RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7847
(170 letters)
>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 = 130 bits (328), Expect = 5e-40
Identities = 50/67 (74%), Positives = 58/67 (86%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
ENDFR+F GDLGN+VTDE+L R FSKYPSF KAKVVRDKRT K+KG+GFVSF DP D++
Sbjct: 3 PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62
Query: 79 RANKEMN 85
+A KEMN
Sbjct: 63 KAMKEMN 69
Score = 125 bits (316), Expect = 3e-38
Identities = 48/65 (73%), Positives = 57/65 (87%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+DFR+F GDLGN+VTDE+L R FSKYPSF KAKVVRDKRT K+KG+GFVSF DP D+++A
Sbjct: 5 NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64
Query: 146 NKEMN 150
KEMN
Sbjct: 65 MKEMN 69
>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 = 80.2 bits (198), Expect = 4e-18
Identities = 44/169 (26%), Positives = 74/169 (43%), Gaps = 45/169 (26%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L V ++ L F+K+ A V++D + +++GF FV+F+ +D +A +EM
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239
Query: 85 ND--------DFRLFCG-----------------------------------DLGNDVTD 101
N +L+ G +L + VTD
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
E L FS+ AKV+ D+ ++GFGFV F +P++ RA EM+
Sbjct: 300 EKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMH 347
Score = 78.7 bits (194), Expect = 1e-17
Identities = 44/174 (25%), Positives = 82/174 (47%), Gaps = 36/174 (20%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L V ++ L TFSK+ + L KV D+ K++G+GFV F+ + A +++
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV 149
Query: 85 N----DDFRLFCG----------------------DLGNDVTDELLIRTFSKYPSFLKAK 118
N +D ++ G +L V ++ L F+K+ A
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209
Query: 119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFPH------LFVGDLKTRS 164
V++D + +++GF FV+F+ +D +A +EMN + L+VG + R+
Sbjct: 210 VMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA 262
Score = 71.0 bits (174), Expect = 6e-15
Identities = 45/149 (30%), Positives = 72/149 (48%), Gaps = 24/149 (16%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ GDL DVT+ L F + L +V RD T ++ G+G+V+F++P D RA + M
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 85 NDD------FRL-----------------FCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
N R+ F +L V ++ L TFSK+ + L KV
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
D+ K++G+GFV F+ + A +++N
Sbjct: 123 DE-NGKSRGYGFVHFEKEESAKAAIQKVN 150
>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 = 68.3 bits (167), Expect = 6e-16
Identities = 27/61 (44%), Positives = 39/61 (63%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F GDL +VTD L FS +PS A+V+ D ++ +++G+GFVSF+ QD A EM
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 85 N 85
N
Sbjct: 62 N 62
Score = 68.3 bits (167), Expect = 6e-16
Identities = 27/61 (44%), Positives = 39/61 (63%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F GDL +VTD L FS +PS A+V+ D ++ +++G+GFVSF+ QD A EM
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 150 N 150
N
Sbjct: 62 N 62
>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 = 67.7 bits (166), Expect = 1e-15
Identities = 33/65 (50%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 22 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
D +F GDL DVTD +L TF ++YPS AKVV D T ++KG+GFV F D + RA
Sbjct: 1 DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60
Query: 81 NKEMN 85
EMN
Sbjct: 61 LTEMN 65
Score = 67.7 bits (166), Expect = 1e-15
Identities = 33/65 (50%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D +F GDL DVTD +L TF ++YPS AKVV D T ++KG+GFV F D + RA
Sbjct: 1 DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60
Query: 146 NKEMN 150
EMN
Sbjct: 61 LTEMN 65
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 65.6 bits (161), Expect = 6e-15
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ GDL DVT+ +L FS L +V RD T ++ G+ +V+F++P D RA +
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 85 NDD 87
N D
Sbjct: 62 NFD 64
Score = 62.9 bits (154), Expect = 7e-14
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ GDL DVT+ +L FS L +V RD T ++ G+ +V+F++P D RA +
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 150 N 150
N
Sbjct: 62 N 62
>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 = 65.5 bits (160), Expect = 6e-15
Identities = 24/61 (39%), Positives = 36/61 (59%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F GDL ++ E L F+ + A+VV+D +T K+KG+GFVSF +D A + M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 85 N 85
N
Sbjct: 62 N 62
Score = 65.5 bits (160), Expect = 6e-15
Identities = 24/61 (39%), Positives = 36/61 (59%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F GDL ++ E L F+ + A+VV+D +T K+KG+GFVSF +D A + M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 150 N 150
N
Sbjct: 62 N 62
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 63.4 bits (155), Expect = 3e-14
Identities = 26/65 (40%), Positives = 37/65 (56%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
LF G+L D T+E L FSK+ ++VRDK T K+KGF FV F+ +D +A +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 149 MNEFP 153
+N
Sbjct: 61 LNGKE 65
Score = 63.4 bits (155), Expect = 4e-14
Identities = 26/62 (41%), Positives = 37/62 (59%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF G+L D T+E L FSK+ ++VRDK T K+KGF FV F+ +D +A +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 84 MN 85
+N
Sbjct: 61 LN 62
>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 = 58.8 bits (143), Expect = 2e-12
Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G+L D T+E L FSK+ ++VRD+ T ++KGF FV F+D +D +A + +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 150 NEF 152
N
Sbjct: 60 NGK 62
Score = 58.4 bits (142), Expect = 3e-12
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G+L D T+E L FSK+ ++VRD+ T ++KGF FV F+D +D +A + +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 85 N 85
N
Sbjct: 60 N 60
>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 = 58.8 bits (143), Expect = 2e-12
Identities = 26/63 (41%), Positives = 38/63 (60%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L N+ TD+ L + F+ + + + AKV DK T ++K FGFVS+ +P+ A K M
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 150 NEF 152
N F
Sbjct: 61 NGF 63
Score = 58.0 bits (141), Expect = 5e-12
Identities = 25/61 (40%), Positives = 37/61 (60%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L N+ TD+ L + F+ + + + AKV DK T ++K FGFVS+ +P+ A K M
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 85 N 85
N
Sbjct: 61 N 61
>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 = 56.2 bits (136), Expect = 3e-11
Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+F LF GDL DV D L FS +YPS AKVV D+ ++G+GFV F D + RA
Sbjct: 1 EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59
Query: 81 NKEMN 85
EM
Sbjct: 60 LTEMQ 64
Score = 56.2 bits (136), Expect = 3e-11
Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+F LF GDL DV D L FS +YPS AKVV D+ ++G+GFV F D + RA
Sbjct: 1 EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59
Query: 146 NKEMN 150
EM
Sbjct: 60 LTEMQ 64
>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 = 55.2 bits (133), Expect = 7e-11
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++P D A
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 84 MN 85
MN
Sbjct: 62 MN 63
Score = 55.2 bits (133), Expect = 7e-11
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++P D A
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 149 MN 150
MN
Sbjct: 62 MN 63
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L T++ L FSK+ + +++D T +++GFGFV+F+ +D A +++
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 85 N 85
N
Sbjct: 64 N 64
Score = 53.8 bits (130), Expect = 2e-10
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L T++ L FSK+ + +++D T +++GFGFV+F+ +D A +++
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 150 N 150
N
Sbjct: 64 N 64
>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 = 53.4 bits (129), Expect = 3e-10
Identities = 24/62 (38%), Positives = 40/62 (64%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F G L TD+ L + FS++ +A V+ D++T K++G+GFV+FKD + RA K+
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 84 MN 85
N
Sbjct: 62 PN 63
Score = 53.4 bits (129), Expect = 3e-10
Identities = 24/62 (38%), Positives = 40/62 (64%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G L TD+ L + FS++ +A V+ D++T K++G+GFV+FKD + RA K+
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 149 MN 150
N
Sbjct: 62 PN 63
>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 = 52.3 bits (126), Expect = 8e-10
Identities = 20/58 (34%), Positives = 29/58 (50%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
L D+T E L F K+VRD+ T ++ G+GFV + D D +A +N F
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65
Score = 50.0 bits (120), Expect = 5e-09
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L D+T E L F K+VRD+ T ++ G+GFV + D D +A +N
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLN 63
>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 = 52.2 bits (126), Expect = 8e-10
Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
LG D+ DE L F KY AKV++D K+KGFGFV+F++ + +A +E+N
Sbjct: 9 LGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64
Score = 51.4 bits (124), Expect = 2e-09
Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
LG D+ DE L F KY AKV++D K+KGFGFV+F++ + +A +E+N
Sbjct: 9 LGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64
>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 = 55.8 bits (134), Expect = 9e-10
Identities = 38/140 (27%), Positives = 58/140 (41%), Gaps = 24/140 (17%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN---- 85
L D+TD L F +++RD +T + G+ FV F D RA K +N
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITV 174
Query: 86 -----------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
D L+ +L +TD+ L F KY ++ ++RDK T
Sbjct: 175 RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP 234
Query: 129 KGFGFVSF---KDPQDFIRA 145
+G FV F ++ Q+ I A
Sbjct: 235 RGVAFVRFNKREEAQEAISA 254
Score = 40.4 bits (94), Expect = 2e-04
Identities = 21/76 (27%), Positives = 36/76 (47%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + E D L+ +L +TD+ L F KY ++ ++RDK T +G FV
Sbjct: 182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVR 241
Query: 71 FKDPQDFIRANKEMND 86
F ++ A +N+
Sbjct: 242 FNKREEAQEAISALNN 257
Score = 33.1 bits (75), Expect = 0.047
Identities = 18/56 (32%), Positives = 26/56 (46%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L D+TD L F +++RD +T + G+ FV F D RA K +N
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLN 170
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM2 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 52.1 bits (125), Expect = 1e-09
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 22 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++ +F GDL +V + L+ F S++PS AK++ D T ++G+GFV F D D RA
Sbjct: 1 EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60
Query: 81 NKEMNDDFRLFCGD 94
EM ++CG
Sbjct: 61 LIEMQG---VYCGG 71
Score = 51.8 bits (124), Expect = 1e-09
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
++ +F GDL +V + L+ F S++PS AK++ D T ++G+GFV F D D RA
Sbjct: 1 EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60
Query: 146 NKEM 149
EM
Sbjct: 61 LIEM 64
>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 = 51.9 bits (125), Expect = 1e-09
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L + + DE L FS + + AKV+ D++ ++KGFGFV F P++ +A EM
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62
Query: 85 N 85
N
Sbjct: 63 N 63
Score = 51.9 bits (125), Expect = 1e-09
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L + + DE L FS + + AKV+ D++ ++KGFGFV F P++ +A EM
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62
Query: 150 N 150
N
Sbjct: 63 N 63
>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 = 51.5 bits (124), Expect = 1e-09
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
+LF G L DVT+E L FS+Y + ++V DK T K +GF FV+F D
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51
Score = 51.5 bits (124), Expect = 1e-09
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+LF G L DVT+E L FS+Y + ++V DK T K +GF FV+F D
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 55.3 bits (132), Expect = 1e-09
Identities = 30/97 (30%), Positives = 48/97 (49%)
Query: 57 DKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLK 116
D TK F F+ + K ++ LF G+L DVT+E L F K+ +
Sbjct: 85 DGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKR 144
Query: 117 AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
++VRD+ T K++GF FV F+ + +A +E+N
Sbjct: 145 VRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE 181
Score = 54.2 bits (129), Expect = 4e-09
Identities = 26/81 (32%), Positives = 42/81 (51%)
Query: 5 RPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 64
S + E + LF G+L DVT+E L F K+ + ++VRD+ T K++
Sbjct: 98 LFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157
Query: 65 GFGFVSFKDPQDFIRANKEMN 85
GF FV F+ + +A +E+N
Sbjct: 158 GFAFVEFESEESAEKAIEELN 178
>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 = 51.2 bits (123), Expect = 2e-09
Identities = 23/63 (36%), Positives = 39/63 (61%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF G+L V DE L F K+ + + A+V+ D+ T +++GFG+V F+ P+D +A +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 84 MND 86
M+
Sbjct: 61 MDG 63
Score = 50.8 bits (122), Expect = 2e-09
Identities = 23/63 (36%), Positives = 39/63 (61%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
LF G+L V DE L F K+ + + A+V+ D+ T +++GFG+V F+ P+D +A +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 149 MNE 151
M+
Sbjct: 61 MDG 63
>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 = 51.2 bits (123), Expect = 2e-09
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF +L ++ L + FSK+ + V DK++ K+KGF +V F DP+D ++A KE
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Query: 84 MNDDFRLFCGDL 95
+ D ++F G L
Sbjct: 64 L--DGKVFQGRL 73
Score = 50.9 bits (122), Expect = 3e-09
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF +L ++ L + FSK+ + V DK++ K+KGF +V F DP+D ++A KE
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Query: 149 MN 150
++
Sbjct: 64 LD 65
>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 = 50.7 bits (122), Expect = 2e-09
Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G+L ++T++ L F + ++ RD T ++KG+GF+ F D +D +A +++
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 150 NEF 152
N F
Sbjct: 61 NGF 63
Score = 49.6 bits (119), Expect = 7e-09
Identities = 18/61 (29%), Positives = 36/61 (59%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L ++T++ L F + ++ RD T ++KG+GF+ F D +D +A +++
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 85 N 85
N
Sbjct: 61 N 61
>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 = 49.5 bits (119), Expect = 8e-09
Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ G+L +VT+E L F ++ A+V+ D+ T +++GFGFV + ++ A ++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 84 MND 86
+N
Sbjct: 61 LNG 63
Score = 48.4 bits (116), Expect = 2e-08
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ G+L +VT+E L F ++ A+V+ D+ T +++GFGFV + ++ A ++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 149 MN 150
+N
Sbjct: 61 LN 62
>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 = 49.1 bits (118), Expect = 9e-09
Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G L D T+E L FSKY + +++D T +++GFGFV+F DP +K +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSS---VDKVL 57
Query: 150 NEFPHL 155
PH+
Sbjct: 58 AAKPHV 63
Score = 46.8 bits (112), Expect = 7e-08
Identities = 22/50 (44%), Positives = 31/50 (62%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
LF G L D T+E L FSKY + +++D T +++GFGFV+F DP
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP 50
>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 = 53.0 bits (127), Expect = 1e-08
Identities = 40/168 (23%), Positives = 70/168 (41%), Gaps = 33/168 (19%)
Query: 18 EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
E E D R +F L + L FSK + ++D+ + ++KG +V F D +
Sbjct: 84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVES 143
Query: 77 FIRA------------------NKEMN--------------DDFRLFCGDLGNDVTDELL 104
I+A E N + +L+ G+L ++T++ L
Sbjct: 144 VIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQEL 203
Query: 105 IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
+ F + ++ RD T ++KGFGF+ F D ++ A + MN F
