16 DLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIEV 72
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 39.9 bits (94), Expect = 9e-05
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-------GFGFVEFEDRRDAEDAVRGFDGREIN 101
S + DI D F YG I ++ R P F +V+F A AV +G+
Sbjct: 11 SFDQSDIRDLFEQYGEILSI---RFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGE 67
Query: 102 GRRVRVEMSNP 112
G ++ V++S+P
Sbjct: 68 GYKLVVKISDP 78
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 39.6 bits (93), Expect = 1e-04
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREING 102
T+E + + F GP++ V + ++P G F FV F+ A++ +G + G
Sbjct: 10 DARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFG 69
Query: 103 RRVRVE 108
R +R++
Sbjct: 70 RELRIK 75
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 43.4 bits (103), Expect = 1e-04
Identities = 33/176 (18%), Positives = 41/176 (23%), Gaps = 5/176 (2%)
Query: 70 VARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQKMRGRSNGRSGGDRGY 129
A E + E RG R R E R++ +
Sbjct: 110 AAAAAAAEAASAPEAAQARERRERGEAARR-GAARKAGEGGEQPATEARADAAERTEEEE 168
Query: 130 RGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQK 189
R R RG + + RG R R G + G R
Sbjct: 169 RDERRRRGDREDRQAE----AERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGG 224
Query: 190 MRGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRR 245
R R R + DD G RG RD R GG
Sbjct: 225 DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGG 280
Score = 34.9 bits (81), Expect = 0.055
Identities = 24/162 (14%), Positives = 35/162 (21%), Gaps = 9/162 (5%)
Query: 85 RRDAEDAVRGFDGREINGRRVRVEMSNPQKMRGRSNGRSGGDRGYRGSVRARGRPFNPDD 144
+A A E ++ + R G+ RG+ R G
Sbjct: 94 AAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEG-GEQP 152
Query: 145 KCYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNGRSGGDRGY 204
+ G R R + + R GD
Sbjct: 153 ATEARADAAERTEEEERDERRRRGD--------REDRQAEAERGERGRREERGRDGDDRD 204
Query: 205 RGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRRR 246
R R +G + RG R R G R
Sbjct: 205 RRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRED 246
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDG 97
++V + + E++ F +G I+ ++ A GF V + D R A A R G
Sbjct: 3 TLFVRNINSNVED--EELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60
Query: 98 REINGRRVRVEMSNP 112
E+ GR++ + S P
Sbjct: 61 TELGGRKLDIHFSIP 75
>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 = 39.2 bits (91), Expect = 2e-04
Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+ + T+E +E AF +G ++ V + + F+ F++R A A+ +G+E+ G +
Sbjct: 10 ANTVTEEILEKAFGQFGKLERV---KKLKDYAFIHFDERDGAVKAMEEMNGKELEGENIE 66
Query: 107 VEMSNP 112
+ + P
Sbjct: 67 IVFAKP 72
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 39.0 bits (91), Expect = 2e-04
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP-GFGFVEFEDRRDAEDAVRGFDG 97
IY++ S T+ED+ + F +GP+ +V + FGFV FE+ + V+
Sbjct: 1 IYLTFPADSRF-TEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFEN----AETVKRILS 55
Query: 98 RE----INGRRVRV 107
+ I G RVRV
Sbjct: 56 KGNPHFICGSRVRV 69
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 38.9 bits (90), Expect = 2e-04
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
+ T+E+++ F G I++ + R+ G+GFV + D +DAE A+ +G + +
Sbjct: 15 NMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 74
Query: 104 RVRVEMSNP 112
++V + P
Sbjct: 75 TIKVSYARP 83
>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 = 38.7 bits (91), Expect = 2e-04
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 10/67 (14%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ED+ F YG I+ V + R+ G FV+F R +A+ A+ ++G+
Sbjct: 12 TEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI-----EALHGKVT 66
Query: 106 RVEMSNP 112
S P
Sbjct: 67 MPGASRP 73
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 42.2 bits (99), Expect = 2e-04
Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 8/61 (13%)
Query: 53 EDIEDAFSYYGPIKNVWVAR-NP-----PGFG--FVEFEDRRDAEDAVRGFDGREINGRR 104
ED++ FS YGP+ N+ + R N PG G F+E+ D R AE A+ G +GR+ N R
Sbjct: 434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRV 493
Query: 105 V 105
V
Sbjct: 494 V 494
Score = 28.7 bits (64), Expect = 4.2
Identities = 10/63 (15%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
++ I++ +G +K + ++ G+ F E++D + A+ +G++ ++
Sbjct: 308 GEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKL 367
Query: 106 RVE 108
V+
Sbjct: 368 HVQ 370
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 45 LCSTSSTKE---DIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAVRGFDGRE 99
L ++ S E + + FS YG + V V R+ + FV+F + DA++A+ G
Sbjct: 10 LPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAKGQGTI 69
Query: 100 INGRRVRVEM 109
++GR +R E
Sbjct: 70 LDGRHIRCER 79
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 40.6 bits (95), Expect = 3e-04
Identities = 23/95 (24%), Positives = 31/95 (32%), Gaps = 18/95 (18%)
Query: 145 KCYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNGRSGGDRGY 204
KCY CG GH +RDC + C R + + +G
Sbjct: 99 KCYNCGETGHLSRDCNPSKDQQKSC-FDCN----STRHSSEDCPSIWKHYVLNNGDGHPI 153
Query: 205 RGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRS 239
+ CY CG GH+ DC+ RS
Sbjct: 154 KKF-------------CYSCGSAGHFGDDCKEPRS 175
Score = 39.4 bits (92), Expect = 8e-04
Identities = 21/105 (20%), Positives = 29/105 (27%), Gaps = 15/105 (14%)
Query: 132 SVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMR 191
SV + C+ CG GH RDC C +G R +
Sbjct: 49 SVEDVSAIREENPVCFNCGQNGHLRRDCPHSIC------YNCSWDGHRSNHCPKPKKCYN 102
Query: 192 GRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRS 236
G D + C++C H + DC S
Sbjct: 103 CGETGHLSRDCNPSKDQQKS---------CFDCNSTRHSSEDCPS 138
Score = 29.4 bits (66), Expect = 1.8
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 146 CYECGGRGHYARDCRSRRSGGSGRPELC 173
CY CG GH+ DC+ RS S P +C
Sbjct: 157 CYSCGSAGHFGDDCKEPRS--SRVPYVC 182
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 38.4 bits (90), Expect = 3e-04
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAV-RGFDGREINGRRVRV 107
T++D+ D F +G I+++ V FV F R AE A R F+ INGRR+++
Sbjct: 14 TEKDLRDHFYQFGEIRSITVVPRQ-QCAFVTFTTREAAEKAAERLFNKLIINGRRLKL 70
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in a family that represents a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), at
their N-terminus, and an RS domain at their C-terminus.