Sbjct: 204 RQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGF 251
>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 = 48.5 bits (116), Expect = 2e-08
Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G+L D T+E L FSK+ ++VRD + K+KGF FV F+ P+D +A + +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 85 N 85
N
Sbjct: 60 N 60
Score = 48.5 bits (116), Expect = 2e-08
Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G+L D T+E L FSK+ ++VRD + K+KGF FV F+ P+D +A + +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 150 N 150
N
Sbjct: 60 N 60
>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 = 48.4 bits (116), Expect = 2e-08
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF +L T+E L F + + + DK T ++KGF FVSF P+ ++A E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 84 MN 85
++
Sbjct: 61 LD 62
Score = 48.4 bits (116), Expect = 2e-08
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF +L T+E L F + + + DK T ++KGF FVSF P+ ++A E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 149 MN 150
++
Sbjct: 61 LD 62
>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 = 51.9 bits (124), Expect = 2e-08
Identities = 33/119 (27%), Positives = 56/119 (47%), Gaps = 21/119 (17%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQDFIRA----------NKEM--------NDDFR---LF 91
K+VRDK T ++ G+GFV++ P+D +A NK + +D + L+
Sbjct: 34 KLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLY 93
Query: 92 CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L +T L FS + + ++++ D T +KG GF+ F + RA K +N
Sbjct: 94 VSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152
Score = 42.6 bits (100), Expect = 3e-05
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L D + +L + F + + K++RD TN+ KG+GFVS + + A +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 85 N 85
N
Sbjct: 332 N 332
Score = 42.6 bits (100), Expect = 3e-05
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L D + +L + F + + K++RD TN+ KG+GFVS + + A +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 150 N 150
N
Sbjct: 332 N 332
Score = 32.2 bits (73), Expect = 0.10
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ L +T L FS + + ++++ D T +KG GF+ F + RA K +
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151
Query: 85 N 85
N
Sbjct: 152 N 152
>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 = 48.7 bits (116), Expect = 3e-08
Identities = 24/51 (47%), Positives = 34/51 (66%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
+LF G L + T E L R FS+Y + +++DK TN+++GFGFV FKDP
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51
Score = 48.7 bits (116), Expect = 3e-08
Identities = 24/51 (47%), Positives = 34/51 (66%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+LF G L + T E L R FS+Y + +++DK TN+++GFGFV FKDP
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51
>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 = 48.1 bits (115), Expect = 3e-08
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D + +F G L DVT E L FS++ L+ ++ KR N T F F+ F+ Q RA
Sbjct: 2 DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59
Query: 146 NKEMNEFPH 154
+ N
Sbjct: 60 VESENHSML 68
Score = 45.4 bits (108), Expect = 4e-07
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
+ +F G L DVT E L FS++ L+ ++ KR N T F F+ F+ Q RA +
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVE 61
Query: 83 EMN 85
N
Sbjct: 62 SEN 64
>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 = 47.8 bits (114), Expect = 4e-08
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TD+ L FS++ V++D T +++GFGFV+F + +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASE---VDAA 57
Query: 149 MNEFPH 154
MN PH
Sbjct: 58 MNARPH 63
Score = 44.3 bits (105), Expect = 9e-07
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L + TD+ L FS++ V++D T +++GFGFV+F + +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASE---VDAA 57
Query: 84 MND 86
MN
Sbjct: 58 MNA 60
>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 = 47.6 bits (114), Expect = 6e-08
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G L T+E L FS+Y + ++VRD T +KG+ FV ++ +D +RA ++
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 85 N----DDFRLF 91
+ D +F
Sbjct: 66 HKLVIDGSEIF 76
Score = 46.9 bits (112), Expect = 1e-07
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G L T+E L FS+Y + ++VRD T +KG+ FV ++ +D +RA ++
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 150 NE 151
++
Sbjct: 66 HK 67
>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 = 47.2 bits (112), Expect = 8e-08
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G L + TD+ L F ++ V+RD T +++GFGF++FK P+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPK 51
Score = 47.2 bits (112), Expect = 8e-08
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+F G L + TD+ L F ++ V+RD T +++GFGF++FK P+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPK 51
>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 = 46.9 bits (111), Expect = 9e-08
Identities = 26/63 (41%), Positives = 36/63 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L + TD L +TF + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66
Query: 150 NEF 152
N F
Sbjct: 67 NGF 69
Score = 45.4 bits (107), Expect = 4e-07
Identities = 25/61 (40%), Positives = 35/61 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L + TD L +TF + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66
Query: 85 N 85
N
Sbjct: 67 N 67
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 47.6 bits (113), Expect = 9e-08
Identities = 26/52 (50%), Positives = 30/52 (57%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
DF LF +L D T+E L FSK+ S A V DK T + KG GFV FKD
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKD 52
Score = 47.6 bits (113), Expect = 9e-08
Identities = 26/52 (50%), Positives = 30/52 (57%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
DF LF +L D T+E L FSK+ S A V DK T + KG GFV FKD
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKD 52
>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 = 46.4 bits (110), Expect = 1e-07
Identities = 24/63 (38%), Positives = 35/63 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L + D L++ F + + + AKV D+ TN++K FGFVSF +P A + M
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 150 NEF 152
N F
Sbjct: 67 NGF 69
Score = 44.8 bits (106), Expect = 6e-07
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L + D L++ F + + + AKV D+ TN++K FGFVSF +P A + M
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 85 N 85
N
Sbjct: 67 N 67
>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 = 46.2 bits (110), Expect = 2e-07
Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L D + LL + FS + + KV+RD TNK KG+GFV+ + ++ A +
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 150 NEFPH 154
N +
Sbjct: 64 NGYRL 68
Score = 46.2 bits (110), Expect = 2e-07
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+F +L D + LL + FS + + KV+RD TNK KG+GFV+ + ++
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEE 55
>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 = 46.0 bits (109), Expect = 2e-07
Identities = 21/64 (32%), Positives = 30/64 (46%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L VT E L FS A VV D T +++G+GFV+F +D A ++
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 150 NEFP 153
Sbjct: 62 KNKK 65
Score = 45.2 bits (107), Expect = 4e-07
Identities = 21/62 (33%), Positives = 31/62 (50%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L VT E L FS A VV D T +++G+GFV+F +D A ++
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 85 ND 86
+
Sbjct: 62 KN 63
>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 = 45.7 bits (109), Expect = 2e-07
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
F G++ D T+E LI FS+ + ++V D+ T K KG+GF F+D + A + +N
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 86 D 86
Sbjct: 62 G 62
Score = 45.3 bits (108), Expect = 4e-07
Identities = 21/60 (35%), Positives = 34/60 (56%)
Query: 91 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
F G++ D T+E LI FS+ + ++V D+ T K KG+GF F+D + A + +N
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
>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 = 45.8 bits (108), Expect = 2e-07
Identities = 23/62 (37%), Positives = 37/62 (59%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
F +F GDL ++T + + F+ + A+VV+D T K+KG+GFVSF + D A +
Sbjct: 2 FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61
Query: 83 EM 84
+M
Sbjct: 62 QM 63
Score = 45.8 bits (108), Expect = 2e-07
Identities = 23/62 (37%), Positives = 37/62 (59%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
F +F GDL ++T + + F+ + A+VV+D T K+KG+GFVSF + D A +
Sbjct: 2 FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61
Query: 148 EM 149
+M
Sbjct: 62 QM 63
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 46.1 bits (110), Expect = 2e-07
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ GDL + + + F++ K++R+K+T K+ G+GFV F + +A + +
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
Query: 85 N 85
N
Sbjct: 62 N 62
Score = 46.1 bits (110), Expect = 2e-07
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ GDL + + + F++ K++R+K+T K+ G+GFV F + +A + +
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
Query: 150 N 150
N
Sbjct: 62 N 62
>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 = 45.7 bits (109), Expect = 3e-07
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L D T+ L R F +Y + ++VRDK+T K +G+ F+ F+ +D A K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 85 ND 86
+
Sbjct: 64 DG 65
Score = 45.3 bits (108), Expect = 4e-07
Identities = 21/60 (35%), Positives = 32/60 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L D T+ L R F +Y + ++VRDK+T K +G+ F+ F+ +D A K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
>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 = 45.3 bits (108), Expect = 4e-07
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF--IRAN 81
R+F G + D T+E L FS++ S K++ D R +KG+GFV+F+ +D I A
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 82 KEMN 85
+N
Sbjct: 63 GNLN 66
Score = 45.3 bits (108), Expect = 4e-07
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF--IRAN 146
R+F G + D T+E L FS++ S K++ D R +KG+GFV+F+ +D I A
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 147 KEMN 150
+N
Sbjct: 63 GNLN 66
>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 = 44.9 bits (107), Expect = 4e-07
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
L T+ L FS+Y K +VV D++T +++GFGFV F+ +D A + +N
Sbjct: 7 LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63
Score = 44.2 bits (105), Expect = 9e-07
Identities = 20/56 (35%), Positives = 32/56 (57%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L T+ L FS+Y K +VV D++T +++GFGFV F+ +D A + +N
Sbjct: 7 LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62
>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 = 48.1 bits (114), Expect = 5e-07
Identities = 30/161 (18%), Positives = 60/161 (37%), Gaps = 32/161 (19%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G + ++ ++ + R F + + D T K KGF FV ++ P+ A ++
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 84 MNDD--------------------------------FRLFCGDLGNDVTDELLIRTFSKY 111
MN R++ + D+++ + F +
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF 228
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
+K ++ R KG+GF+ + + Q A MN F
Sbjct: 229 GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLF 269
Score = 38.5 bits (89), Expect = 0.001
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
R++ + D+++ + F + +K ++ R KG+GF+ + + Q A
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264
Query: 83 EMNDDFRLFCGDLG 96
MN LF DLG
Sbjct: 265 SMN----LF--DLG 272
>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 = 44.5 bits (106), Expect = 6e-07
Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
F G+L D+ +E L + F ++VRD++T KGFG+V FK
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKD 52
Score = 44.5 bits (106), Expect = 6e-07
Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 91 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
F G+L D+ +E L + F ++VRD++T KGFG+V FK
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKD 52
>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 = 44.7 bits (105), Expect = 7e-07
Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 2 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 55
Score = 44.7 bits (105), Expect = 7e-07
Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 2 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 55
>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 = 44.1 bits (104), Expect = 9e-07
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+LF G L DV + L FS++ KA+V+ DK+T K +GFGFV F++
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50
Score = 44.1 bits (104), Expect = 9e-07
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+LF G L DV + L FS++ KA+V+ DK+T K +GFGFV F++
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50
>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 = 44.3 bits (105), Expect = 1e-06
Identities = 21/58 (36%), Positives = 29/58 (50%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
L +TDE F K+VRDKRT + GFGFV ++ +D RA + +N
Sbjct: 8 LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGL 65
Score = 43.9 bits (104), Expect = 1e-06
Identities = 21/56 (37%), Positives = 29/56 (51%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L +TDE F K+VRDKRT + GFGFV ++ +D RA + +N
Sbjct: 8 LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLN 63
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 24/63 (38%), Positives = 35/63 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L D TDE L FS+ + VV+DK + K +GFG+V+F +D RA +E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 150 NEF 152
+
Sbjct: 62 KKT 64
Score = 43.8 bits (104), Expect = 1e-06
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L D TDE L FS+ + VV+DK + K +GFG+V+F +D RA +E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 85 N 85
Sbjct: 62 K 62
>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 = 43.5 bits (103), Expect = 1e-06
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L DVT+E FS++ + A++++D T +++GFGFV+F
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSES 52
Score = 43.5 bits (103), Expect = 1e-06
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++F G L DVT+E FS++ + A++++D T +++GFGFV+F
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSES 52
>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 = 43.4 bits (103), Expect = 2e-06
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
++ G+L + +T+E L RTFS + + + R K KG+ FV F
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPF------GAIEEVRVFKDKGYAFVRF 43
Score = 43.4 bits (103), Expect = 2e-06
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
++ G+L + +T+E L RTFS + + + R K KG+ FV F
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPF------GAIEEVRVFKDKGYAFVRF 43
>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 = 43.4 bits (103), Expect = 2e-06
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G+L VT+ELL F + + + +D+ T +G+GFV F +D A K M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 85 NDDFRLF 91
N +L+
Sbjct: 61 N-MIKLY 66
Score = 43.0 bits (102), Expect = 2e-06
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G+L VT+ELL F + + + +D+ T +G+GFV F +D A K M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 150 N 150
N
Sbjct: 61 N 61
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 44.6 bits (105), Expect = 2e-06
Identities = 22/62 (35%), Positives = 33/62 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L D L F+ + + AKV+ D+ T +++GFGFV+F D A E
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 84 MN 85
M+
Sbjct: 96 MD 97
Score = 44.6 bits (105), Expect = 2e-06
Identities = 22/62 (35%), Positives = 33/62 (53%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L D L F+ + + AKV+ D+ T +++GFGFV+F D A E
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 149 MN 150
M+
Sbjct: 96 MD 97
>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 = 42.9 bits (101), Expect = 2e-06
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G++ + T+E L FS+ + ++V D+ T K KG+GF +KD + + A + +
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 150 NEF 152
N +
Sbjct: 61 NGY 63
Score = 42.9 bits (101), Expect = 3e-06
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G++ + T+E L FS+ + ++V D+ T K KG+GF +KD + + A + +
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 85 N 85
N
Sbjct: 61 N 61
>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 = 43.1 bits (102), Expect = 3e-06
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSF 71
LF G+L +V ++LL TFS + L+ K++RD T +KGF F+S+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51
Score = 43.1 bits (102), Expect = 3e-06
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSF 136
LF G+L +V ++LL TFS + L+ K++RD T +KGF F+S+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51
>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 = 43.1 bits (101), Expect = 3e-06
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69
Query: 150 NEF 152
N F
Sbjct: 70 NGF 72
Score = 41.6 bits (97), Expect = 1e-05
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69
Query: 85 N 85
N
Sbjct: 70 N 70
>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 = 42.7 bits (101), Expect = 4e-06
Identities = 21/59 (35%), Positives = 31/59 (52%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
L + T E L FSKY + + + R K T KGF F+ F+ P++ +A K +N P
Sbjct: 7 LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNPP 65
Score = 40.4 bits (95), Expect = 2e-05
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
L + T E L FSKY + + + R K T KGF F+ F+ P++ +A K +N+
Sbjct: 7 LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNN 63
>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 = 42.5 bits (100), Expect = 4e-06
Identities = 18/62 (29%), Positives = 35/62 (56%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G L + ++ L + FS++ + +V R K+T +K +GF+ F +P+ A K M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 85 ND 86
N+
Sbjct: 62 NN 63
Score = 41.7 bits (98), Expect = 8e-06
Identities = 18/63 (28%), Positives = 35/63 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G L + ++ L + FS++ + +V R K+T +K +GF+ F +P+ A K M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 150 NEF 152
N +
Sbjct: 62 NNY 64
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 42.7 bits (100), Expect = 4e-06
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +LG D + +L + F + + KV+RD TNK KGFGFV+ + ++ A +
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 150 NEF 152
N +
Sbjct: 64 NGY 66
Score = 42.4 bits (99), Expect = 5e-06
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +LG D + +L + F + + KV+RD TNK KGFGFV+ + ++ A +
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 85 N 85
N
Sbjct: 64 N 64
>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 = 42.5 bits (101), Expect = 4e-06
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
L D ++ L F + + + +DK T +++GF FV+F +D RA +++N F
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
Score = 42.1 bits (100), Expect = 5e-06
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L D ++ L F + + + +DK T +++GF FV+F +D RA +++N
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 24 RLF--CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
RLF CG VT++ L F+ + VV+DK+T ++KG +V F RA
Sbjct: 5 RLFIVCG---KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
Query: 82 KEMND 86
+EMN
Sbjct: 62 EEMNG 66
Score = 41.5 bits (98), Expect = 9e-06
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 89 RLF--CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
RLF CG VT++ L F+ + VV+DK+T ++KG +V F RA
Sbjct: 5 RLFIVCG---KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
Query: 147 KEMN 150
+EMN
Sbjct: 62 EEMN 65
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN----DDFRL 90
TDE L FS++ +V+RDK+T + + F+ F+ +D A +M+ DD R+
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75
Score = 41.5 bits (98), Expect = 9e-06
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
TDE L FS++ +V+RDK+T + + F+ F+ +D A +M+
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66
>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 = 42.2 bits (100), Expect = 6e-06
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 95 LGNDVTDELLIRTFSKYPSF--LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
L T+E +++ S S +++RDK T ++GF FV F +D + +N
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69
Query: 153 PHLFVGD 159
+
Sbjct: 70 DPFVIDG 76
Score = 39.5 bits (93), Expect = 6e-05
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 30 LGNDVTDELLIRTFSKYPSF--LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD 87
L T+E +++ S S +++RDK T ++GF FV F +D + +N+
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69
Query: 88 FRLF 91
Sbjct: 70 DPFV 73
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 41.8 bits (99), Expect = 8e-06
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +LG + T+E L + FS+ P F + K+ KG G V F + +D A + +
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQAL 57
Query: 150 NEF 152
N
Sbjct: 58 NSL 60
Score = 40.3 bits (95), Expect = 3e-05
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +LG + T+E L + FS+ P F + K+ KG G V F + +D A + +
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQAL 57
Query: 85 N 85
N
Sbjct: 58 N 58
>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 = 41.5 bits (97), Expect = 1e-05
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L D T+E L +F + A++V D+ T +KGFGFV F +D A + M
Sbjct: 3 LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 85 ND 86
D
Sbjct: 60 ED 61
Score = 39.6 bits (92), Expect = 5e-05
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L D T+E L +F + A++V D+ T +KGFGFV F +D A + M
Sbjct: 3 LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 150 NE 151
+
Sbjct: 60 ED 61
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 20/61 (32%), Positives = 38/61 (62%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G L ++T+ ++ FS+Y + +VRDK+T K+KGF F++++D + I A +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 85 N 85
N
Sbjct: 72 N 72
Score = 41.5 bits (98), Expect = 1e-05
Identities = 20/61 (32%), Positives = 38/61 (62%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G L ++T+ ++ FS+Y + +VRDK+T K+KGF F++++D + I A +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 150 N 150
N
Sbjct: 72 N 72
>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 = 40.9 bits (96), Expect = 1e-05
Identities = 21/50 (42%), Positives = 29/50 (58%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
+F G L T E L FSK+ + V+RD T +++GFGFV+F DP
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP 50
Score = 40.9 bits (96), Expect = 1e-05
Identities = 21/50 (42%), Positives = 29/50 (58%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+F G L T E L FSK+ + V+RD T +++GFGFV+F DP
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP 50
>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 = 40.9 bits (96), Expect = 2e-05
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T + + FS K++RDK T ++ G+GFV++ DP+D +A +N
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLN 64
Score = 40.9 bits (96), Expect = 2e-05
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T + + FS K++RDK T ++ G+GFV++ DP+D +A +N
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLN 64
>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 = 40.3 bits (95), Expect = 2e-05
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
TDE L + + + K + DK+TNK KG+GFV F P+
Sbjct: 13 TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54
Score = 40.3 bits (95), Expect = 2e-05
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
TDE L + + + K + DK+TNK KG+GFV F P+
Sbjct: 13 TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 21/65 (32%), Positives = 34/65 (52%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+F G++ V+D+ + + K L K V+D T K K FGF F+DP+ +RA +
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61
Query: 149 MNEFP 153
+N
Sbjct: 62 LNGLE 66
Score = 39.9 bits (94), Expect = 4e-05
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+F G++ V+D+ + + K L K V+D T K K FGF F+DP+ +RA
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRA 58
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 40.4 bits (94), Expect = 2e-05
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ +
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE---VDAA 60
Query: 149 MNEFPH 154
MN PH
Sbjct: 61 MNARPH 66
Score = 38.9 bits (90), Expect = 1e-04
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+LF G L + TDE L F ++ + V+RD T +++GFGFV++
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 51
>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 = 40.5 bits (95), Expect = 3e-05
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF +L T+E L + FSKY + + DK T K KGF FV++ P+ ++A E
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 84 MN 85
++
Sbjct: 64 LD 65
Score = 40.5 bits (95), Expect = 3e-05
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF +L T+E L + FSKY + + DK T K KGF FV++ P+ ++A E
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 149 MN 150
++
Sbjct: 64 LD 65
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 40.1 bits (93), Expect = 4e-05
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+LF G L + TD+ L F K+ + V+RD +T +++GFGFV++
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51
Score = 40.1 bits (93), Expect = 4e-05
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+LF G L + TD+ L F K+ + V+RD +T +++GFGFV++
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 39.9 bits (93), Expect = 4e-05
Identities = 21/51 (41%), Positives = 29/51 (56%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G+LG + +E L R F K ++VRD +TN KGF +V FKD
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDEN 52
Score = 39.9 bits (93), Expect = 4e-05
Identities = 21/51 (41%), Positives = 29/51 (56%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+F G+LG + +E L R F K ++VRD +TN KGF +V FKD
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDEN 52
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
T++ L FS + L +V +D +T ++KGFGFV F D +D ++
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57
Score = 39.7 bits (93), Expect = 4e-05
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
T++ L FS + L +V +D +T ++KGFGFV F D +D ++
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57
>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 = 39.5 bits (93), Expect = 4e-05
Identities = 20/63 (31%), Positives = 32/63 (50%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V +++L F + ++ D T K +GF FV F++P+D A M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 150 NEF 152
NE
Sbjct: 61 NES 63
Score = 38.7 bits (91), Expect = 7e-05
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V +++L F + ++ D T K +GF FV F++P+D A M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 85 ND 86
N+
Sbjct: 61 NE 62
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in
the system using SV40 DNA. MSSP-2 is identical with
Scr3, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 75
Score = 39.7 bits (92), Expect = 4e-05
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 53
Score = 39.7 bits (92), Expect = 4e-05
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 53
>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 = 39.9 bits (94), Expect = 4e-05
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK------GFGFVSFKDPQDFI 78
LF +L T+E L + F K + + K+ K G+GFV FK +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAK-KKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 79 RANKEMN 85
+A K +
Sbjct: 62 KALKRLQ 68
Score = 39.9 bits (94), Expect = 4e-05
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK------GFGFVSFKDPQDFI 143
LF +L T+E L + F K + + K+ K G+GFV FK +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAK-KKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 144 RANKEMN 150
+A K +
Sbjct: 62 KALKRLQ 68
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 39.7 bits (92), Expect = 5e-05
Identities = 20/63 (31%), Positives = 33/63 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L D + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 150 NEF 152
N +
Sbjct: 66 NGY 68
Score = 39.3 bits (91), Expect = 7e-05
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L D + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 85 N 85
N
Sbjct: 66 N 66
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 39.8 bits (92), Expect = 5e-05
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
L+ L + TD+ L++ Y + K + DK TNK KG+GFV F P
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59
Score = 39.8 bits (92), Expect = 5e-05
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
L+ L + TD+ L++ Y + K + DK TNK KG+GFV F P
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59
>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 = 39.4 bits (92), Expect = 6e-05
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
LF G+L + T++ L F + + +++ + + K KGF FV F++ +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51
Score = 39.4 bits (92), Expect = 6e-05
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
LF G+L + T++ L F + + +++ + + K KGF FV F++ +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 80
Score = 39.4 bits (91), Expect = 6e-05
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
L+ L TD+ LI+ Y + K + DK TN+ KG+GFV F P
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSP 56
Score = 39.4 bits (91), Expect = 6e-05
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
L+ L TD+ LI+ Y + K + DK TN+ KG+GFV F P
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSP 56
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 39.2 bits (92), Expect = 6e-05
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFP 153
VT E L R F P + RD T K+KGF +V++ +P I A +++N E+P
Sbjct: 11 VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEYP 67
Score = 36.9 bits (86), Expect = 5e-04
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
VT E L R F P + RD T K+KGF +V++ +P I A +++N
Sbjct: 11 VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 2 (Musashi-2 ) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 76
Score = 39.3 bits (91), Expect = 7e-05
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
++F G L + + L FSK+ + V+RD T +++GFGFV+F DP
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51
Score = 39.3 bits (91), Expect = 7e-05
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
++F G L + + L FSK+ + V+RD T +++GFGFV+F DP
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 16/52 (30%), Positives = 32/52 (61%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L + T+E + F K+ + ++ ++ DK+TNK +GF F++F +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52
Score = 38.5 bits (90), Expect = 1e-04
Identities = 16/52 (30%), Positives = 32/52 (61%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++F G L + T+E + F K+ + ++ ++ DK+TNK +GF F++F +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52
>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 = 37.9 bits (89), Expect = 2e-04
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L + ++ L TFS + + L KV D+ +KG+GFV F+ + +RA +++
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63
Query: 85 N 85
N
Sbjct: 64 N 64
Score = 37.9 bits (89), Expect = 2e-04
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L + ++ L TFS + + L KV D+ +KG+GFV F+ + +RA +++
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63
Query: 150 N 150
N
Sbjct: 64 N 64
>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 = 37.9 bits (88), Expect = 2e-04
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R+F G + + L + FS+Y + + K+V D R +KG+GFV+F+ +D + +E
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62
Query: 84 MN 85
N
Sbjct: 63 AN 64
Score = 37.9 bits (88), Expect = 2e-04
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R+F G + + L + FS+Y + + K+V D R +KG+GFV+F+ +D + +E
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62
Query: 149 MN 150
N
Sbjct: 63 AN 64
>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 = 37.7 bits (88), Expect = 2e-04
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
LF G+L VT+E+L F + K+ +D K K F FV+FK
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHE 52
Score = 37.7 bits (88), Expect = 2e-04
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
LF G+L VT+E+L F + K+ +D K K F FV+FK
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHE 52
>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 = 37.6 bits (88), Expect = 2e-04
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
F L V + L FSK +++RD+ + ++KG +V F D + A
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57
Score = 37.6 bits (88), Expect = 2e-04