Length = 70
Score = 38.3 bits (89), Expect = 3e-04
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 50 STKE-DIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+T+ D+E F YG + NV + RN F FV++E + DA A+ + ++ R + VE
Sbjct: 11 NTRTRDLERHFEPYGKLVNVRIRRN---FAFVQYETQEDATKALESTNMSKVLDRVISVE 67
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 38.1 bits (88), Expect = 4e-04
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGP--IKNVWVARNPPGFGFVEFEDRRDAEDAVRGF 95
V+YV ++ ST T+E I+ F+ + P ++ V R+ + FV F +R DA A+
Sbjct: 3 VLYVRNLMIST--TEETIKAEFNKFKPGVVERVKKLRD---YAFVHFFNREDAVAAMSVM 57
Query: 96 DGREINGRRVRVEMSNP 112
+G+ I+G + V ++ P
Sbjct: 58 NGKCIDGASIEVTLAKP 74
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 37.9 bits (89), Expect = 4e-04
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREIN-GRRVRVEMS 110
G+ FV + ++ A+ AV+ EI G+R+ V +S
Sbjct: 43 GYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCIS 78
>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 = 38.0 bits (89), Expect = 5e-04
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
T++ + + F G + +V V R G FGFV F+ DA+ AV+ F+ I+ ++
Sbjct: 13 TEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKIS 72
Query: 107 VEM 109
VE+
Sbjct: 73 VEL 75
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 38.1 bits (88), Expect = 5e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREING 102
+ T++D+ED FS +G I N V + G F+ F+ R +AE+A+ F+G + G
Sbjct: 11 TMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGHKPPG 69
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 38.0 bits (89), Expect = 5e-04
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVR 93
I+V + +T + + FS +G I+ V + G+GFV F+D+ AE A +
Sbjct: 3 IFVGGL--PYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 94 G----FDGREIN 101
DGR+ N
Sbjct: 61 DPNPIIDGRKAN 72
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 37.6 bits (88), Expect = 5e-04
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T E + S +G ++ ++ + G+GFVE+ + A A DG++I GR++
Sbjct: 12 TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
Query: 106 RV 107
+V
Sbjct: 72 QV 73
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 38.0 bits (88), Expect = 6e-04
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 13/74 (17%)
Query: 49 SSTKEDIEDAFSYYGPIK----------NVWVARN---PPGFGFVEFEDRRDAEDAVRGF 95
+ T E++ D F + G +K N++ + P G V +ED A+ AV F
Sbjct: 11 NVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPSAKAAVEWF 70
Query: 96 DGREINGRRVRVEM 109
DG++ G +++V +
Sbjct: 71 DGKDFQGSKLKVSL 84
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 77
Score = 37.8 bits (88), Expect = 6e-04
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGRE-INGRR 104
T++D++D FS +G + V V ++P GFGFV F D ED V+ R I+GR
Sbjct: 12 TEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKVLSQRHMIDGRW 68
Query: 105 VRVEMSNPQ 113
V++ N +
Sbjct: 69 CDVKIPNSK 77
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 37.8 bits (88), Expect = 6e-04
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP------GFGFVEFEDRRDAEDAVRGF-DGREING 102
+T +++ + FS +G +K V + + GFGFV+F ++DA+ A + + G
Sbjct: 12 ATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYG 71
Query: 103 RRVRVE 108
RR+ +E
Sbjct: 72 RRLVLE 77
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 37.4 bits (87), Expect = 6e-04
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 53 EDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ I AFS +GPIK++ ++ +P GF FVE+E A+ A+ +G + GR ++V
Sbjct: 15 DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74
>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 = 37.6 bits (88), Expect = 6e-04
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
FS YGP+ +V + R G V F+ A+ AV GR++ GR+++V
Sbjct: 28 FSRYGPVVHVVIDRQR-GQALVFFDKVEAAQAAVNEMKGRKLGGRKLQV 75
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 37.7 bits (87), Expect = 6e-04
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSN 111
K D+E FS YG + V + G+ FV++ + R A AV G +GR + G+ + + M+
Sbjct: 16 KSDVETIFSKYGRVVGCSVHK---GYAFVQYSNERHARGAVIGENGRVLAGQTLDINMAG 72
Query: 112 PQK 114
K
Sbjct: 73 EPK 75
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 37.7 bits (87), Expect = 6e-04
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGP--IKNVWVARNPPGFGFVEFEDRRDAEDAVRGF 95
++YV ++ TS ++ I+ F + P ++ V R+ + FV F R DA A+
Sbjct: 3 ILYVRNLMIETS--EDTIKKTFGQFNPGCVERVKKIRD---YAFVHFTSREDAVHAMNNL 57
Query: 96 DGREINGRRVRVEMSNP 112
+G E+ G + V ++ P
Sbjct: 58 NGTELEGSCIEVTLAKP 74
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 37.4 bits (87), Expect = 6e-04
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
G F F +A+ V +G EI+GRR+RVE
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVE 76
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 37.5 bits (87), Expect = 6e-04
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GFV F ++DAE+A+ +G+ + R +R
Sbjct: 42 GYGFVSFRSQQDAENAINEMNGKWLGSRPIRC 73
>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 = 37.8 bits (88), Expect = 7e-04
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNV-----WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++++ F +G + V P FGFV F+D + + R+
Sbjct: 16 TEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPIYFRGDHRL 75
Query: 106 RVE 108
VE
Sbjct: 76 NVE 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 = 37.2 bits (87), Expect = 7e-04
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVR 93
+++++ FS YG + +V V+ G VEF ++ AE AV
Sbjct: 17 SEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVE 59
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 37.5 bits (87), Expect = 8e-04
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++ F YG ++ + R GF FV + R++AE A+ +G EI+GR V V+
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75
>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 = 37.2 bits (86), Expect = 9e-04
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T+E++ F YG +++ ++ GFGF+ E R AE A D + G+++RV
Sbjct: 14 TEEEMRKLFEKYGKAGEIFIHKDK-GFGFIRLETRTLAEIAKAELDNMPLRGKQLRV 69
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 36.9 bits (86), Expect = 9e-04
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 51 TKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ED+ + FS YG +++V + GF FV F+D D D + ING RV
Sbjct: 12 TEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD-YDPVDKIVLQKYHTINGHRV 70
Query: 106 RV 107
V
Sbjct: 71 EV 72
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 36.8 bits (86), Expect = 0.001
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 63 GPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
GP+ NV + + G+GFVEF DA+ A++ + ++ G+ +RV
Sbjct: 23 GPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.0 bits (86), Expect = 0.001
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ D+ FS +G + V V + P GFGF+ FE D+ D V +ING++V
Sbjct: 15 TETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQVVNEHFHDINGKKV 73
Query: 106 RVEMSNP 112
V+ + P
Sbjct: 74 EVKRAEP 80
>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 = 36.8 bits (86), Expect = 0.001
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 59 FSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
FS +G + + ++R+ G+ FVEFE A+ + + R ++ +
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74
>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 = 36.5 bits (85), Expect = 0.001
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRG 94
++VS + S ++++ FS G I +V + +N G+ +VEFE+ ++A+
Sbjct: 2 VFVSNL--DYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-K 58
Query: 95 FDGREINGR 103
D I GR
Sbjct: 59 LDRELIKGR 67
>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 = 36.4 bits (84), Expect = 0.001
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T T+ED + F YG V++ R+ GFGF+ E R AE A DG + R +R+
Sbjct: 11 TDITEEDFKKLFEKYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDGTILKNRPLRI 69
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 36.5 bits (85), Expect = 0.002
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
GF +VEFED ++A+ +DG + R +RV+++
Sbjct: 43 GFCYVEFEDVESLKEALE-YDGALFDDRSLRVDIA 76
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 36.4 bits (85), Expect = 0.002
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG----FDG 97
S +T+E + + FS YG + + + ++P GFGFV F D + + DG
Sbjct: 7 SWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDG 66
Query: 98 REI 100
REI
Sbjct: 67 REI 69
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 36.2 bits (84), Expect = 0.002
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDG 97
++VS TS + + D FS +GP+ NV + ++ + VEF+ ++ D V
Sbjct: 4 SVFVSGFKRGTSEEQ--LMDYFSAFGPVMNVIMDKDKGVYAIVEFDS-KEGVDKVLSEPQ 60
Query: 98 REINGRRVRV 107
+NG R+RV
Sbjct: 61 HTLNGHRLRV 70
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 36.6 bits (85), Expect = 0.002
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG----FDG 97
S +T + +++ FS +G I + V ++P GFGFV F + + A+ DG
Sbjct: 8 SYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDG 67
Query: 98 REINGRR 104
RE+ +R
Sbjct: 68 REVEPKR 74
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 35.1 bits (82), Expect = 0.002
Identities = 12/17 (70%), Positives = 12/17 (70%)
Query: 145 KCYECGGRGHYARDCRS 161
KCY CG GH ARDC S
Sbjct: 1 KCYNCGKEGHIARDCPS 17
Score = 35.1 bits (82), Expect = 0.002
Identities = 12/17 (70%), Positives = 12/17 (70%)
Query: 220 KCYECGGRGHYARDCRS 236
KCY CG GH ARDC S
Sbjct: 1 KCYNCGKEGHIARDCPS 17
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 36.4 bits (84), Expect = 0.002
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 52 KEDIEDA-----FSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
K D+ + FS +GP++ V + GFGFV F++ D+ D IN
Sbjct: 8 KGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN-HDSADKAAVVKFHPIN 66
Query: 102 GRRVRVEMSNPQK 114
G RV V+ + P++
Sbjct: 67 GHRVEVKKAVPKE 79
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 36.2 bits (84), Expect = 0.002
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 44 VLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEF 82
V+ S T+ED+ + F +G I+ V + ++ GFG+V+F
Sbjct: 6 VVIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
>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 = 36.2 bits (84), Expect = 0.002
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 47 STSSTKEDIEDAFSYYG-PIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
S+ + D+ F + P+ +V V + G+ FV+ D+ A+ A+ +G+ + G+ +
Sbjct: 7 SSDVNESDLRQLFEEHKIPVSSVLVKKG--GYAFVDCPDQSWADKAIEKLNGKILQGKVI 64
Query: 106 RVEMSNPQK 114
VE S P+K
Sbjct: 65 EVEHSVPKK 73
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 36.3 bits (84), Expect = 0.002
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 77 FGFVEFEDRRDAEDAVRGFDGREINGRR--VRVEMS 110
F FVE+E RDAEDA GR + V+ +
Sbjct: 42 FAFVEYESHRDAEDAYEEMHGRRFPDTGDTLHVQWA 77
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 36.2 bits (83), Expect = 0.002
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E+ F G I++ + R+ G+GFV + D +DAE A+ +G + + +
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 106 RVEMSNP 112
+V + P
Sbjct: 75 KVSYARP 81
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 38.8 bits (90), Expect = 0.002
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E+I F+ G I++ + R+ G+GFV + DAE AV +G + + +
Sbjct: 16 TQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI 75
Query: 106 RVEMSNP 112
+V + P
Sbjct: 76 KVSYARP 82
Score = 32.6 bits (74), Expect = 0.21
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 59 FSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
F +G ++NV + R+ G+GFV + +A A+ +G + R ++V
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343
Score = 32.2 bits (73), Expect = 0.30
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVR 93
+YVS + + T+ ++E FS +G I + + G GF+ F+ R +A+ A++
Sbjct: 92 LYVSGL--PKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIK 149
Query: 94 GFDG 97
+G
Sbjct: 150 TLNG 153
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 35.8 bits (82), Expect = 0.002
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKN----VWVARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
S T+ I FS GP K+ + A N P + FVEF + R A ++ +GR+I G
Sbjct: 8 SRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-YCFVEFFEHRHAAASLAAMNGRKIMG 66
Query: 103 RRVRV 107
+ V+V
Sbjct: 67 KEVKV 71
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or P-CIP2,
is a serine/threonine protein kinase functionally
related to RNA metabolism and neurite outgrowth. It
contains an N-terminal kinase domain and a C-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), with
high homology to the corresponding motif of the
mammalian U2 small nuclear ribonucleoprotein auxiliary
factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1
targets two key regulators of cell proliferation and
migration, the cyclin-dependent kinase (CDK) inhibitor
p27Kip1 and the microtubule-destabilizing protein
stathmin. It plays a critical role during vascular wound
repair by preventing excessive vascular smooth muscle
cell (VSMC) migration into the vascular lesion.