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 91 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
F L V + L FSK +++RD+ + ++KG +V F D + A
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57
>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 = 37.6 bits (87), Expect = 3e-04
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L +T++ L + F Y + ++ ++RDK T +G FV + ++ A +
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 150 N-EFPH 154
N P
Sbjct: 63 NGTIPP 68
Score = 37.2 bits (86), Expect = 4e-04
Identities = 15/64 (23%), Positives = 31/64 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L +T++ L + F Y + ++ ++RDK T +G FV + ++ A +
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 85 NDDF 88
N
Sbjct: 63 NGTI 66
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+++ G+LG T L F KY V R GF FV F+DP+D A +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55
Query: 84 MNDDFRLFCGD 94
+ D R CG+
Sbjct: 56 L--DGRRICGN 64
Score = 36.4 bits (85), Expect = 5e-04
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+++ G+LG T L F KY V R GF FV F+DP+D A +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55
Query: 149 MN 150
++
Sbjct: 56 LD 57
>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 = 37.7 bits (87), Expect = 3e-04
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
Score = 37.7 bits (87), Expect = 3e-04
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
>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 = 37.3 bits (87), Expect = 3e-04
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G+L V + L FS++ V DK T +KG+GFVSF
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGL---ENA 57
Query: 149 MNEFPHLFVG 158
+ + H+ G
Sbjct: 58 LQKQKHILEG 67
Score = 36.9 bits (86), Expect = 5e-04
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G+L V + L FS++ V DK T +KG+GFVSF A ++
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ GDL + + + R F+ + L K++R+K T G+ FV F D R +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
Query: 84 MN 85
+N
Sbjct: 62 LN 63
Score = 37.7 bits (88), Expect = 3e-04
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ GDL + + + R F+ + L K++R+K T G+ FV F D R +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
Query: 149 MN 150
+N
Sbjct: 62 LN 63
>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 = 37.8 bits (87), Expect = 3e-04
Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L + + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 150 NEF 152
N +
Sbjct: 64 NGY 66
Score = 37.4 bits (86), Expect = 4e-04
Identities = 19/61 (31%), Positives = 32/61 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L + + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 85 N 85
N
Sbjct: 64 N 64
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 37.3 bits (87), Expect = 3e-04
Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
T+ L + FSKY +K +V+DK T K+KG F+ F D +D + K +N+
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNN 65
Score = 36.9 bits (86), Expect = 4e-04
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T+ L + FSKY +K +V+DK T K+KG F+ F D +D + K +N
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALN 64
>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 = 37.3 bits (86), Expect = 3e-04
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D LF G+L V +E+L F + K + +DK K K FGFV FK + A
Sbjct: 1 DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59
Query: 82 KEMN 85
+N
Sbjct: 60 ALLN 63
Score = 37.3 bits (86), Expect = 3e-04
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D LF G+L V +E+L F + K + +DK K K FGFV FK + A
Sbjct: 1 DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59
Query: 147 KEMN 150
+N
Sbjct: 60 ALLN 63
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 37.5 bits (87), Expect = 4e-04
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L +D L R F++Y + V+ D T +++GFGF++F + A++
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADE---ADEA 60
Query: 149 MNEFPH 154
M PH
Sbjct: 61 MEAQPH 66
Score = 36.3 bits (84), Expect = 9e-04
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+LF G L +D L R F++Y + V+ D T +++GFGF++F
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITF 51
>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 = 37.2 bits (87), Expect = 4e-04
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
D T+E L FS++ A++V+DK T +KG FV FK +
Sbjct: 11 DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54
Score = 37.2 bits (87), Expect = 4e-04
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
D T+E L FS++ A++V+DK T +KG FV FK +
Sbjct: 11 DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 15/64 (23%), Positives = 31/64 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L G+L + TDE S + + + +V + T ++KG+GFV + ++A ++
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 150 NEFP 153
+
Sbjct: 62 DGKQ 65
Score = 36.5 bits (85), Expect = 6e-04
Identities = 15/61 (24%), Positives = 31/61 (50%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L G+L + TDE S + + + +V + T ++KG+GFV + ++A ++
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 85 N 85
+
Sbjct: 62 D 62
>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 = 36.8 bits (86), Expect = 4e-04
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 24 RLFCGDLGNDVTDE---LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
++F G L N ++++ L+ +F K +F +V+D T +KG+ F + DP
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAF---NLVKDSATGLSKGYAFCEYLDP 52
Score = 36.8 bits (86), Expect = 4e-04
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 89 RLFCGDLGNDVTDE---LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
++F G L N ++++ L+ +F K +F +V+D T +KG+ F + DP
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAF---NLVKDSATGLSKGYAFCEYLDP 52
>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 = 37.4 bits (86), Expect = 4e-04
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L ++T E L F K+VRDK T ++ G+GFV++ DP+D +A +N
Sbjct: 12 LPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67
Score = 37.4 bits (86), Expect = 4e-04
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L ++T E L F K+VRDK T ++ G+GFV++ DP+D +A +N
Sbjct: 12 LPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 37.4 bits (86), Expect = 4e-04
Identities = 20/63 (31%), Positives = 33/63 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L D + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 150 NEF 152
N +
Sbjct: 66 NGY 68
Score = 37.0 bits (85), Expect = 5e-04
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L D + +L + F + + KV+RD TNK KGFGFV+ + + A +
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 85 N 85
N
Sbjct: 66 N 66
>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 = 36.6 bits (85), Expect = 6e-04
Identities = 15/63 (23%), Positives = 27/63 (42%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G+L D ++ + F +Y ++ D + + KGFG+V F + A +
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 150 NEF 152
Sbjct: 61 GGT 63
Score = 35.0 bits (81), Expect = 0.002
Identities = 15/63 (23%), Positives = 27/63 (42%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G+L D ++ + F +Y ++ D + + KGFG+V F + A +
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 85 NDD 87
Sbjct: 61 GGT 63
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 36.4 bits (85), Expect = 6e-04
Identities = 18/62 (29%), Positives = 34/62 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L T+E + F +Y + + ++RDK T ++KG FV F ++ +A +
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 84 MN 85
++
Sbjct: 61 LH 62
Score = 36.4 bits (85), Expect = 6e-04
Identities = 18/62 (29%), Positives = 34/62 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L T+E + F +Y + + ++RDK T ++KG FV F ++ +A +
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 149 MN 150
++
Sbjct: 61 LH 62
>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 = 36.4 bits (85), Expect = 6e-04
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
RLF G L VT+ L FS++ + ++++ K +GF ++ + +
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA 53
Score = 36.4 bits (85), Expect = 6e-04
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
RLF G L VT+ L FS++ + ++++ K +GF ++ + +
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA 53
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate
RNA-binding protein 7 (RBM7). This subfamily
corresponds to the RRM of RBM7, a ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. RBM7 interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20. It may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM7 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
.
Length = 75
Score = 36.4 bits (84), Expect = 7e-04
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
D LF G+L VT+EL+ F + +K K+ +DK K K F FV+FK
Sbjct: 1 DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFK 50
Score = 36.4 bits (84), Expect = 7e-04
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
D LF G+L VT+EL+ F + +K K+ +DK K K F FV+FK
Sbjct: 1 DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFK 50
>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 = 36.5 bits (84), Expect = 7e-04
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ L +T + L + FS+Y + ++++RD+ T ++G GF+ F + A K +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 85 N 85
N
Sbjct: 63 N 63
Score = 36.5 bits (84), Expect = 7e-04
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ L +T + L + FS+Y + ++++RD+ T ++G GF+ F + A K +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 150 N 150
N
Sbjct: 63 N 63
>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 = 36.2 bits (83), Expect = 0.001
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L VT+E+L ++FS++ +R K K + FV F++ +RA EM
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEERDAAVRAMDEM 55
Query: 85 N 85
N
Sbjct: 56 N 56
Score = 36.2 bits (83), Expect = 0.001
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L VT+E+L ++FS++ +R K K + FV F++ +RA EM
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEERDAAVRAMDEM 55
Query: 150 N 150
N
Sbjct: 56 N 56
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM1 of hnRNP A2/B1 which is an RNA trafficking
response element-binding protein that interacts with
the hnRNP A2 response element (A2RE). Many mRNAs, such
as myelin basic protein (MBP), myelin-associated
oligodendrocytic basic protein (MOBP), carboxyanhydrase
II (CAII), microtubule-associated protein tau, and
amyloid precursor protein (APP) are trafficked by hnRNP
A2/B1. hnRNP A2/B1 also functions as a splicing factor
that regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Moreover, the overexpression of hnRNP A2/B1 has been
described in many cancers. It functions as a nuclear
matrix protein involving in RNA synthesis and the
regulation of cellular migration through alternatively
splicing pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 81
Score = 36.2 bits (83), Expect = 0.001
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+LF G L + T+E L + ++ V+RD + +++GFGFV+F
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51
Score = 36.2 bits (83), Expect = 0.001
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+LF G L + T+E L + ++ V+RD + +++GFGFV+F
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51
>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 = 0.001
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L ++T E F K+VRDK T ++ G+GFV++ DP+D +A +N
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65
Score = 36.2 bits (83), Expect = 0.001
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L ++T E F K+VRDK T ++ G+GFV++ DP+D +A +N
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65
>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 = 38.1 bits (88), Expect = 0.001
Identities = 38/164 (23%), Positives = 71/164 (43%), Gaps = 36/164 (21%)
Query: 17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDP 74
C ++ RLF G + + E ++ FSK + +V +K K GF FV ++
Sbjct: 133 CISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESH 192
Query: 75 Q-----------------------DFIRANKEMNDDFR-----LFCGDLGNDVTDELLIR 106
+ D+ +E+++D L+ +L T+E++ +
Sbjct: 193 RAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEK 252
Query: 107 TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+FS+ F KV +R K + + FV F+D +D ++A E+N
Sbjct: 253 SFSE---FKPGKV---ERVKKIRDYAFVHFEDREDAVKAMDELN 290
Score = 36.5 bits (84), Expect = 0.004
Identities = 30/132 (22%), Positives = 58/132 (43%), Gaps = 19/132 (14%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G + D+ ++ L+ F K + +++ D + + +G+ FV+F ++ A K +
Sbjct: 61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLL 119
Query: 85 N----------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
N D+ RLF G + + E ++ FSK + +V +K
Sbjct: 120 NNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKK 179
Query: 129 K--GFGFVSFKD 138
K GF FV ++
Sbjct: 180 KNRGFAFVEYES 191
>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 = 35.9 bits (83), Expect = 0.001
Identities = 17/48 (35%), Positives = 32/48 (66%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
++F G L + T++ + + FS++ A ++ DK+TN+ +GFGFV+F
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
Score = 35.9 bits (83), Expect = 0.001
Identities = 17/48 (35%), Positives = 32/48 (66%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
++F G L + T++ + + FS++ A ++ DK+TN+ +GFGFV+F
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 35.7 bits (82), Expect = 0.001
Identities = 16/67 (23%), Positives = 36/67 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G + +T++ + F ++ + L+ +++DKRT +G FV + + RA +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60
Query: 84 MNDDFRL 90
+++ L
Sbjct: 61 LHNQRTL 67
Score = 35.3 bits (81), Expect = 0.002
Identities = 15/62 (24%), Positives = 34/62 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G + +T++ + F ++ + L+ +++DKRT +G FV + + RA +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60
Query: 149 MN 150
++
Sbjct: 61 LH 62
>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 = 35.4 bits (81), Expect = 0.002
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 4 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 58
Query: 82 KEMNDDFRLFCG 93
+E+ D R CG
Sbjct: 59 REL--DGRTLCG 68
Score = 32.3 bits (73), Expect = 0.024
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 4 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 58
Query: 147 KEMN 150
+E++
Sbjct: 59 RELD 62
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 35.4 bits (81), Expect = 0.002
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+LF G + D + L F +Y +++ D+++ K +GFGFV+F D
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51
Score = 35.4 bits (81), Expect = 0.002
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+LF G + D + L F +Y +++ D+++ K +GFGFV+F D
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51
>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 = 35.0 bits (80), Expect = 0.002
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L N VT+E+L + F ++ +R K K + F+ F + ++A +EM
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 55
Query: 85 N 85
N
Sbjct: 56 N 56
Score = 35.0 bits (80), Expect = 0.002
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L N VT+E+L + F ++ +R K K + F+ F + ++A +EM
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 55
Query: 150 N 150
N
Sbjct: 56 N 56
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 35.0 bits (80), Expect = 0.002
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ--DFIRAN 81
++F G L D + + L F+K+ + D T +++GFGF+ FKD + +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 82 KEMNDDFRL 90
KE D RL
Sbjct: 61 KEHRLDGRL 69
Score = 33.8 bits (77), Expect = 0.007
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
++F G L D + + L F+K+ + D T +++GFGF+ FKD
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDA 51
>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 = 34.9 bits (81), Expect = 0.002
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
T+ L + FS + + + R K K KGF FV F D +A K +N
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVNG 62
Score = 34.9 bits (81), Expect = 0.003
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T+ L + FS + + + R K K KGF FV F D +A K +N
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVN 61
>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 = 35.1 bits (80), Expect = 0.003
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L ++T + L FS AK++RDK + G+GFV++ + +D RA +N
Sbjct: 9 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLN 64
Score = 35.1 bits (80), Expect = 0.003
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L ++T + L FS AK++RDK + G+GFV++ + +D RA +N
Sbjct: 9 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLN 64
>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 = 34.6 bits (80), Expect = 0.003
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
RLF G+L ND+T+E FSKY V + NK KGFGF+
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGE------VSEVFLNKEKGFGFI 42
Score = 34.6 bits (80), Expect = 0.003
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 134
RLF G+L ND+T+E FSKY V + NK KGFGF+
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGE------VSEVFLNKEKGFGFI 42
>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 = 34.5 bits (80), Expect = 0.003
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L G L +V + L FS Y + + D+ N +G+ +V F+ P+D +A K M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 85 N 85
+
Sbjct: 61 D 61
Score = 34.5 bits (80), Expect = 0.003
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L G L +V + L FS Y + + D+ N +G+ +V F+ P+D +A K M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 150 N 150
+
Sbjct: 61 D 61
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 34.9 bits (81), Expect = 0.003
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 116 KAKVVRDKR------TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF 156
+ K++RD + K+KG+GFV F + + ++A + +N P +F
Sbjct: 38 QVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALNNNPEIF 84
Score = 32.2 bits (74), Expect = 0.031
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 6/41 (14%)
Query: 51 KAKVVRDKR------TNKTKGFGFVSFKDPQDFIRANKEMN 85
+ K++RD + K+KG+GFV F + + ++A + +N
Sbjct: 38 QVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALN 78
>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 = 34.7 bits (79), Expect = 0.004
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
++F G L + E + + F ++ A ++ DK TN+ +GFGFV+F+
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53
Score = 34.7 bits (79), Expect = 0.004
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
++F G L + E + + F ++ A ++ DK TN+ +GFGFV+F+
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53
>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 = 34.3 bits (79), Expect = 0.004
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
D +LF G+L +D+T++ L F ++ + L+ ++ + FGFV F DP+
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56
Score = 32.8 bits (75), Expect = 0.015
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
LF G+L +D+T++ L F ++ + L+ ++ + FGFV F DP+
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56
>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 = 34.3 bits (79), Expect = 0.004
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
T+E L F ++ +V+DK T ++KGFG+V F P
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP 52
Score = 34.3 bits (79), Expect = 0.004
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
T+E L F ++ +V+DK T ++KGFG+V F P
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP 52
>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 = 34.3 bits (78), Expect = 0.005
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L ++T E F K+VRDK T ++ G+GFV++ DP D +A +N
Sbjct: 11 LPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLN 66
Score = 34.3 bits (78), Expect = 0.005
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 95 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L ++T E F K+VRDK T ++ G+GFV++ DP D +A +N
Sbjct: 11 LPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLN 66
>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 = 33.9 bits (78), Expect = 0.005
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
F LF G+L D T E L+ F + +++ DK+T K+KG FV F +
Sbjct: 1 FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEA 54
Score = 33.9 bits (78), Expect = 0.005
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
F LF G+L D T E L+ F + +++ DK+T K+KG FV F +
Sbjct: 1 FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEA 54
>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 = 33.9 bits (78), Expect = 0.005
Identities = 13/44 (29%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
F ++ L +++ ++R +KGFGFV+F + D RA ++++
Sbjct: 21 FGQFGPILDVEIIFNER--GSKGFGFVTFANSADADRAREKLHG 62
Score = 33.5 bits (77), Expect = 0.008
Identities = 13/43 (30%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
F ++ L +++ ++R +KGFGFV+F + D RA ++++
Sbjct: 21 FGQFGPILDVEIIFNER--GSKGFGFVTFANSADADRAREKLH 61
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 33.7 bits (78), Expect = 0.006
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L VT+E L FS Y ++VR+K ++ +GF FV F P+D A K++
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58
Query: 85 ND 86
N
Sbjct: 59 NG 60
Score = 33.3 bits (77), Expect = 0.007
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
L+ +L VT+E L FS Y ++VR+K ++ +GF FV F P+D
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPED 50
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 33.8 bits (77), Expect = 0.006
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L D T+E + F + ++ D +TN+ +GF FV++ D +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52
Score = 33.8 bits (77), Expect = 0.006
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++F G L D T+E + F + ++ D +TN+ +GF FV++ D +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog
of DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 34.0 bits (78), Expect = 0.006
Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 25 LFCGDLGNDVT-DELLIRT-FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+F G G D+ DE IR+ F+KY S + K++ D RT +KG+GFVSF D D
Sbjct: 8 VFVG--GIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVD 58
Score = 34.0 bits (78), Expect = 0.006
Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 90 LFCGDLGNDVT-DELLIRT-FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+F G G D+ DE IR+ F+KY S + K++ D RT +KG+GFVSF D D
Sbjct: 8 VFVG--GIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVD 58
>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 = 33.9 bits (78), Expect = 0.006
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L +VT+ L + FS++ + + V+ D + +GFGF++F+
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED 55
Score = 33.9 bits (78), Expect = 0.006
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++F G L +VT+ L + FS++ + + V+ D + +GFGF++F+
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED 55
>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 = 33.4 bits (77), Expect = 0.007
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
T + L R F KY + RD+ T +++GF FV F D +D
Sbjct: 9 RTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRD 52
Score = 33.4 bits (77), Expect = 0.007
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
T + L R F KY + RD+ T +++GF FV F D +D
Sbjct: 9 RTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRD 52
>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 = 33.7 bits (78), Expect = 0.007
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
FS++ + + ++ R K+T K+KG+ FV F+ P
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
Score = 33.7 bits (78), Expect = 0.007
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
FS++ + + ++ R K+T K+KG+ FV F+ P
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
>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 = 33.5 bits (77), Expect = 0.007
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++VRDK T+K KGF +V F+D + A
Sbjct: 31 RLVRDKETDKFKGFCYVEFEDVESLKEA 58
Score = 33.5 bits (77), Expect = 0.007
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
++VRDK T+K KGF +V F+D + A
Sbjct: 31 RLVRDKETDKFKGFCYVEFEDVESLKEA 58
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 33.1 bits (75), Expect = 0.010
Identities = 12/47 (25%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
++CG + + +T++L+ +TFS + ++ +V + KG+ F+ F
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRF 43
Score = 33.1 bits (75), Expect = 0.010
Identities = 12/47 (25%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
++CG + + +T++L+ +TFS + ++ +V + KG+ F+ F
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRF 43
>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 = 33.0 bits (76), Expect = 0.012
Identities = 16/65 (24%), Positives = 31/65 (47%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
R++ + D++++ + F + + D T K KG+GF+ +++PQ A
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 148 EMNEF 152
MN F
Sbjct: 61 SMNLF 65
Score = 32.2 bits (74), Expect = 0.025
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
R++ + D++++ + F + + D T K KG+GF+ +++PQ A
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 83 EMNDDFRLFCGDLG 96
MN LF DLG
Sbjct: 61 SMN----LF--DLG 68
>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 = 33.1 bits (75), Expect = 0.012
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L + T E + + F ++ A ++ DK TN+ +GFGFV+F+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
Score = 33.1 bits (75), Expect = 0.012
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L + T E + + F ++ A ++ DK TN+ +GFGFV+F+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>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 = 33.0 bits (76), Expect = 0.013
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R+ +L VT++ L F KV+R R K++ FGFV FK +D +A K
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMR-TRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 84 MNDDF 88
N F
Sbjct: 61 FNKTF 65
Score = 31.8 bits (73), Expect = 0.027
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R+ +L VT++ L F KV+R R K++ FGFV FK +D +A K
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMR-TRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 149 MN 150
N
Sbjct: 61 FN 62
>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 = 34.9 bits (80), Expect = 0.013
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 6 PGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 65
T D D R++ G+L + ++ + + +++D T +KG
Sbjct: 280 KNVEKLVNSTTVLDSKD-RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKG 338
Query: 66 FGFVSFKDPQD 76
+ F +KDP
Sbjct: 339 YAFCEYKDPSV 349
Score = 34.5 bits (79), Expect = 0.021
Identities = 11/53 (20%), Positives = 25/53 (47%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
R++ G+L + ++ + + +++D T +KG+ F +KDP
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSV 349
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 32.9 bits (75), Expect = 0.015
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + + F+ + S + V+RD+ +++G FV+F Q + A K
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61
Query: 149 MNE 151
M+
Sbjct: 62 MHH 64
Score = 32.9 bits (75), Expect = 0.016
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L + + F+ + S + V+RD+ +++G FV+F Q + A K
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61
Query: 84 MN 85
M+
Sbjct: 62 MH 63
>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 = 32.6 bits (75), Expect = 0.015
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L T+E L FS+Y + K ++D + FV F++ D ++A +EM
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 85 ND 86
N
Sbjct: 56 NG 57
Score = 31.8 bits (73), Expect = 0.027
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L T+E L FS+Y + K ++D + FV F++ D ++A +EM
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 150 N 150
N
Sbjct: 56 N 56
>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 = 32.5 bits (74), Expect = 0.015
Identities = 19/49 (38%), Positives = 27/49 (55%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+F G L D T + L FSK+ + + D T +++GFGFV FKD
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49
Score = 32.5 bits (74), Expect = 0.015
Identities = 19/49 (38%), Positives = 27/49 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+F G L D T + L FSK+ + + D T +++GFGFV FKD
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49
>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 = 32.5 bits (74), Expect = 0.016
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L VT+++L + F K++ DK NK +GFV + D A + +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 85 N 85
N
Sbjct: 60 N 60
Score = 32.5 bits (74), Expect = 0.016
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G+L VT+++L + F K++ DK NK +GFV + D A + +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 150 N 150
N
Sbjct: 60 N 60
>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 = 32.6 bits (74), Expect = 0.017
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FS+Y VV D+RT +++GF FV F+ D A + N
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHAN 62
Score = 32.6 bits (74), Expect = 0.017
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T+ L FS+Y VV D+RT +++GF FV F+ D A + N
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHAN 62
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 32.7 bits (74), Expect = 0.017
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L D + + L S++ L + D T +++GFGFV FKD
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKD 50
Score = 32.7 bits (74), Expect = 0.017
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L D + + L S++ L + D T +++GFGFV FKD
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKD 50
>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 = 32.2 bits (73), Expect = 0.019
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF G+L D+T++ + F+KY + + NK KGFGF+ + A E
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56
Query: 149 MNEFP 153
+++ P
Sbjct: 57 LDDTP 61
Score = 31.8 bits (72), Expect = 0.032
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF G+L D+T++ + F+KY + + NK KGFGF+ + A E
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56
Query: 84 MND 86
++D
Sbjct: 57 LDD 59
>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 = 32.7 bits (74), Expect = 0.021
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 72
Score = 32.7 bits (74), Expect = 0.021
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 72
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 32.4 bits (74), Expect = 0.022
Identities = 15/72 (20%), Positives = 37/72 (51%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
D++ +LF G + ++ ++ L F ++ + V++DK T KG F+++ + +
Sbjct: 2 DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61
Query: 79 RANKEMNDDFRL 90
+A +++ L
Sbjct: 62 KAQSALHEQKTL 73
Score = 32.0 bits (73), Expect = 0.032
Identities = 15/66 (22%), Positives = 34/66 (51%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D +LF G + ++ ++ L F ++ + V++DK T KG F+++ + ++A
Sbjct: 4 DAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
Query: 146 NKEMNE 151
++E
Sbjct: 64 QSALHE 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 = 32.3 bits (74), Expect = 0.023
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
FSKY + AK+V + R+ + FGFV+
Sbjct: 20 FSKYGKVVGAKIVTNARSPGARCFGFVTMAS 50
Score = 32.3 bits (74), Expect = 0.023
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
FSKY + AK+V + R+ + FGFV+
Sbjct: 20 FSKYGKVVGAKIVTNARSPGARCFGFVTMAS 50
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 32.3 bits (73), Expect = 0.024
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
++CG + + +T++L+ +TFS + ++ +V D KG+ FV F
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRF 43
Score = 32.3 bits (73), Expect = 0.024
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
++CG + + +T++L+ +TFS + ++ +V D KG+ FV F
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRF 43
>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 = 31.9 bits (73), Expect = 0.028
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L VT++LL FS+ K++R+ + + FV + D + A + M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57
Query: 85 N 85
N
Sbjct: 58 N 58
Score = 31.9 bits (73), Expect = 0.028
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G+L VT++LL FS+ K++R+ + + FV + D + A + M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57
Query: 150 N 150
N
Sbjct: 58 N 58
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), in the middle and
an RGG box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 31.9 bits (72), Expect = 0.029
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L D +E + F + ++ D +TNK +GF F++FK+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKE 50
Score = 31.9 bits (72), Expect = 0.029