Moreover, UHMK1 may control cell migration and neurite
outgrowth by interacting with and phosphorylating the
splicing factor SF1, thereby probably contributing to
the control of protein expression. Furthermore, UHMK1
may be functionally related to microtubule dynamics and
axon development. It localizes to RNA granules,
interacts with three proteins found in RNA granules
(KIF3A, NonO, and eEF1A), and further enhances the local
translation. UHMK1 is highly expressed in regions of the
brain implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 36.1 bits (83), Expect = 0.002
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPPGFG--FVEFEDRRDAEDAVRGFDGREINGRRV 105
EDI++ YGP+ ++ + + PG G FVE+ + D++ A + GR +G+ V
Sbjct: 28 EDIKEECQKYGPVVSLLIPKENPGKGQVFVEYANAGDSKAAQKLLTGRIFDGKFV 82
>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 = 35.7 bits (83), Expect = 0.003
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDG 97
+YV T+E ++ AFS +G I N+ + + GFV FE A+ A+ +G
Sbjct: 6 TLYVH----GYGLTEEILKKAFSPFGNIINISMEK-EKNCGFVTFEKMESADRAIAELNG 60
Query: 98 REINGRRVRVEMS 110
+ G +++V ++
Sbjct: 61 TTVQGVQLKVSLA 73
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 35.9 bits (82), Expect = 0.003
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV----ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
S T+ I FS GP K+ + N P + FVEF + RDA A+ +GR+I G
Sbjct: 8 SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMNGRKILG 66
Query: 103 RRVRV 107
+ V+V
Sbjct: 67 KEVKV 71
>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 = 35.7 bits (83), Expect = 0.003
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPG-FGFVEFEDRRDAEDAV-RGFDGREINGRRVR 106
+T+ I F G I+ V + + G +EFE +A A+ + D + + G +
Sbjct: 11 DTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTK--DHKRLGGNEIS 68
Query: 107 VE 108
V
Sbjct: 69 VS 70
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 77
Score = 35.8 bits (82), Expect = 0.003
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 49 SSTKEDIEDAFSYYG-PIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGR-EINGRRVR 106
S T D+E F + ++ ++ G+ FV+ D + A A+ F G+ E++G+R+
Sbjct: 12 SVTPADLEKVFEDHKISYSGQFLVKS--GYAFVDCPDEQWAMKAIETFSGKVELHGKRLE 69
Query: 107 VEMSNPQK 114
+E S P+K
Sbjct: 70 IEHSVPKK 77
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 35.5 bits (82), Expect = 0.003
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+++I FS G I++ + R+ G+GFV + D DAE A+ +G + + +
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTI 73
Query: 106 RV 107
+V
Sbjct: 74 KV 75
>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 = 35.4 bits (82), Expect = 0.003
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP------PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
T+EDI++ F + +V + R P GFG+ EFEDR A+ + + RR
Sbjct: 14 TEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL-SLNDESLKNRR 71
Query: 105 VRVEMS 110
+RV+++
Sbjct: 72 IRVDIA 77
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved in
eukaryotic gene regulation, such as C. elegans GLH-1.
Structure is an 18-residue zinc finger.
Length = 18
Score = 34.0 bits (79), Expect = 0.003
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 145 KCYECGGRGHYARDCRS 161
KCY CG GH ARDC
Sbjct: 2 KCYNCGKEGHLARDCPE 18
Score = 34.0 bits (79), Expect = 0.003
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 220 KCYECGGRGHYARDCRS 236
KCY CG GH ARDC
Sbjct: 2 KCYNCGKEGHLARDCPE 18
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 35.4 bits (82), Expect = 0.004
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+ + + FS G I V + + GF ++EF+ E A+ DG ++ G +
Sbjct: 17 RRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLV 75
Query: 107 VE 108
V+
Sbjct: 76 VD 77
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 35.1 bits (81), Expect = 0.004
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
S +T E + + FS +G IK V R+P GFGFV F D + D V E++
Sbjct: 7 SWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSD-PASVDKVLAQGPHELD 65
Query: 102 GRRV 105
G+++
Sbjct: 66 GKKI 69
>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 = 35.3 bits (82), Expect = 0.004
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 51 TKEDIEDAFSYYGPIKNV-WVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN--GRRVRV 107
+ ++E F +G I+ + + + ++E+E A+ A G + GRR+RV
Sbjct: 11 SLAELEREFDRFGAIRRIDYDPGRN--YAYIEYESIEAAQAAKEALRGFPLGGPGRRLRV 68
Query: 108 EMSN 111
+ ++
Sbjct: 69 DFAD 72
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 35.3 bits (81), Expect = 0.004
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVAR----NPPGFGFVEFEDRRDAEDAVRGFDGREING 102
S +T+E ++++F G I V + GFGFV+F DA+ A + EI+G
Sbjct: 9 SEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDG 66
Query: 103 RRVRVEMSNPQ 113
+V ++ + P+
Sbjct: 67 NKVTLDFAKPK 77
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 35.1 bits (80), Expect = 0.005
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 11/60 (18%)
Query: 51 TKEDIEDAFSYYGPI--------KNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
T++++E FS YG I + V+R G GF+ F+ R +AE+A++G +G++ +G
Sbjct: 15 TQKELEQLFSQYGRIITSRILVDQVTGVSR---GVGFIRFDKRIEAEEAIKGLNGQKPSG 71
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 35.2 bits (81), Expect = 0.005
Identities = 13/52 (25%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRGFDG 97
+T++++E+ FS YG ++++++ R+ G FV++ + A+ A++ +G
Sbjct: 11 ATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNG 62
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 35.1 bits (81), Expect = 0.005
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 51 TKEDIEDAFSYYGPIKNVWVAR-----NPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ F G I+ V + GF FV+FE+ A +A G+ +NGR +
Sbjct: 11 TEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---LKGKHLNGRAL 67
Query: 106 RVE 108
RVE
Sbjct: 68 RVE 70
>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 = 35.3 bits (81), Expect = 0.005
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREING 102
T++++E FS YG I + R+ G GF+ F+ R +AE+A++G +G++ G
Sbjct: 13 TQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEG 69
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 35.2 bits (82), Expect = 0.005
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDG 97
G+ FVEF +A++AV+ +G
Sbjct: 51 GYAFVEFATPEEAKEAVKALNG 72
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 34.9 bits (81), Expect = 0.006
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 53 EDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRGFDGREINGR 103
E + + FS +G I + V + GFGFV F +A AV +GR I G+
Sbjct: 16 ERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGK 70
>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 = 34.6 bits (80), Expect = 0.007
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIK--NVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
S T+ED+++ F YG I+ ++ R G +V E R+DA A++ ++ G++
Sbjct: 11 SKKVTEEDLKNLFEEYGEIQSIDMIPPR---GCAYVCMETRQDAHRALQKLRNVKLAGKK 67
Query: 105 VRV 107
++V
Sbjct: 68 IKV 70
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 34.7 bits (79), Expect = 0.007
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E+ + F G I++ + R+ G+GFV + D DA+ A+ +G ++ + +
Sbjct: 16 TQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTI 75
Query: 106 RVEMSNP 112
+V + P
Sbjct: 76 KVSYARP 82
>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 = 34.5 bits (80), Expect = 0.007
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 51 TKEDIEDAFSYYGPIKNV-WVARNPPGFGFVEFEDRRDAEDAVRGFDGREI 100
TKE +E F+ + K V V R G FVEFE A A++ G +I
Sbjct: 15 TKEMLEMLFNQFPGFKEVRLVPR--RGIAFVEFETEEQATVALQALQGFKI 63
>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 = 0.007
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 42 SIVLCSTSST--KEDIEDAFSYYGP-IKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGR 98
+I L + S T +E I+ F GP ++ + + + G VEFE DA A +G
Sbjct: 2 TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG-ALVEFESPSDAGKASLSLNGS 60
Query: 99 EINGRRVRV 107
+ G+ +++
Sbjct: 61 QFGGKTIKI 69
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 34.6 bits (79), Expect = 0.007
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 7/66 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVR 93
+YVS L T S KE +E FS YG I + + G GF+ F+ R +AE+A++
Sbjct: 4 LYVS-GLPKTMSQKE-MEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61
Query: 94 GFDGRE 99
G +G++
Sbjct: 62 GLNGQK 67
>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 = 37.6 bits (87), Expect = 0.007
Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ F +G I++V + R+P GFGF++F D +A++A+ +G E+ GR +
Sbjct: 199 TEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPI 258
Query: 106 RVEMSNPQKMRGRSNGRSGGDRGYRGS 132
+V + + +
Sbjct: 259 KVGYAQDSTYLLDAANTFEDIDKQQQM 285
Score = 32.2 bits (73), Expect = 0.38
Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 52 KEDIEDAFSYYGPIKNVWV-ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
+D+++ S YG + +++V +N G +++F A A + +GR G+
Sbjct: 386 LDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGK 438
>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 = 34.6 bits (80), Expect = 0.008
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
++ + F +G I +V + G FGFV ++ +A+ A++ F+ I+ ++
Sbjct: 13 KEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKIT 72
Query: 107 VE 108
VE
Sbjct: 73 VE 74
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 34.9 bits (81), Expect = 0.008