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L D +E + F + ++ D +TNK +GF F++FK+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKE 50
>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 = 31.4 bits (72), Expect = 0.033
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 24 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
R+F G+L D V+ E L FSKY L + KG+GFV F + +D
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEED 47
Score = 31.4 bits (72), Expect = 0.033
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 89 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
R+F G+L D V+ E L FSKY L + KG+GFV F + +D
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEED 47
>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 = 31.5 bits (71), Expect = 0.037
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G L D T + L FSK+ + + D T +++GFGFV FK+ +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 51
Score = 31.5 bits (71), Expect = 0.037
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+F G L D T + L FSK+ + + D T +++GFGFV FK+ +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 51
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 31.9 bits (72), Expect = 0.037
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G + D + L F KY +V+ D+++ K +GF FV+F D
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDD 51
Score = 31.9 bits (72), Expect = 0.037
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G + D + L F KY +V+ D+++ K +GF FV+F D
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDD 51
>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 = 31.4 bits (72), Expect = 0.041
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
LF +L + T E+L F+++P F + ++V +G FV F+
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFET 47
Score = 31.4 bits (72), Expect = 0.041
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
LF +L + T E+L F+++P F + ++V +G FV F+
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFET 47
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 31.5 bits (71), Expect = 0.045
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G + D + L F +Y +++ D+ + K +GF FV+F D
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51
Score = 31.5 bits (71), Expect = 0.045
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G + D + L F +Y +++ D+ + K +GF FV+F D
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51
>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 = 31.5 bits (71), Expect = 0.048
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
LF ++ +D E L R F +Y + V D T + +GF +V F+D +D
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRD 54
Score = 31.5 bits (71), Expect = 0.048
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
LF ++ +D E L R F +Y + V D T + +GF +V F+D +D
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRD 54
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 31.0 bits (70), Expect = 0.059
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D +LF G+L +DV L F +Y + ++ +R K FGFV F D +
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEP---V 55
Query: 146 NKEMNEFPHLFVGDLK 161
K ++ P +F GD++
Sbjct: 56 QKILSNRPIMFRGDVR 71
Score = 26.8 bits (59), Expect = 2.0
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+LF G+L +DV L F +Y + ++ +R K FGFV F D +
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSE 53
>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 = 30.9 bits (70), Expect = 0.059
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RL+ D ++ + FS Y + + K++ F FV F+ + IRA
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52
Query: 149 MNEFP 153
++
Sbjct: 53 VHGKV 57
Score = 29.3 bits (66), Expect = 0.24
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL+ D ++ + FS Y + + K++ F FV F+ + IRA
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52
Query: 84 MN 85
++
Sbjct: 53 VH 54
>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 = 31.2 bits (71), Expect = 0.060
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G+L +T+E L R F +Y + R R + FV F + RA M
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQ-GNAYAFVKFLNLDMAHRAKVAM 63
Query: 85 N 85
+
Sbjct: 64 S 64
Score = 31.2 bits (71), Expect = 0.060
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G+L +T+E L R F +Y + R R + FV F + RA M
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQ-GNAYAFVKFLNLDMAHRAKVAM 63
Query: 150 N 150
+
Sbjct: 64 S 64
>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 = 30.9 bits (70), Expect = 0.071
Identities = 16/62 (25%), Positives = 32/62 (51%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G + ++ ++ + + FS + + D T K KGF FV ++ P+ A ++
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61
Query: 84 MN 85
MN
Sbjct: 62 MN 63
Score = 30.9 bits (70), Expect = 0.071
Identities = 16/62 (25%), Positives = 32/62 (51%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R++ G + ++ ++ + + FS + + D T K KGF FV ++ P+ A ++
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61
Query: 149 MN 150
MN
Sbjct: 62 MN 63
>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 = 30.8 bits (69), Expect = 0.085
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+ F + A
Sbjct: 2 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
Query: 82 KEMN 85
K +N
Sbjct: 62 KGLN 65
Score = 30.8 bits (69), Expect = 0.085
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+ F + A
Sbjct: 2 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
Query: 147 KEMN 150
K +N
Sbjct: 62 KGLN 65
>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 = 30.8 bits (70), Expect = 0.087
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF L VT E L + F K+ ++V + R+ K KG +V +++ +A +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLK 62
Query: 149 MNE 151
M+
Sbjct: 63 MDG 65
Score = 30.1 bits (68), Expect = 0.12
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF L VT E L + F K+ ++V + R+ K KG +V +++ +A +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLK 62
Query: 84 MN 85
M+
Sbjct: 63 MD 64
>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 = 30.3 bits (69), Expect = 0.089
Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G LG + L R F ++ + +R + + + ++ ++ + A + +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGA------IRRIDYDPGRNYAYIEYESIEAAQAAKEAL 54
Query: 150 NEFP 153
FP
Sbjct: 55 RGFP 58
Score = 28.3 bits (64), Expect = 0.47
Identities = 9/61 (14%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G LG + L R F ++ + +R + + + ++ ++ + A + +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGA------IRRIDYDPGRNYAYIEYESIEAAQAAKEAL 54
Query: 85 N 85
Sbjct: 55 R 55
>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 = 30.5 bits (68), Expect = 0.100
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +D A M
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59
Query: 85 N 85
N
Sbjct: 60 N 60
Score = 30.5 bits (68), Expect = 0.100
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +D A M
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59
Query: 150 N 150
N
Sbjct: 60 N 60
>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 = 30.3 bits (69), Expect = 0.10
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
RL +L DVT+E L F + K K+ D R+ +++G V F+ +D RA K
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIK 59
Query: 83 EMND 86
+ N
Sbjct: 60 QFNG 63
Score = 30.3 bits (69), Expect = 0.12
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
RL +L DVT+E L F + K K+ D R+ +++G V F+ +D RA K
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIK 59
Query: 148 EMN 150
+ N
Sbjct: 60 QFN 62
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 30.4 bits (68), Expect = 0.10
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+++ G+LG L R FS Y + R+ GF FV F+DP+D A +
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 55
Query: 84 MNDDFRLFCG 93
+ D ++ CG
Sbjct: 56 L--DGKVICG 63
Score = 30.0 bits (67), Expect = 0.14
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+++ G+LG L R FS Y + R+ GF FV F+DP+D
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRD 48
>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 = 30.5 bits (68), Expect = 0.11
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+ F + A
Sbjct: 5 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
Query: 82 KEMN 85
K +N
Sbjct: 65 KGLN 68
Score = 30.5 bits (68), Expect = 0.11
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+ F + A
Sbjct: 5 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
Query: 147 KEMN 150
K +N
Sbjct: 65 KGLN 68
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 30.5 bits (69), Expect = 0.12
Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRAN 81
++F G + +++ L F +Y + + V+RD+ N ++KG FV+F + + A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 82 KEMND 86
+++
Sbjct: 63 NALHN 67
Score = 30.1 bits (68), Expect = 0.15
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRAN 146
++F G + +++ L F +Y + + V+RD+ N ++KG FV+F + + A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 147 KEM 149
+
Sbjct: 63 NAL 65
>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 = 30.0 bits (68), Expect = 0.16
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ ++ + + L R F KY + + D T + +GF +V F+D +D A
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY-- 60
Query: 85 NDDFRLFCG 93
D F G
Sbjct: 61 YLDRTRFLG 69
Score = 28.9 bits (65), Expect = 0.42
Identities = 15/61 (24%), Positives = 29/61 (47%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ ++ + + L R F KY + + D T + +GF +V F+D +D A +
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 150 N 150
+
Sbjct: 63 D 63
>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 = 29.8 bits (67), Expect = 0.16
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
RLF G+L D+T+E + + F KY KA + +K KGFGF+
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYG---KAGEI---FIHKDKGFGFI 42
Score = 29.8 bits (67), Expect = 0.16
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 134
RLF G+L D+T+E + + F KY KA + +K KGFGF+
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYG---KAGEI---FIHKDKGFGFI 42
>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 = 29.9 bits (68), Expect = 0.16
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFIRA 80
RL+ G+L + +T+ L++ FSKY K + K G+ FV+F+ ++ +A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 81 NKEMND 86
K +N
Sbjct: 61 LKSLNG 66
Score = 29.6 bits (67), Expect = 0.19
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFIRA 145
RL+ G+L + +T+ L++ FSKY K + K G+ FV+F+ ++ +A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 146 NKEMN 150
K +N
Sbjct: 61 LKSLN 65
>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 = 29.5 bits (66), Expect = 0.18
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G L V ++ + R F Y L+ + G+GFV F+D +D A E
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52
Query: 84 MNDDFRLFCGD 94
+N + CG+
Sbjct: 53 LNG--KDLCGE 61
Score = 29.1 bits (65), Expect = 0.24
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R++ G L V ++ + R F Y L+ + G+GFV F+D +D A E
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52
Query: 149 MN 150
+N
Sbjct: 53 LN 54
>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 = 29.8 bits (68), Expect = 0.18
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 123 KRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
+T K +G FV FKD + A + + FP
Sbjct: 36 SKTLKMRGQAFVVFKDVESATNALRALQGFP 66
Score = 26.0 bits (58), Expect = 4.4
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 58 KRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLF 91
+T K +G FV FKD + A + + F +
Sbjct: 36 SKTLKMRGQAFVVFKDVESATNALRALQ-GFPFY 68
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 29.7 bits (67), Expect = 0.19
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN----KTKGFGFVSFKDPQDFI 78
+ + G+L DVT+E + F L VR R + +GFG+ F+D +
Sbjct: 2 YTAYLGNLPYDVTEEDIKEFFRG----LNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLL 57
Query: 79 RA 80
+A
Sbjct: 58 QA 59
Score = 29.7 bits (67), Expect = 0.19
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN----KTKGFGFVSFKDPQDFI 143
+ + G+L DVT+E + F L VR R + +GFG+ F+D +
Sbjct: 2 YTAYLGNLPYDVTEEDIKEFFRG----LNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLL 57
Query: 144 RA 145
+A
Sbjct: 58 QA 59
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important
role in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 80
Score = 29.6 bits (66), Expect = 0.24
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L + T+E + F ++ ++ D +TNK +GF F++FK+
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE 55
Score = 29.6 bits (66), Expect = 0.24
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L + T+E + F ++ ++ D +TNK +GF F++FK+
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE 55
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 29.7 bits (67), Expect = 0.24
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+++R K T ++GF FV F ++ R
Sbjct: 34 RLMRRKTTGASRGFAFVEFMSLEEATR 60
Score = 29.7 bits (67), Expect = 0.24
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+++R K T ++GF FV F ++ R
Sbjct: 34 RLMRRKTTGASRGFAFVEFMSLEEATR 60
>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 = 0.30
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G L D+ ++ LI K + +++ D N +G+ FV+F + Q+ A K++
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQL 62
Query: 150 NEF 152
N +
Sbjct: 63 NNY 65
Score = 28.8 bits (64), Expect = 0.46
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G L D+ ++ LI K + +++ D N +G+ FV+F + Q+ A K++
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQL 62
Query: 85 ND 86
N+
Sbjct: 63 NN 64
>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 = 29.2 bits (66), Expect = 0.31
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 29 DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+L V++ELL + FS++ +A V+ D R ++ G G V F
Sbjct: 6 NLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEF 47
Score = 29.2 bits (66), Expect = 0.31
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 94 DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+L V++ELL + FS++ +A V+ D R ++ G G V F
Sbjct: 6 NLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEF 47
>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 = 28.7 bits (64), Expect = 0.32
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
RLF G+L D+T+E + F KY + + RD +GFGF+
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFI 42
Score = 28.7 bits (64), Expect = 0.32
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 134
RLF G+L D+T+E + F KY + + RD +GFGF+
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFI 42
>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 = 29.2 bits (66), Expect = 0.32
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVV-----RDKRTNKTKGF-GFVSFKDPQDFI 143
L+ G+L VT+E+L + F ++ K++ ++R N+ GF F++ D + +
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 144 RA--NKEMNEFP 153
K++ +
Sbjct: 64 DELDGKDVMGYE 75
Score = 28.8 bits (65), Expect = 0.40
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF----GFVSFKDPQDFIRA 80
L+ G+L VT+E+L + F ++ K++ RT + + GFV+F + D RA
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMW-PRTEEERRRNRNCGFVAFMNRADAERA 62
Query: 81 NKEMND 86
E++
Sbjct: 63 LDELDG 68
>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 = 28.6 bits (64), Expect = 0.36
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F G++ D + E L F Y + L V+R F FV + RA +E
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEE 53
Query: 84 MN 85
+N
Sbjct: 54 LN 55
Score = 28.6 bits (64), Expect = 0.36
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G++ D + E L F Y + L V+R F FV + RA +E
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEE 53
Query: 149 MN 150
+N
Sbjct: 54 LN 55
>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 = 28.6 bits (64), Expect = 0.41
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
R++ G+L +DV ++ L F KY + + + K F FV F+DP+D
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYG---RIRDIELKNRRGLVPFAFVRFEDPRD 50
Score = 28.6 bits (64), Expect = 0.41
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
R++ G+L +DV ++ L F KY + + + K F FV F+DP+D
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYG---RIRDIELKNRRGLVPFAFVRFEDPRD 50
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a
specific inhibitory effect on oestrogen action, SLTM is
shown to exert a generalized inhibitory effect on gene
expression associated with induction of apoptosis in a
wide range of cell lines. .