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+D+ F +G + V N G +V+++ +A A + F+GR G+++ E
Sbjct: 43 DDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCE 102
Query: 109 MSN 111
S
Sbjct: 103 FSP 105
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 34.2 bits (79), Expect = 0.008
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 53 EDIEDAFSYYGPIKNV-WVARNPPGFG-FVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
ED++ S YG +KN V V +E A+ AV +G E G +++V
Sbjct: 15 EDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNGHEYEGSKLKVSYI 74
Query: 111 N 111
Sbjct: 75 P 75
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 34.2 bits (78), Expect = 0.009
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDR 85
S +T+E + + F +G +K V R+P GFGFV F D+
Sbjct: 9 SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 34.4 bits (79), Expect = 0.009
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 49 SSTKEDIEDAFSY-----YGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGR 98
S+T + + DAF + + +K + P GFGFV F+ + A+ A++ DG
Sbjct: 11 STTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQAALKAMDGF 70
Query: 99 EINGRRVRVEMS 110
++G + V+ S
Sbjct: 71 VLDGHTLVVKFS 82
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically bind mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone and play a key role in
cell growth and differentiation. DND1 is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 34.6 bits (80), Expect = 0.009
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 51 TKEDIEDAFSYYGP-IKNVWVARNPP------GFGFVEFEDRRDAEDAVR 93
TKE+I + FS + +V V R+P GF FVE+E R A A R
Sbjct: 14 TKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARR 63
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 34.1 bits (79), Expect = 0.009
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGR 103
+ E++ D F YG I+ + + G FV +ED DA++A G + R
Sbjct: 13 KISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGFNVANR 69
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 34.3 bits (79), Expect = 0.009
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 80 VEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
EFED E V ++G+E+NG ++ VE+
Sbjct: 43 FEFEDPSILEKVVEKYNGKELNGAKIEVEI 72
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 33.9 bits (78), Expect = 0.010
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 47 STSSTKEDIEDAFSYYGPI--KNVWVARN---PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
T+E+ ++ FS +G + + + GFGFV F+ A + V E+
Sbjct: 8 PPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSAGMLELG 66
Query: 102 GRRVRVEM 109
G++V V+
Sbjct: 67 GKQVEVKR 74
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 33.8 bits (78), Expect = 0.012
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGR 98
++T ED+E +G I + G+GFV+F+ A A+ G +GR
Sbjct: 11 NTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 34.2 bits (79), Expect = 0.012
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRG----FDGR 98
+T+E++ D FS +G +K+V + + G+GFV FE + DAE + F G+
Sbjct: 11 PPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGNLNFRGK 70
Query: 99 EIN-GRRVR 106
++N G +R
Sbjct: 71 KLNIGPAIR 79
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 34.4 bits (78), Expect = 0.013
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREING 102
T++++E FS YG I + + G GF+ F+ R +AE+A++G +G++ G
Sbjct: 18 TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPG 74
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 33.7 bits (78), Expect = 0.014
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T E + AFS Y + V R+ G+GFV F D D A++ +G+ + R +
Sbjct: 19 TDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPI 78
Query: 106 RVEMS 110
++ S
Sbjct: 79 KLRKS 83
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 33.5 bits (77), Expect = 0.014
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 45 LCSTSSTKEDIEDAFSYYGPIKNVWVARNP--PGFGFVEFEDRRDAEDAVRGFDGREING 102
L T+ T D+ +AF +G I ++ + + P + F+++ D A+R DG +
Sbjct: 10 LEKTT-TYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDGEYLGN 68
Query: 103 RRVRV 107
RV++
Sbjct: 69 NRVKL 73
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 33.5 bits (77), Expect = 0.014
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
ST+++I FSY G I+ + + P G F+ F+ A+ A+ DG ++ GR
Sbjct: 9 YSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-LDGEDMGGR 67
Query: 104 RVRVE 108
++VE
Sbjct: 68 FLKVE 72
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding
Raly-like protein (RALYL). This subgroup corresponds to
the RRM of RALYL, also termed heterogeneous nuclear
ribonucleoprotein C-like 3, or hnRNP core protein C-like
3, a putative RNA-binding protein that shows high
sequence homology with Raly, an RNA-binding protein
playing a critical role in embryonic development. The
biological role of RALYL remains unclear. Like Raly,
RALYL contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain. .
Length = 69
Score = 33.5 bits (76), Expect = 0.015
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
K DIE F+ YG I V + G+ FV++ R A AV G + R I G+
Sbjct: 16 KADIEAIFAKYGKIVGCSVHK---GYAFVQYISERHARAAVAGENARIIAGQ 64
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 33.7 bits (77), Expect = 0.015
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAV----RGFDG 97
S +TK+D+++ FS +G + + + +P GFGFV F+D E + DG
Sbjct: 7 SWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLDG 66
Query: 98 REINGRR 104
R I+ +R
Sbjct: 67 RVIDPKR 73
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 33.3 bits (77), Expect = 0.015
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVR 93
FS +G I N+ V NP V+F +A+ A R
Sbjct: 23 FSKFGTIVNIQVNYNPES-ALVQFSTSEEAKKAYR 56
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 33.5 bits (76), Expect = 0.020
Identities = 16/67 (23%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ FS G +++ + R+ G+GFV + + +DAE A+ +G + + +
Sbjct: 14 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTI 73
Query: 106 RVEMSNP 112
+V + P
Sbjct: 74 KVSYARP 80
>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 = 33.1 bits (76), Expect = 0.020
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
+T ED+ F G +V + G FVEF+ A++ +
Sbjct: 9 PYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-LHHTLLK 67
Query: 102 GRRVRVE 108
GR++ VE
Sbjct: 68 GRKINVE 74
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.4 bits (77), Expect = 0.021
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 53 EDIEDAF-----SYYGPIKNVW------VARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
E + D F G + + W FGF EFED A A+R +G E+
Sbjct: 10 EGVSDDFIRKLLEKCGKVLS-WKRVKDPSTGKLKAFGFCEFEDPEGALRALRLLNGLELG 68
Query: 102 GRRVRV 107
G+++ V
Sbjct: 69 GKKLLV 74
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 33.0 bits (76), Expect = 0.021
Identities = 18/63 (28%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVA--RN--PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+ +DI++ F+ +G +K V R+ G V FE R DA A++ ++G ++GR ++
Sbjct: 13 SDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYNGVPLDGRPMK 72
Query: 107 VEM 109
+++
Sbjct: 73 IQL 75
>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subgroup corresponds to the RRM2 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, an essential splicing
regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 33.0 bits (75), Expect = 0.022
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S+ + +D++D G + + G +EF D + A+ DG EINGR++R
Sbjct: 9 SSRCSWQDLKDFMRQAGEVTYADAHKERANEGVIEFRSYSDMKRALEKLDGTEINGRKIR 68
Query: 107 V 107
+
Sbjct: 69 L 69
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 33.3 bits (76), Expect = 0.023
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
ST E++E FS GPI V + + +P G+ ++EF RD+ +A D GR
Sbjct: 11 STAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVALDESSFRGRV 69
Query: 105 VRV 107
++V
Sbjct: 70 IKV 72
>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 = 33.0 bits (76), Expect = 0.023
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 51 TKEDIEDAFSYYG--PIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
T ED+E A + G +K++ + GF +VEF A +GRE NG+
Sbjct: 11 TDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGK 70
Query: 104 RVRV 107
+ V
Sbjct: 71 KCVV 74
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 33.0 bits (76), Expect = 0.023
Identities = 18/59 (30%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNP-PGFG--FVEFEDRRDAEDAVRGFDGREINGRRVRV 107
K +E FS YG I +V P F V F +A A G G +RV
Sbjct: 17 KAALESLFSSYGEI-ATFV---YLPSFRRARVVFSSPEEAALARIELHGTVFEGSVLRV 71
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 33.4 bits (76), Expect = 0.024
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 13/70 (18%)
Query: 51 TKEDIEDAFSYYGPIK----------NVWVARN---PPGFGFVEFEDRRDAEDAVRGFDG 97
T E + D F G IK N++ R G V F+D A+ A+ FDG
Sbjct: 15 TIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG 74
Query: 98 REINGRRVRV 107
+E +G ++V
Sbjct: 75 KEFSGNPIKV 84
>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 = 33.0 bits (76), Expect = 0.025
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
GFG V FE DA+ A+ F+G ++ GR + V
Sbjct: 40 GFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71
>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 = 33.0 bits (76), Expect = 0.029
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREING 102
T++++E FS YG I + + G GF+ F+ R +AE A++ +G G
Sbjct: 13 TQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPG 69
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily
corresponds to the RRM2 of La and LARP7. La is a highly
abundant nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. LARP7 is an oligopyrimidine-binding
protein that binds to the highly conserved 3'-terminal
U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable
component of the 7SK small nuclear ribonucleoprotein
(7SK snRNP), intimately associates with all the nuclear
7SK and is required for 7SK stability. LARP7 also acts
as a negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. LARP7 plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. Both La and LARP7 contain an N-terminal
La motif (LAM), followed by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 32.7 bits (75), Expect = 0.029
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 41 VSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPG-FGFVEFEDRRDAEDAVRGF 95
+ I T+EDI+ F+ +G +K +V G++ F+ A+ A F
Sbjct: 4 LKITSIGPGVTREDIKAVFAQFGEVK--YVDFTEGADTGYIRFKTPEAAQKAREAF 57
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 33.5 bits (77), Expect = 0.029
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 79 FVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
FVEF +AE A++ +GR GR+V+ E+
Sbjct: 56 FVEFSLPSEAEKAIQALNGRWFGGRKVKAEL 86
>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM2 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5), is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 75
Score = 32.7 bits (74), Expect = 0.030
Identities = 17/61 (27%), Positives = 31/61 (50%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S+ + +D++D G + R G VEF D ++A+ G+EINGR+++
Sbjct: 12 SSRVSWQDLKDFMRQAGEVTFADAHRPKLNEGVVEFASYSDLKNAIEKLSGKEINGRKIK 71
Query: 107 V 107
+
Sbjct: 72 L 72
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 32.6 bits (75), Expect = 0.030
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 44 VLCSTSSTK---EDIEDAFSYYGPIKNVW-----VARNPPGFGFVEFEDRRDAEDAVRGF 95
V S K D+ + FS G +++V +R G +VEF D A+ G
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60
Query: 96 DGREINGRRVRV 107
G+ + G+ + V
Sbjct: 61 TGQRLLGQPIMV 72
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 32.8 bits (75), Expect = 0.031
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG----FDG 97
+ ++ + F+ YG + V +P GFGF+ F +A++A+ DG
Sbjct: 11 NLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSIDG 70
Query: 98 REINGRR 104
+I +R
Sbjct: 71 NQIELKR 77
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although
their biological roles remain unclear, these proteins
show high sequence similarity to the fission yeast
Vip1. Like Vip1 protein, members in this family contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 69
Score = 32.4 bits (74), Expect = 0.031
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFG----FVEFEDRRDAEDAV 92
S +T+ DI D FS+ G I+ V + R+ G +V F+D + E A+
Sbjct: 7 SPKATERDIYDFFSFSGDIEYVEIQRS--GEQSQTAYVTFKDPQAQETAL 54
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 35.6 bits (82), Expect = 0.036
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 193 RSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRRRSA 248
R GG RG+ G R GR F+ + + GGRG R RR G RR +
Sbjct: 567 TGGERRGGGRGFGGERREGGRNFSGERR---EGGRGDGRRFSGERREGRAPRRDDS 619
Score = 29.4 bits (66), Expect = 2.5
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 118 RSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPE 171
R GG RG+ G R GR F+ + + GGRG R RR G + R +
Sbjct: 567 TGGERRGGGRGFGGERREGGRNFSGERR---EGGRGDGRRFSGERREGRAPRRD 617
>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 = 32.6 bits (74), Expect = 0.036
Identities = 17/52 (32%), Positives = 24/52 (46%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
FS YG I + + N P ++ D AE AV G + G+R+ V S
Sbjct: 23 FSNYGNIVRIKLLHNKPDHALIQMGDGFQAELAVNYLKGAMLFGKRMEVNFS 74
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 98
Score = 32.9 bits (75), Expect = 0.039
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQKMRGRSNGRS 123
GF VE+E AE+ DG I G R+++ P + GRS
Sbjct: 45 GFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPG-----APGRS 87
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 75
Score = 32.0 bits (73), Expect = 0.048
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIK-NVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T E+I D F Y I +V + N P G V F+ R+A AVR +GR I R+V
Sbjct: 13 TIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVRELNGRPIGTRKV 72
Query: 106 RV 107
++
Sbjct: 73 KL 74
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of
specific mRNAs during gametogenesis. .
Length = 81
Score = 32.5 bits (74), Expect = 0.050
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAE 89
I+V + T + D+ FS YG +K V + + G+GFV FE + DA+
Sbjct: 5 IFVGGIDFKT--NENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQ 57
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 32.3 bits (74), Expect = 0.050
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 57 DAFSYYGPI-KNVWVARNP-----PGFGFVEFEDRRDAED-AVRGFDGREINGRRVRVE 108
D FS +G I + + R+P GF F+ + D +A D A+ +G+ + R + V
Sbjct: 20 DTFSAFGVILQTPKIMRDPDTGNSKGFAFISY-DSFEASDAAIEAMNGQYLCNRPITVS 77
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 32.0 bits (73), Expect = 0.052
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
GFG V+F D + A++ DG + GR +R+
Sbjct: 41 GFGHVDFADEESLDAALK-LDGTVLCGRPIRI 71
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 32.6 bits (75), Expect = 0.053
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 53 EDIEDAFSYYGPIKNVWVARN--PPGFG--FVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
ED+ S +G I+++ V N G +V+FE DAE A++ +GR GR + E
Sbjct: 40 EDVFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99
Query: 109 MSN 111
+S
Sbjct: 100 LSP 102
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4), a splicing
regulatory serine/arginine (SR) protein that plays an
important role in both constitutive splicing and
alternative splicing of many pre-mRNAs. For instance, it
interacts with heterogeneous nuclear ribonucleoproteins,
hnRNP G and hnRNP E2, and further regulates the 5'
splice site of tau exon 10, whose misregulation causes
frontotemporal dementia. SFRS4 also induces production
of HIV-1 vpr mRNA through the inhibition of the
5'-splice site of exon 3. In addition, SRSF4 activates
splicing of the cardiac troponin T (cTNT) alternative
exon by direct interactions with the cTNT exon 5
enhancer RNA. SRSF4 can shuttle between the nucleus and
cytoplasm. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 32.0 bits (72), Expect = 0.054
Identities = 16/61 (26%), Positives = 30/61 (49%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S+ + +D++D G + + G +EF D + A+ DG E+NGR++R
Sbjct: 9 SSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALEKLDGTEVNGRKIR 68
Query: 107 V 107
+
Sbjct: 69 L 69
>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 = 31.8 bits (72), Expect = 0.062
Identities = 18/65 (27%), Positives = 28/65 (43%)
Query: 40 YVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGRE 99
+ ++ T+ + F YG ++ V R G V F D RDA+ AVR GR
Sbjct: 3 SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRH 62
Query: 100 INGRR 104
+ +
Sbjct: 63 MQQQA 67
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions as
a translational regulator that activates translation in
an mRNA-specific manner. DAZAP1 was initially identified
as a binding partner of Deleted in Azoospermia (DAZ). It
also interacts with numerous hnRNPs, including hnRNP U,
hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D,
suggesting DAZAP1 might associate and cooperate with
hnRNP particles to regulate adenylate-uridylate-rich
elements (AU-rich element or ARE)-containing mRNAs.
DAZAP1 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
proline-rich domain. .
Length = 82
Score = 32.1 bits (73), Expect = 0.062
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 9/64 (14%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG----FDG 97
S +T+E + FS YG + + + ++ GFGFV+F+D + G DG
Sbjct: 8 SWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDG 67
Query: 98 REIN 101
R I+
Sbjct: 68 RTID 71
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 34.3 bits (78), Expect = 0.063
Identities = 32/166 (19%), Positives = 56/166 (33%), Gaps = 16/166 (9%)
Query: 1 MWNKMSHFKLKLLLCFSSLCQEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIE---- 56
K+ K LL ++ E E +D +I R VI I + T +
Sbjct: 36 NQRKLGSGKDFDLLFYNGETNE-EYDDDYFVIPRSTSVIVSRIPAWKSKGTAARYKGGAP 94
Query: 57 ---DAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQ 113
A Y + + P G + + + + F R + +MS+
Sbjct: 95 KTTGARGYNVKRPRMLQKKAPITSGELNSQSSSEDAAIQQMFQVSSDQWRETQDKMSSAT 154
Query: 114 KMRGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDC 159
+ + R G + +P P CY CG +GH+ ++C
Sbjct: 155 PIYKPNQHRIGAQK--------HNKPPPPGYVCYRCGQKGHWIQNC 192
Score = 30.5 bits (68), Expect = 1.1
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 205 RGSVRARGRPFNPDDKCYECGGRGHYARDC 234
R + +P P CY CG +GH+ ++C
Sbjct: 163 RIGAQKHNKPPPPGYVCYRCGQKGHWIQNC 192
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 32.3 bits (74), Expect = 0.070
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPPGFG-------FVEFEDRRDAEDAVRGFDGREINGRRV 105
EDI + S +G ++ + V N G +V+F D A A++ GR +GR +
Sbjct: 41 EDIFEELSKFGEVEALNVCDN---LGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPI 97
Query: 106 RVEMS 110
VE S
Sbjct: 98 IVEFS 102
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 31.9 bits (73), Expect = 0.070