Length = 74
Score = 28.9 bits (64), Expect = 0.41
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
F KY L AKVV + R+ K +G V+ + R
Sbjct: 20 FGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVAR 56
Score = 28.9 bits (64), Expect = 0.41
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
F KY L AKVV + R+ K +G V+ + R
Sbjct: 20 FGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVAR 56
>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 = 28.2 bits (64), Expect = 0.44
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 39 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCG 93
L + FS + V + K K GF FV F + +A + +N LF G
Sbjct: 1 LYKLFSPF-----GNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNG--VLFGG 48
Score = 27.5 bits (62), Expect = 0.76
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
L + FS + V + K K GF FV F + +A + +N
Sbjct: 1 LYKLFSPF-----GNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNG 43
>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 = 28.5 bits (63), Expect = 0.45
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
FSKY + AKVV + R+ + +GFV+ ++ +
Sbjct: 22 FSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATK 58
Score = 28.5 bits (63), Expect = 0.45
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
FSKY + AKVV + R+ + +GFV+ ++ +
Sbjct: 22 FSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATK 58
>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 = 28.7 bits (65), Expect = 0.46
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 125 TNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
T KTKG+ FV F P++ A K +N +
Sbjct: 46 TGKTKGYAFVEFATPEEAKEAVKALNGYK 74
Score = 28.7 bits (65), Expect = 0.47
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 60 TNKTKGFGFVSFKDPQDFIRANKEMN 85
T KTKG+ FV F P++ A K +N
Sbjct: 46 TGKTKGYAFVEFATPEEAKEAVKALN 71
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.8 bits (64), Expect = 0.49
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G + DV ++ L+ F + +++ D K +G+ FV + + RA +E+
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVREL 62
Query: 150 NEF 152
N +
Sbjct: 63 NNY 65
Score = 27.2 bits (60), Expect = 1.3
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G + DV ++ L+ F + +++ D K +G+ FV + + RA +E+
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVREL 62
Query: 85 ND 86
N+
Sbjct: 63 NN 64
>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 = 28.4 bits (64), Expect = 0.51
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
++F G L D+T+E L + FS++ + + R F FV+F DP+
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFR-----AFAFVTFADPEV 49
Score = 28.4 bits (64), Expect = 0.51
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
++F G L D+T+E L + FS++ + + R F FV+F DP+
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFR-----AFAFVTFADPEV 49
>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 = 28.1 bits (62), Expect = 0.67
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
V++ELL + FS++ +A V+ D R T G GFV F
Sbjct: 11 VSNELLEQAFSQFGPVERAVVIVDDRGRPT-GKGFVEF 47
Score = 28.1 bits (62), Expect = 0.67
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
V++ELL + FS++ +A V+ D R T G GFV F
Sbjct: 11 VSNELLEQAFSQFGPVERAVVIVDDRGRPT-GKGFVEF 47
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 28.3 bits (64), Expect = 0.69
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 122 DKRTNKTKGFGFVSFKDPQ---DFIRA--NKEMNEFPHLFVGDLK 161
D + G+ F++F +P+ F +A K+ F V D+
Sbjct: 36 DFKNKCNVGYAFINFVNPEYAEKFYKAFNGKKWKNFKSKKVCDIT 80
>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 = 28.3 bits (63), Expect = 0.70
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD---KRTNKT--KGFGFVSFKDPQDFIR 144
LF +L T++ L F F+ A+V KR +T GFGFV FK +
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 145 ANKEMNEF 152
A K M+ F
Sbjct: 63 ALKAMDGF 70
Score = 27.9 bits (62), Expect = 0.85
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD---KRTNKT--KGFGFVSFKDPQDFIR 79
LF +L T++ L F F+ A+V KR +T GFGFV FK +
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 80 ANKEMN 85
A K M+
Sbjct: 63 ALKAMD 68
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 29.7 bits (67), Expect = 0.73
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 120 VRDKRTNKTKGFGFVSFKD--PQDFIRA--NKEMNEFPHLFVGDLKTRSSITLKG 170
VR KR++K F+ D I+A N E N + + L T SS+++ G
Sbjct: 25 VRTKRSSK--KIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTG 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 = 27.7 bits (62), Expect = 0.75
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
++ G+L D E +R F K ++ DK T + KGFG V F D + A K
Sbjct: 1 TVYIGNLAWD-ITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK 58
Score = 27.7 bits (62), Expect = 0.75
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
++ G+L D E +R F K ++ DK T + KGFG V F D + A K
Sbjct: 1 TVYIGNLAWD-ITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK 58
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 86
Score = 28.3 bits (63), Expect = 0.76
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQD 76
++++DK+T + +GF FV +
Sbjct: 35 RLIKDKQTQQNRGFAFVQLSSALE 58
Score = 28.3 bits (63), Expect = 0.76
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQD 141
++++DK+T + +GF FV +
Sbjct: 35 RLIKDKQTQQNRGFAFVQLSSALE 58
>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 = 28.2 bits (63), Expect = 0.78
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 25 LFCGDLGNDVTDELL----IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+F L +D+ L FSKY + + KV+RD R + + FV F + D A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWR---QRPYAFVQFTNDDDAKNA 61
Score = 28.2 bits (63), Expect = 0.78
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 90 LFCGDLGNDVTDELL----IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+F L +D+ L FSKY + + KV+RD R + + FV F + D A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWR---QRPYAFVQFTNDDDAKNA 61
>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 = 27.8 bits (62), Expect = 0.80
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G++ T E L F S + ++ DK + KGF ++ F D ++ +R +
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTALAL 60
Query: 85 NDDFRLFCG 93
++ LF G
Sbjct: 61 DES--LFRG 67
Score = 25.1 bits (55), Expect = 7.4
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G++ T E L F S + ++ DK + KGF ++ F D ++ +R +
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTALAL 60
Query: 150 NEFPHLFVG 158
+E LF G
Sbjct: 61 DE--SLFRG 67
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 28.1 bits (62), Expect = 0.82
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 51 KAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ +++R+K + +++GF FV F QD R
Sbjct: 32 EVRLMRNKSSGQSRGFAFVEFNHLQDATR 60
Score = 28.1 bits (62), Expect = 0.82
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+ +++R+K + +++GF FV F QD R
Sbjct: 32 EVRLMRNKSSGQSRGFAFVEFNHLQDATR 60
>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 = 27.7 bits (62), Expect = 0.88
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G L + + R F Y R + N GFGFV F+DP+D A E
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYG--------RIREINLKNGFGFVEFEDPRDADDAVYE 52
Query: 84 MN 85
+N
Sbjct: 53 LN 54
Score = 27.7 bits (62), Expect = 0.88
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R++ G L + + R F Y R + N GFGFV F+DP+D A E
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYG--------RIREINLKNGFGFVEFEDPRDADDAVYE 52
Query: 149 MN 150
+N
Sbjct: 53 LN 54
>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 = 27.7 bits (61), Expect = 0.92
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
L+ G+L DVT+ L+++ FS+ K++ D N + FV F
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEF 46
Score = 27.7 bits (61), Expect = 0.92
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
L+ G+L DVT+ L+++ FS+ K++ D N + FV F
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEF 46
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 27.6 bits (62), Expect = 0.99
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L VT + L F + + L+A V D ++KGFG V F+ P+D RA +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59
Query: 150 NE 151
N
Sbjct: 60 NG 61
Score = 26.8 bits (60), Expect = 1.6
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L VT + L F + + L+A V D ++KGFG V F+ P+D RA +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59
Query: 85 N 85
N
Sbjct: 60 N 60
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar
proteins. This subfamily corresponds to the RRM1 of
RBM19 and MRD1. RBM19, also termed RNA-binding domain-1
(RBD-1), is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 77
Score = 27.6 bits (62), Expect = 1.0
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
RL +L +T+ L FSK K++R + K++ F+ +K ++
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEE 54
Score = 27.6 bits (62), Expect = 1.0
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
RL +L +T+ L FSK K++R + K++ F+ +K ++
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEE 54
>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 = 27.4 bits (61), Expect = 1.1
Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 9/58 (15%)
Query: 24 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
RLF G+L V+ E L R FS Y + +GFV F P+ A
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQ--------IVLKNAYGFVQFDSPESCANA 50
Score = 27.4 bits (61), Expect = 1.1
Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 9/58 (15%)
Query: 89 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
RLF G+L V+ E L R FS Y + +GFV F P+ A
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQ--------IVLKNAYGFVQFDSPESCANA 50
>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 = 27.6 bits (62), Expect = 1.1
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L ++ E L F KY + + +R T +T+G FV ++D D A +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQ---IRIGNTKETRGTAFVVYEDIYDAKNACDHL 61
Query: 150 NEF 152
+ F
Sbjct: 62 SGF 64
Score = 26.4 bits (59), Expect = 2.9
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L ++ E L F KY + + +R T +T+G FV ++D D A +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQ---IRIGNTKETRGTAFVVYEDIYDAKNACDHL 61
Query: 85 N 85
+
Sbjct: 62 S 62
>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 = 27.2 bits (61), Expect = 1.2
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 34 VTDELLIRTFSKYPSFLKAKV---VRDKRTNKTKGFGFVSFKDPQDFIRA 80
+ ++ L FSK+ ++ +K+ GF FV+FKD A
Sbjct: 12 LDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Score = 27.2 bits (61), Expect = 1.2
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 99 VTDELLIRTFSKYPSFLKAKV---VRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ ++ L FSK+ ++ +K+ GF FV+FKD A
Sbjct: 12 LDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 72
Score = 27.3 bits (61), Expect = 1.2
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L + DV+ L F K K V+ +KG VSF D + I+A K++
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDV-KGIFVKKLL---SKGIVIVSFHDLRQAIKAYKDL 59
Score = 27.3 bits (61), Expect = 1.2
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L + DV+ L F K K V+ +KG VSF D + I+A K++
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDV-KGIFVKKLL---SKGIVIVSFHDLRQAIKAYKDL 59
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 27.6 bits (61), Expect = 1.2
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
D +LF G+L +D+ + L F + + ++ ++ K FGFV F D + R
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
Score = 26.1 bits (57), Expect = 4.7
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+LF G+L +D+ + L F + + ++ ++ K FGFV F D + R
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
>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 = 27.3 bits (60), Expect = 1.3
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
LF ++ + E L R F +Y + V D T + +GF ++ F+D +D
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRD 54
Score = 27.3 bits (60), Expect = 1.3
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
LF ++ + E L R F +Y + V D T + +GF ++ F+D +D
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRD 54
>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 = 27.3 bits (60), Expect = 1.4
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
D L+ L ++ + + + FS+Y + ++++ D+ T ++G GF+ F
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF 50
Score = 27.3 bits (60), Expect = 1.4
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
D L+ L ++ + + + FS+Y + ++++ D+ T ++G GF+ F
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF 50
>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 = 27.1 bits (61), Expect = 1.5
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 12/69 (17%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+E D++ ++ DV +E SK+ KV DK N +G +V FK +
Sbjct: 14 EETEDEWDD---EIKEDVLEEC-----SKFGPVEHIKV--DK--NSPEGVVYVKFKTVEA 61
Query: 142 FIRANKEMN 150
+ + +N
Sbjct: 62 AQKCIQALN 70
Score = 26.4 bits (59), Expect = 3.5
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 11/65 (16%)
Query: 29 DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDF 88
++ DV +E SK+ KV DK N +G +V FK + + + +N
Sbjct: 23 EIKEDVLEEC-----SKFGPVEHIKV--DK--NSPEGVVYVKFKTVEAAQKCIQALNG-- 71
Query: 89 RLFCG 93
R F G
Sbjct: 72 RWFDG 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 = 27.1 bits (61), Expect = 1.6
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDP 74
ED+ ++ ++ DV +E KY L + R + G FV F D
Sbjct: 16 EDDEEYE----EILEDVKEE-----CGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADV 66
Query: 75 QDFIRANKEMNDDFRLFCG 93
+D +A + R F G
Sbjct: 67 EDAQKAQLALAG--RKFDG 83
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM2 of RBM5, also termed protein
G15, or putative tumor suppressor LUCA15, or renal
carcinoma antigen NY-REN-9, a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor. RBM5 shows high sequence
similarity to RNA-binding protein 6 (RBM6 or NY-LU-12
or g16 or DEF-3). Both, RBM5 and RBM6, specifically
bind poly(G) RNA. They contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), two C2H2-type zinc
fingers, a nuclear localization signal, and a
G-patch/D111 domain. .