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVA---RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
++T + + + FS G +K V +A P + FVEF ++ +A++ +G GR +
Sbjct: 15 TTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK-LNGAMFGGRPL 73
Query: 106 RVEMSN 111
+V SN
Sbjct: 74 KVNHSN 79
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 31.8 bits (73), Expect = 0.070
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 42 SIVLC----STSSTKEDIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAVRGF 95
+V+ ++E++ F YG ++++ + PPG + FV + DA A
Sbjct: 3 HLVVANGGLGNGVSREELLRVFEKYGTVEDLVM---PPGKPYCFVSYSSIEDAAAAYDAL 59
Query: 96 DGREIN 101
+G+E+
Sbjct: 60 NGKELE 65
>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 = 31.4 bits (71), Expect = 0.078
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T+++ + F+ YG V++ + GFGF++ E R AE A D + GR++RV
Sbjct: 14 TEDEFKKLFAKYGEPGEVFINKGK-GFGFIKLESRALAEIAKAELDDTPMRGRQLRV 69
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 31.6 bits (72), Expect = 0.082
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 51 TKEDIEDAF-SYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRGFDGREINGRR- 104
T+ I + F S GPIK V ++ N G + F+ DA A F+GR +G R
Sbjct: 12 TEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRK 71
Query: 105 VRVEM 109
++VE+
Sbjct: 72 MKVEV 76
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 31.2 bits (70), Expect = 0.10
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
S ++ + + D FS +G I+ V R+P GFGFV F D D V E++
Sbjct: 8 SWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASV-DKVLAQPHHELD 66
Query: 102 GRRV 105
+ +
Sbjct: 67 SKTI 70
>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 = 0.10
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
T++++ F YG I + R+ P G FV ++ R +A+ A+ +G G
Sbjct: 13 TEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 31.1 bits (70), Expect = 0.12
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAV----RGFDG 97
S ++K+D++D F+ +G + + + +P GFGF+ F+D E + DG
Sbjct: 8 SWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDG 67
Query: 98 REINGRR 104
R I+ ++
Sbjct: 68 RLIDPKK 74
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 31.9 bits (73), Expect = 0.12
Identities = 22/83 (26%), Positives = 31/83 (37%), Gaps = 20/83 (24%)
Query: 43 IVLCSTSSTKED-IEDAFSYYGPIKNVWVARN--------PPGFGFVEFEDRRDAED--- 90
+V ST ED I++ FS +G I + RN P G +++ D
Sbjct: 6 VVWGFQPSTSEDIIKNYFSSFGEIAEI---RNFNDPNTAVPLGIYLIKYYGSPGKPDRAA 62
Query: 91 -----AVRGFDGREINGRRVRVE 108
AVR I G +VE
Sbjct: 63 KAALKAVRKAQDCRIGGAEFKVE 85
>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 = 31.4 bits (72), Expect = 0.13
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 59 FSYYGPI-KNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
FS YG + K + +N V+F+ AE+A + +GR I
Sbjct: 22 FSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNIY 65
>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 = 31.0 bits (71), Expect = 0.14
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 59 FSYYGPIKNVWVARNPP---GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
FS +GP+ ++ VA G FV F+D A +A+R G + +R++
Sbjct: 24 FSQFGPVLDI-VASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQ 75
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 31.2 bits (70), Expect = 0.15
Identities = 10/37 (27%), Positives = 24/37 (64%)
Query: 77 FGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQ 113
FGFV +++ A+ A++ +G +I +R++V++ +
Sbjct: 51 FGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSK 87
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition, steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway. It binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 76
Score = 30.6 bits (69), Expect = 0.16
Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG---FDGREIN 101
+T + + + F +G + + V R+ GFGF+ F+ + + ++ DG+ I+
Sbjct: 10 TTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDGKIID 69
Query: 102 GRR 104
+R
Sbjct: 70 PKR 72
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 92
Score = 31.0 bits (70), Expect = 0.16
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
GF +E+E AE + DG + G +RV P
Sbjct: 45 GFAVLEYESAEMAEMVQQQADGLSLAGSHIRVSFCAP 81
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 30.7 bits (70), Expect = 0.17
Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 62 YGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+G +K + ++ G+ F E+ D + A+ G +G ++ +++ V
Sbjct: 24 FGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTV 74
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 30.8 bits (69), Expect = 0.17
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 47 STSSTKEDIEDAFSYYGPI---KNVWVARNPPG--FGFVEFEDRRDAEDAVRGFDGREIN 101
S+++ D+++ FS YG + K V AR+P +GFV +A + E++
Sbjct: 10 SSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELH 69
Query: 102 GRRVRVE 108
GR + VE
Sbjct: 70 GRMISVE 76
>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 = 30.8 bits (70), Expect = 0.17
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREINGR 103
+ T+E++ AF YG +++V + R P G + FV+F + A A G+ I
Sbjct: 12 ITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRN 71
Query: 104 RVRV 107
++++
Sbjct: 72 QIKI 75
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 30.8 bits (69), Expect = 0.18
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAV 92
+ E +E AFS +GP++ V + P G GFVEF + A A+
Sbjct: 12 SNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57
>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 = 30.6 bits (69), Expect = 0.20
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
KE EDA P ++ G ++EF+ +AE A+ G E++GR + V+
Sbjct: 19 ELKEVFEDAVDIRLPSGKDGSSK---GIAYIEFKTEAEAEKALEEKQGAEVDGRSIVVD 74
>gnl|CDD|240698 cd12252, RRM_DbpA, RNA recognition motif in the DbpA subfamily of
prokaryotic DEAD-box rRNA helicases. This subfamily
corresponds to the C-terminal RRM homology domain of
dbpA proteins implicated in ribosome biogenesis. They
bind with high affinity and specificity to RNA
substrates containing hairpin 92 of 23S rRNA (HP92),
which is part of the ribosomal A-site. The majority of
dbpA proteins contain two N-terminal ATPase catalytic
domains and a C-terminal RNA binding domain, an atypical
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNPs (ribonucleoprotein domain). The
catalytic domains bind to nearby regions of RNA to
stimulate ATP hydrolysis and disrupt RNA structures. The
C-terminal domain is responsible for the high-affinity
RNA binding. Several members of this family lack
specificity for 23S rRNA. These proteins can generally
be distinguished by a basic region that extends beyond
the C-terminal domain.
Length = 71
Score = 30.2 bits (69), Expect = 0.21
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 77 FGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
F FVE AE + +G++I G++VRVE
Sbjct: 41 FSFVEV-PEEVAEKVIEALNGKKIKGKKVRVE 71
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 30.4 bits (68), Expect = 0.25
Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPI--KNVWVARN---PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T D+ F +G + V++ + FGFV +++ A+ A++ +G +I +R+
Sbjct: 17 TDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRL 76
Query: 106 RVE 108
+V+
Sbjct: 77 KVQ 79
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 30.0 bits (68), Expect = 0.26
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVW-----VARNPPGFGFVEFEDRRDAEDAV 92
S +T+E I + F +G I + GF F+ F D+E+ V
Sbjct: 8 SPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPV 54
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 30.4 bits (68), Expect = 0.27
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
K+ + FS +G I ++ V+R+ G FV F++ A +A+R G + +R++
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 110 S 110
+
Sbjct: 81 A 81
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 30.3 bits (69), Expect = 0.28
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 79 FVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQKMR 116
FVEFE A AV +GR GR V+ + ++ R
Sbjct: 55 FVEFERVESAIKAVVDLNGRFFGGRTVKASFYDEERFR 92
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 30.0 bits (67), Expect = 0.29
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAV----RGFDG 97
S +TK+D++D FS +G + + + +P GFGFV F++ + + +G
Sbjct: 7 SWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNG 66
Query: 98 REINGRR 104
+ I+ +R
Sbjct: 67 KVIDPKR 73
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 30.3 bits (69), Expect = 0.31
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 56 EDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+D YG ++ V + +P G V F+ + A+ V + + G+ ++V
Sbjct: 20 KDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVF 77
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 30.0 bits (68), Expect = 0.31
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 43 IVLCSTSS--TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRD-------- 87
I++ S T + I F +G I+ + +P G V F
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 88 AEDAVRGFDGREINGRRVRVEM 109
A+ AV G +GR I G+RVRVE+
Sbjct: 61 AKAAVDGLNGRRIGGKRVRVEL 82
>gnl|CDD|130716 TIGR01655, yxeA_fam, conserved hypothetical protein TIGR01655.
This model represents a family of small (about 115
amino acids) uncharacterized proteins with N-terminal
signal sequences, found exclusively in Gram-positive
organisms. Most genomes that have any members of this
family have at least two members [Hypothetical
proteins, Conserved].
Length = 114
Score = 30.5 bits (69), Expect = 0.32
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 36 MLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWV 70
+L + V I + + D F+YY IKN +
Sbjct: 8 LLALIVVITIVGIEISHPVYSDRFNYYIKIKNDYK 42
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 29.7 bits (67), Expect = 0.33
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 79 FVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++ FE DA A+ +GR +GR V+ E
Sbjct: 41 YITFERSEDAARAIVDLNGRYFDGRLVKAE 70
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 29.8 bits (67), Expect = 0.35
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVR 93
+YV V +T E++E F G + V + + P GF ++EF D +++
Sbjct: 2 VYVGNV--DYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTAL 58
Query: 94 GFDGREINGRRVRV 107
D GR+++V
Sbjct: 59 ALDESLFRGRQIKV 72
>gnl|CDD|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM1 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 70
Score = 29.5 bits (66), Expect = 0.38
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
ST +++ D Y +K +V RN FV + A+DA+R F + G+ + V++
Sbjct: 11 STNQEVHDLLKDY-ELKYCYVDRNK-RTAFVTLLNGEQAQDAIRTFHQTSVRGKDINVQL 68
>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 = 29.2 bits (65), Expect = 0.45
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
F YG I+ V + PG VE D E AV + ++ G+R+ V
Sbjct: 21 FCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 69
>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 = 31.7 bits (72), Expect = 0.47
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQ 113
F YG ++ V +N +E D A+ A+ +G ++ G+ +RV S Q
Sbjct: 297 FCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ 351
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 29.6 bits (67), Expect = 0.48
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 59 FSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
FS +G + NV V R+ G+GFV + +A A+ +G + GR ++V
Sbjct: 22 FSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQV 75
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 29.3 bits (66), Expect = 0.48
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
G G V+FE +A A+ F+G+ + R +RV+M
Sbjct: 40 GMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVKM 73
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 29.4 bits (66), Expect = 0.49
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 77 FGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
FGFV F++ A+ A++ +G +I +R++V+
Sbjct: 48 FGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ 79
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 29.3 bits (66), Expect = 0.53
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPG---FGFVEFEDRRDAEDAVR 93
+YVS + T+E + FS G + + V +P F F+EF D A A+
Sbjct: 5 VYVSDI--DQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 29.2 bits (66), Expect = 0.56
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 47 STSSTKEDIEDAFSYYGPI-------KNVWVARNPPGFGFVEFEDRRDAEDA 91
S +T+E + F + G I + +A FV++ED D A
Sbjct: 8 SPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVA 59
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 29.2 bits (65), Expect = 0.57
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 73 NPPGFGFVEFEDRRDAEDAVRGFDGREI-NGRRVRV 107
N G+ FV F ++++A++A++ + EI NGR + V
Sbjct: 40 NNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGV 75
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 29.2 bits (66), Expect = 0.57
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREING 102
++D+E YG + + + R+ G GF E R ED + F+G+ + G
Sbjct: 13 DEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFNGKYLKG 68
>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 = 29.3 bits (66), Expect = 0.61
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVR 93
S ++E++ + +GPI + + + FV F +A V
Sbjct: 14 SYSEEELREDLEKFGPIDQIKIVKE-KNIAFVHFLSIANAIKVVT 57
>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 = 29.5 bits (67), Expect = 0.61
Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 13/71 (18%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP---GFGF---------VEFEDRRDAEDAVRGFDG 97
T ED+ + F Y P + +W+ R V + ++ +
Sbjct: 14 VTDEDLREFFKDYNP-QEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEETLDEIIESLKS 72
Query: 98 REINGRRVRVE 108
+++NG+++ ++
Sbjct: 73 KKLNGKKISLK 83
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 29.1 bits (65), Expect = 0.66
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 82 FEDRRDAEDAVRGFDGREINGRRVRVEM 109
F+ DA AV+ +G ++G ++V M
Sbjct: 43 FDRASDALLAVKKMNGGVLSGLSIKVRM 70
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 29.3 bits (66), Expect = 0.68
Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 13/67 (19%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAV------------RGFDGREI 100
I D F +G K+V + + GFV FE R AE +
Sbjct: 17 YKIRDYFEQFGKSKSV-IVNHRAKCGFVRFETREAAEKFAAAISENGLNAGLSRGGLLVL 75
Query: 101 NGRRVRV 107
G +RV
Sbjct: 76 EGCPLRV 82
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 30.8 bits (70), Expect = 0.69
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAV 92
S +T+ DI++ FS+ G I+ V + +V F+D + AE A+
Sbjct: 13 SLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETAL 60
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 28.9 bits (65), Expect = 0.72
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAVRGFDG 97
T++D+ F +G I+ + R P G FV+F +A+ A+ G
Sbjct: 14 TEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 28.7 bits (65), Expect = 0.74
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP----GFGFVEFEDRRDAE 89
+T +DI++ F +G + N+ + R+ G FVEF+ DA+
Sbjct: 11 ATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAK 54
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 28.8 bits (64), Expect = 0.82
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
S ++T ED++ F +G + + + + GFGFV FE D + V EIN
Sbjct: 8 SVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEIHFHEIN 66
Query: 102 GRRV 105
+ V
Sbjct: 67 NKMV 70
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 28.8 bits (65), Expect = 0.96
Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 21/78 (26%)
Query: 49 SSTKEDIEDAFSYYGPIKNV---------------WVARNP-PG---FGFVEFEDRRDAE 89
ST E + + FS G I + + +R+P G VEFE A
Sbjct: 12 ESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAAR 71
Query: 90 DAVRGFDGRE--INGRRV 105
AV R+ +G +V
Sbjct: 72 KAVEELSARDDWRDGIKV 89
>gnl|CDD|214341 CHL00032, ndhA, NADH dehydrogenase subunit 1.
Length = 363
Score = 30.7 bits (70), Expect = 1.0
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 42 SIVLCSTSSTKEDIEDAFSYYGPIK-NVWVARNPPGF 77
SI L S S + DI +A S YG N+W R P GF
Sbjct: 181 SISLLSNSLSTVDIVEAQSKYGFWGWNLW--RQPIGF 215
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 28.5 bits (63), Expect = 1.1
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 43 IVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGF----GFVEFEDRRDAEDAVRG 94
I + S + DI FS +G I+ + R P G FV F R A+ A++
Sbjct: 6 IGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 61
>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 = 28.5 bits (64), Expect = 1.1
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN--GRRVR 106
T+ D+ +A S +GPI V + VEFED DA+ V + GR+
Sbjct: 13 GVTEADLVEALSEFGPISYVTMMPKKRQ-ALVEFEDISDAKACVNHAQQNPVYIAGRQAY 71
Query: 107 VEMSNPQKM 115
S Q++
Sbjct: 72 FNYSTSQEI 80
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 28.8 bits (64), Expect = 1.1
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 55 IEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
+ D YG ++ V + NP G V F + A+DAV+ + G + VE+
Sbjct: 19 LTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDAVQHLHNTSVMGNIIHVEL 78
Query: 110 SNPQKMRGR 118
+ R R
Sbjct: 79 DTKGETRMR 87
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 28.8 bits (64), Expect = 1.1
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPG----FGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
++ ++ AF YG I+ V + R G + F++F++ A A GR I ++
Sbjct: 21 SEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIK 80
Query: 107 V 107
+
Sbjct: 81 I 81
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 28.0 bits (63), Expect = 1.2
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG----FDGR 98
T +KE +++ FS +G +K+ V + G+GFV F R E+A++ +G
Sbjct: 10 TVGSKE-LKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGN 68
Query: 99 EIN 101
++
Sbjct: 69 KLQ 71
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 28.4 bits (64), Expect = 1.3
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDG-REINGRRVRVEMSNP 112
G+GFV F D + + A+ G + G+ +RV ++ P
Sbjct: 44 GYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIP 81
>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 = 30.4 bits (68), Expect = 1.4
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 59 FSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
F GPI + R+ G+ FV+F D++ A++ +G + +R++V + P
Sbjct: 128 FRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP 186
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 28.1 bits (63), Expect = 1.4
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 38 VIYVSIVLCSTSSTKEDIE----DAFSYYGPIKNVWVARNPPGFG-----FVEFEDRRDA 88
+YV + S T+E+I AFS +G + +V V N FV+F R A
Sbjct: 2 TLYVWGI--SPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAA 59
Query: 89 EDAVRGFDGRE-INGRRVRV 107
A + +G+ G ++V
Sbjct: 60 SRAQKACNGKWLFQGSPLKV 79
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 28.0 bits (63), Expect = 1.6
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVR 93
+ E +E AFS +G ++ V + G G VEF + A+ A++
Sbjct: 12 SNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIK 58
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 28.1 bits (62), Expect = 1.7
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
G G V F+ AE A R +G +INGR + V +
Sbjct: 40 GCGTVRFDSPESAEKACRLMNGIKINGREIDVRL 73
>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 = 27.8 bits (62), Expect = 1.7
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 74 PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G G VEF+D+ + A+ + E+ GR++ V
Sbjct: 40 SRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 28.0 bits (62), Expect = 1.8
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAV 92
+ E +E+AFS +G ++ V + P G G VEF + A A+
Sbjct: 12 SNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 27.6 bits (61), Expect = 1.9
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 52 KEDIEDAFSYYGPIKNVWVAR----NPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+E + + F GP+ V + + P FGFV F+ A+ +G + GR ++V
Sbjct: 15 EEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIKV 74
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 27.6 bits (61), Expect = 1.9
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
G G V FE AE A R +G ++NGR + V +
Sbjct: 40 GCGVVRFESPEVAERACRMMNGYKLNGREIDVRI 73
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 27.3 bits (61), Expect = 2.3
Identities = 12/50 (24%), Positives = 21/50 (42%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREI 100
+ + +G ++ V + G V F D R AEDA+R + +
Sbjct: 14 PETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIRAQHL 63
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 27.3 bits (60), Expect = 2.5
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREIN 101
S ++ ED++ F +G +++ + + GFGFV FE D + V EIN
Sbjct: 12 SANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE-NEDVVEKVCEIHFHEIN 70
Query: 102 GRRV 105
+ V
Sbjct: 71 NKMV 74
>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
Length = 421
Score = 29.4 bits (66), Expect = 2.5
Identities = 24/101 (23%), Positives = 36/101 (35%), Gaps = 21/101 (20%)
Query: 129 YRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKI-NGRRVRVEMSNP 187
Y G++R N D C C G G G CK+ NG+ +RV++
Sbjct: 138 YNGAMRKLA--INKDVICANCEGHG-----------GPKDAFVDCKLCNGQGIRVQIRQM 184
Query: 188 QKMRGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRG 228
M ++ G +G+ KC C G+G
Sbjct: 185 GSMIHQTQSTCNSCNG-------QGKIIPESKKCKNCSGKG 218
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 27.2 bits (61), Expect = 2.7
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGRE--INGRRVRVE 108
T+ ++ +G + + N F+E E DA+ V + I G+ ++V
Sbjct: 14 TEAELLKLAEPFGKVDHYIFLPNR-NKAFIEMESPEDAQALVSFYKTYPLTIGGKSIKVA 72
Query: 109 MSN 111
+S
Sbjct: 73 LST 75
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 156
Score = 28.4 bits (63), Expect = 2.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREI 100
G+GF+EF + A A+R +G +
Sbjct: 90 GYGFMEFISHKYALMALRWLNGHAV 114
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 27.3 bits (61), Expect = 3.0
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPG--FGFVEFEDRRDAEDAV 92
VIYV + +T+ ++ F +G I+ + + G +GFV + DA A+
Sbjct: 4 VIYVGKI--PIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI 58
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 27.4 bits (60), Expect = 3.3
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 59 FSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNPQ 113
F +G + NV V R+ GFGFV + +A A+ +G + R ++V +
Sbjct: 22 FGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTSK 81
Query: 114 KMRG 117
+ +
Sbjct: 82 QHKA 85
>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 = 26.8 bits (60), Expect = 3.3
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 59 FSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
F YG + + ++ PG V+ D + AE A+ +G + G+++ V
Sbjct: 21 FCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEV 69
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 26.8 bits (60), Expect = 3.4
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGF---DGREING 102
+++ED+++AF +G + V AR G+V F++ A++A+ +I G
Sbjct: 9 VGEQTSREDLKEAFEEFGEVAWVDFARGQTE-GYVRFKEENAAKEALEKLKEAKNLKIKG 67
Query: 103 RRVRVEM 109
V V++
Sbjct: 68 SEVTVKL 74
>gnl|CDD|239745 cd03776, MATH_TRAF6, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily,
TRAF domain, C-terminal MATH subdomain; composed of
proteins with similarity to human TRAF6, including the
Drosophila protein DTRAF2. TRAF molecules serve as
adapter proteins that link TNFRs and downstream kinase
cascades resulting in the activation of transcription
factors and the regulation of cell survival,
proliferation and stress responses. TRAF6 is the most
divergent in its TRAF domain among the mammalian TRAFs.
In addition to mediating TNFR family signaling, it is
also an essential signaling molecule of the
interleukin-1/Toll-like receptor superfamily. Whereas
other TRAF molecules display similar and overlapping
TNFR-binding specificities, TRAF6 binds completely
different sites on receptors such as CD40 and RANK.
TRAF6 serves as a molecular bridge between innate and
adaptive immunity and plays a central role in
osteoimmunology. DTRAF2, as an activator of nuclear
factor-kappaB, plays a pivotal role in Drosophila
development and innate immunity. TRAF6 contains a RING
finger domain, five zinc finger domains, and a TRAF
domain. The TRAF domain can be divided into a more
divergent N-terminal alpha helical region (TRAF-N), and
a highly conserved C-terminal MATH subdomain (TRAF-C)
with an eight-stranded beta-sandwich structure. TRAF-N
mediates trimerization while TRAF-C interacts with
receptors.
Length = 147
Score = 28.1 bits (63), Expect = 3.5
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEF 82
T +K ++ AF P RNP GFG+VEF
Sbjct: 96 TMMSKPEL-LAFQR--PT----TDRNPKGFGYVEF 123
>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 = 27.0 bits (60), Expect = 3.5
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 7/55 (12%)
Query: 53 EDIEDAFSYYGPIKNVWVARNPPGFG----FVEFEDRRDAE---DAVRGFDGREI 100
E I + F YG +++V + G FV+F D + A+ +AV R++
Sbjct: 14 ERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVNKMGDRDL 68
>gnl|CDD|240990 cd12546, RRM_RBM43, RNA recognition motif in vertebrate
RNA-binding protein 43 (RBM43). This subgroup
corresponds to the RRM of RBM43, a putative RNA-binding
protein containing one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). Although its biological
function remains unclear, RBM43 shows high sequence
homology to poly [ADP-ribose] polymerase 10 (PARP-10),
which is a novel oncoprotein c-Myc-interacting protein
with poly(ADP-ribose) polymerase activity. .
Length = 77
Score = 26.9 bits (60), Expect = 3.9
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 63 GPIKNVWVARNPPGFGFVEFEDRRDAEDAVR 93
G ++NV G +V FE+ DAE+ ++
Sbjct: 33 GDVENVTYPTRTKGVAYVTFEEEEDAENVLK 63
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 27.3 bits (61), Expect = 4.1
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 56 EDAF----SYYGPIKNVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
ED F YG I+ + V N G +V+F DAE AV + R NG+ +
Sbjct: 41 EDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQPIYA 100
Query: 108 EMS 110
E+S
Sbjct: 101 ELS 103
>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 = 26.8 bits (60), Expect = 4.5
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFE 83
S T+ D+E+ FS +G + +V + + GF +++
Sbjct: 10 SVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 28.6 bits (64), Expect = 4.7
Identities = 14/62 (22%), Positives = 19/62 (30%)
Query: 120 NGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGSGRPELCKINGRR 179
NGR G RG RG+ + + R G +P + RR
Sbjct: 389 NGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRR 448
Query: 180 VR 181
R
Sbjct: 449 PR 450
>gnl|CDD|184603 PRK14282, PRK14282, chaperone protein DnaJ; Provisional.
Length = 369
Score = 28.6 bits (64), Expect = 4.7
Identities = 22/66 (33%), Positives = 26/66 (39%), Gaps = 15/66 (22%)
Query: 146 CYECGGRGHYARDCRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNG-----RSGG 200
C CGG G + GGSGR RRVR + P G +G GG
Sbjct: 198 CERCGGTGKIPGE-YCHECGGSGRIR------RRVRTTVKIPA---GVEDGTVLRITGGG 247
Query: 201 DRGYRG 206
+ GY G
Sbjct: 248 NAGYYG 253
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 26.5 bits (59), Expect = 4.8
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GFV F D + + A+ +G + R +RV
Sbjct: 45 GYGFVRFGDEDERDRALTEMNGVYCSSRPMRV 76
>gnl|CDD|202795 pfam03880, DbpA, DbpA RNA binding domain. This RNA binding domain
is found at the C-terminus of a number of DEAD helicase
proteins. It is sufficient to confer specificity for
hairpin 92 of 23S rRNA, which is part of the ribosomal
A-site. However, several members of this family lack
specificity for 23S rRNA. These can proteins can
generally be distinguished by a basic region that
extends beyond this domain [Karl Kossen, unpublished
data].
Length = 74
Score = 26.3 bits (59), Expect = 5.0
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 75 PGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
F FVE A+ ++ +I GR++++E
Sbjct: 40 DNFSFVEV-PEDMADKVLKALKKGKIKGRKLKIE 72
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also
stimulate translation initiation. It contains a five
stranded beta sheet which forms an atypical RNA
recognition motif.
Length = 102
Score = 26.9 bits (60), Expect = 6.0
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRG 94
+++EDI++AFS +G +K V G+V F+ A+ A+
Sbjct: 13 TSREDIKEAFSQHGEVKYVDFLEGDKE-GYVRFKTPEAAKKALEK 56
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 28.2 bits (63), Expect = 6.5
Identities = 19/59 (32%), Positives = 19/59 (32%), Gaps = 5/59 (8%)
Query: 191 RGRSNGRSGGDRGYRGSVRARGRPFNPDDKCYECGGRGHYARDCRSRRSGGGGRRRSAV 249
G GR GG G G R G GGRG R GGGG V
Sbjct: 4 GGFGGGRGGGRGGGGGGGRGGGGRGGGRG-----GGRGRGRGGGGGGRGGGGGGGPGKV 57
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 26.4 bits (59), Expect = 7.2
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 17/63 (26%)
Query: 59 FSYYGPIKNVWVARNPPGF-----------------GFVEFEDRRDAEDAVRGFDGREIN 101
S YG + +++ P G+VEFED++ A+ + I
Sbjct: 21 LSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80
Query: 102 GRR 104
G++
Sbjct: 81 GKK 83
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 27.9 bits (62), Expect = 7.3
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 140 FNPDDKCYECGGRGHYARD-CRSRRSGGSGRPELCKINGRRVRVEMSNPQKMRGRSNGRS 198
F+ + C +C GRG A D C + GSGR + + R+ +S+ Q++R R G
Sbjct: 202 FSLSEPCPDCKGRGLIADDPCLVCK--GSGRAKSSRTMQVRIPAGVSDGQRIRLRGKGAP 259
Query: 199 GGDRGYRG 206
G G G
Sbjct: 260 GERGGPAG 267
>gnl|CDD|206088 pfam13917, zf-CCHC_3, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved in
eukaryotic gene regulation, such as C. elegans GLH-1.
Structure is an 18-residue zinc finger.
Length = 40
Score = 24.6 bits (54), Expect = 9.8
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 140 FNPDDKCYECGGRGHYARDCRSRR 163
N +C +C +GH+ +C++ R
Sbjct: 1 ANASARCQKCLKKGHWTYECKNER 24
Score = 24.6 bits (54), Expect = 9.8
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 215 FNPDDKCYECGGRGHYARDCRSRR 238
N +C +C +GH+ +C++ R
Sbjct: 1 ANASARCQKCLKKGHWTYECKNER 24
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
0.321 0.139 0.439
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,371,783
Number of extensions: 1585274
Number of successful extensions: 1971
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1792
Number of HSP's successfully gapped: 377
Length of query: 312
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 215
Effective length of database: 6,635,264
Effective search space: 1426581760
Effective search space used: 1426581760
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: 59 (26.6 bits)