Length = 86
Score = 27.2 bits (60), Expect = 1.7
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQD 76
++++DK+T + +GF FV +
Sbjct: 35 RLIKDKQTQQNRGFAFVQLSSALE 58
Score = 27.2 bits (60), Expect = 1.7
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQD 141
++++DK+T + +GF FV +
Sbjct: 35 RLIKDKQTQQNRGFAFVQLSSALE 58
>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 = 26.8 bits (59), Expect = 1.8
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN-KTKGFGFVSFKDPQDFIRANKE 83
LF ++ DVT+ L R F Y VR +T ++G V F D +D RA +E
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGD------VRGVQTERISEGIVTVHFYDIRDAKRAVRE 57
Query: 84 M 84
+
Sbjct: 58 L 58
Score = 26.8 bits (59), Expect = 1.8
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN-KTKGFGFVSFKDPQDFIRANKE 148
LF ++ DVT+ L R F Y VR +T ++G V F D +D RA +E
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGD------VRGVQTERISEGIVTVHFYDIRDAKRAVRE 57
Query: 149 M 149
+
Sbjct: 58 L 58
>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 = 26.7 bits (59), Expect = 1.8
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+FCG+ D + R F KY R R + GF FV +D +D A + +
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYG--------RVDRVDMKSGFAFVYMEDERDAEDAIRGL 54
Query: 150 NEFP 153
+ F
Sbjct: 55 DNFE 58
Score = 25.6 bits (56), Expect = 5.9
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+FCG+ D + R F KY R R + GF FV +D +D
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYG--------RVDRVDMKSGFAFVYMEDERD 46
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 87
Score = 27.3 bits (60), Expect = 1.9
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQD 76
+V++DK+T +GF F+ +
Sbjct: 35 RVIKDKQTQLNRGFAFIQLSTIVE 58
Score = 27.3 bits (60), Expect = 1.9
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQD 141
+V++DK+T +GF F+ +
Sbjct: 35 RVIKDKQTQLNRGFAFIQLSTIVE 58
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 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 = 85
Score = 27.0 bits (59), Expect = 2.2
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDPQDFIRAN 81
RLF G + T E ++ FSK L ++ + +K K GF F+ ++D + +A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQAR 63
Query: 82 KEM 84
+ +
Sbjct: 64 RRL 66
Score = 27.0 bits (59), Expect = 2.2
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDPQDFIRAN 146
RLF G + T E ++ FSK L ++ + +K K GF F+ ++D + +A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQAR 63
Query: 147 KEM 149
+ +
Sbjct: 64 RRL 66
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 26.6 bits (59), Expect = 2.2
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
D +LF G L T++ + R F + + + ++R N +KG FV F +
Sbjct: 1 DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFSSHAE 54
Score = 26.6 bits (59), Expect = 2.2
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
D +LF G L T++ + R F + + + ++R N +KG FV F +
Sbjct: 1 DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFSSHAE 54
>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 = 26.8 bits (60), Expect = 2.4
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 25 LFCGDLGNDVTD-ELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
LF L D +L + FS+ P+F + + + + +GF FV + +D A
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN---GQPRGFAFVEYATAEDAEEAQ 61
Query: 82 KEMND 86
+ +N
Sbjct: 62 QALNG 66
Score = 26.5 bits (59), Expect = 3.6
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 90 LFCGDLGNDVTD-ELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
LF L D +L + FS+ P+F + + + + +GF FV + +D A
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN---GQPRGFAFVEYATAEDAEEAQ 61
Query: 147 KEMN 150
+ +N
Sbjct: 62 QALN 65
>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 = 26.4 bits (59), Expect = 2.6
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 28 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
G LGN V+ E L+R F KY + + K + FVS+ +D A +N
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPG------KPYCFVSYSSIEDAAAAYDALNG 61
Score = 26.0 bits (58), Expect = 4.1
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 93 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
G LGN V+ E L+R F KY + + K + FVS+ +D A
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPG------KPYCFVSYSSIEDAAAA 55
>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 = 26.2 bits (58), Expect = 3.1
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 125 TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF 156
T +GFGFV F QD RA K + HL+
Sbjct: 39 TGSHRGFGFVDFITKQDAKRAFKALCHSTHLY 70
>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 = 26.1 bits (57), Expect = 3.1
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R+F G L ++ + R F Y R + + +GFGFV F DP+D A E
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYG--------RIRDIDLKRGFGFVEFDDPRDADDAVYE 52
Query: 84 MN 85
++
Sbjct: 53 LD 54
Score = 26.1 bits (57), Expect = 3.1
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R+F G L ++ + R F Y R + + +GFGFV F DP+D A E
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYG--------RIRDIDLKRGFGFVEFDDPRDADDAVYE 52
Query: 149 MN 150
++
Sbjct: 53 LD 54
>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 = 26.1 bits (58), Expect = 3.3
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 31 GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
G +T+E+L + FS + + + + ++K GFV+F+ + RA E+N
Sbjct: 11 GYGLTEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAELNG 60
Score = 26.1 bits (58), Expect = 3.4
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 96 GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL 155
G +T+E+L + FS + + + + ++K GFV+F+ + RA E+N
Sbjct: 11 GYGLTEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAELNG---T 61
Query: 156 FVGDLKTRSSITLK 169
V ++ + S+ K
Sbjct: 62 TVQGVQLKVSLARK 75
>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 = 26.2 bits (58), Expect = 3.4
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++ G+L ++E L K+ + K+V++ K FV F + I+
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKV 55
Score = 26.2 bits (58), Expect = 3.4
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
++ G+L ++E L K+ + K+V++ K FV F + I+
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKV 55
>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 = 26.1 bits (58), Expect = 3.4
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL +L + ++ L + F + + ++ K K + FGFV +K ++ +A K
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALKH 60
Query: 84 MNDDF 88
N+ F
Sbjct: 61 FNNSF 65
Score = 25.0 bits (55), Expect = 8.1
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RL +L + ++ L + F + + ++ K K + FGFV +K ++ A K
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEE---AQKA 57
Query: 149 MNEFPHLFVGDLK 161
+ F + F+ K
Sbjct: 58 LKHFNNSFIDTSK 70
>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM2 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. It 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 = 85
Score = 26.2 bits (57), Expect = 3.4
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 11/84 (13%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDPQDFIRAN 81
RLF G + + T E ++ FSK L ++ + +K K GF F+ ++D + +A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQAR 63
Query: 82 KEMNDDFRLFCGDL---GNDVTDE 102
+ RL G + GN VT E
Sbjct: 64 R------RLMSGKVKVWGNVVTVE 81
Score = 26.2 bits (57), Expect = 3.6
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDPQDFIRAN 146
RLF G + + T E ++ FSK L ++ + +K K GF F+ ++D + +A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQAR 63
Query: 147 KEM 149
+ +
Sbjct: 64 RRL 66
>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 = 26.2 bits (58), Expect = 3.5
Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF G+L T L F ++ + + K+ + F+ + D ++A ++M
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 85 NDDF 88
+ ++
Sbjct: 62 DGEY 65
Score = 25.8 bits (57), Expect = 3.8
Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF G+L T L F ++ + + K+ + F+ + D ++A ++M
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 150 N 150
+
Sbjct: 62 D 62
>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 = 26.4 bits (58), Expect = 3.7
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 13/60 (21%)
Query: 16 TCEDENDFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
T E+ DF CG + N T + ++ ++ DK T K KG VS++DP
Sbjct: 13 TLEELADFFKHCGVVKINKRTGQPMVNIYT------------DKETGKPKGDATVSYEDP 60
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 27.5 bits (61), Expect = 3.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 141 DFIRANKEMNEFPHLFVGDL 160
+F+RA PHLFVG+L
Sbjct: 143 EFMRAGLYEGWLPHLFVGNL 162
>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 = 25.7 bits (57), Expect = 4.3
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
+L +L V+D+ + F+++ + KA V D R+ ++ G V F+ D ++A K
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMK 59
Query: 148 EMNEFP 153
+ N P
Sbjct: 60 QYNGVP 65
>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 = 25.8 bits (57), Expect = 4.4
Identities = 9/49 (18%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
L+ +L + ++ L Y + +++RD + ++G GF +
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ-SRGVGFARMES 50
Score = 25.8 bits (57), Expect = 4.4
Identities = 9/49 (18%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
L+ +L + ++ L Y + +++RD + ++G GF +
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ-SRGVGFARMES 50
>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 = 25.7 bits (57), Expect = 4.9
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G L VT++ L F + + K+ KG GFV F A +++
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQQL 57
Query: 150 NEFP 153
Sbjct: 58 QGTI 61
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes.
Since the Hu proteins share high homology with the
Drosophila embryonic lethal abnormal vision (ELAV)
protein, the Hu family is sometimes referred to as the
ELAV family. Drosophila ELAV is exclusively expressed
in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress.
Moreover, HuR has an anti-apoptotic function during
early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Hu proteins
perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 79
Score = 25.7 bits (57), Expect = 4.9
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
FS Y + ++++ D T ++G GF+ F + RA K +N
Sbjct: 21 FSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALN 63
Score = 25.7 bits (57), Expect = 4.9
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
FS Y + ++++ D T ++G GF+ F + RA K +N
Sbjct: 21 FSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALN 63
>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 = 25.6 bits (57), Expect = 5.1
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 58 KRTNKTKGFGFVSFKDPQDFIRA----NKEMNDDFRL 90
R NKT+ F +V F P+ A N ++ + ++L
Sbjct: 35 LRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKL 71
>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 = 25.6 bits (56), Expect = 5.3
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G+L + T++ + F +Y L+ ++ K +GFV D A +
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53
Query: 149 MNEF 152
++ +
Sbjct: 54 LHHY 57
Score = 25.2 bits (55), Expect = 7.0
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+LF G+L + T++ + F +Y L+ ++ K +GFV D
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDD 43
>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 = 25.4 bits (56), Expect = 5.7
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
R++ G+L D+ + + F KY K + K + F FV F+DP+D
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYG---PIKAIDLKNRRRGPPFAFVEFEDPRD 50
Score = 25.4 bits (56), Expect = 5.7
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
R++ G+L D+ + + F KY K + K + F FV F+DP+D
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYG---PIKAIDLKNRRRGPPFAFVEFEDPRD 50
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 25.8 bits (56), Expect = 5.7
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+FC L + L FS +++ D+ + ++KG +V F D
Sbjct: 4 VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52
Score = 25.8 bits (56), Expect = 5.7
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+FC L + L FS +++ D+ + ++KG +V F D
Sbjct: 4 VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 25.7 bits (56), Expect = 5.9
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+F G + D+ ++ L+ F K +++ D T +G+ FV+F
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF 50
Score = 25.7 bits (56), Expect = 5.9
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+F G + D+ ++ L+ F K +++ D T +G+ FV+F
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF 50
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 25.7 bits (56), Expect = 5.9
Identities = 10/47 (21%), Positives = 25/47 (53%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+F G + D+ ++ L+ F K +++ D + + +G+ F++F
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF 50
Score = 25.7 bits (56), Expect = 5.9
Identities = 10/47 (21%), Positives = 25/47 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+F G + D+ ++ L+ F K +++ D + + +G+ F++F
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF 50
>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 = 25.7 bits (57), Expect = 6.2
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 18/60 (30%)
Query: 24 RLFCGDLGNDVTDELLIRTFSK----------YPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
RLF G + T E ++ FSK Y S DK NK +GF FV ++
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRS------PDDK--NKNRGFAFVEYES 54
Score = 25.7 bits (57), Expect = 6.2
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 18/60 (30%)
Query: 89 RLFCGDLGNDVTDELLIRTFSK----------YPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
RLF G + T E ++ FSK Y S DK NK +GF FV ++
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRS------PDDK--NKNRGFAFVEYES 54
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 25.4 bits (56), Expect = 6.3
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 91 FCGDLGNDVT-DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
F G L +T EL Y ++ D+ G V+F + Q +I+A E+
Sbjct: 4 FVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAVSEV 63
Query: 150 N-EFPH 154
E P
Sbjct: 64 FVELPF 69
Score = 25.0 bits (55), Expect = 8.2
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 26 FCGDLGNDVT-DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
F G L +T EL Y ++ D+ G V+F + Q +I+A E
Sbjct: 4 FVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAVSE 62
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 77
Score = 25.3 bits (55), Expect = 7.3
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
E L+R F + + +V + T +KG+GFV + RA ++
Sbjct: 17 EELVRPFG---NLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
Score = 25.3 bits (55), Expect = 7.3
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
E L+R F + + +V + T +KG+GFV + RA ++
Sbjct: 17 EELVRPFG---NLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
>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 = 25.3 bits (55), Expect = 7.4
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F +L D T ++L F++ L A + K+KG G V F+ P+ RA +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58
Query: 84 MN 85
MN
Sbjct: 59 MN 60
Score = 25.3 bits (55), Expect = 7.4
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F +L D T ++L F++ L A + K+KG G V F+ P+ RA +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58
Query: 149 MN 150
MN
Sbjct: 59 MN 60
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 25.4 bits (56), Expect = 7.6
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKY-PS--FLKAKVVRDKRTNKTKGFG--FVSFKDPQDFI 143
R++ +L ++E L + P + ++ VR R+ + + G + F P+
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 144 RANKEMNE 151
+ K++N
Sbjct: 61 KVVKDLNG 68
Score = 25.0 bits (55), Expect = 9.5
Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY-PS--FLKAKVVRDKRTNKTKGFG--FVSFKDPQDFI 78
R++ +L ++E L + P + ++ VR R+ + + G + F P+
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 79 RANKEMN 85
+ K++N
Sbjct: 61 KVVKDLN 67
>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 = 25.2 bits (56), Expect = 8.2
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 11/69 (15%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-----TNKTKGFGFVSFKDPQDFIR 144
+F G + D+ ++ L+ P F KA + + R + +G+ FV++ + + R
Sbjct: 4 VFVGKIPRDLFEDELV------PLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQR 57
Query: 145 ANKEMNEFP 153
A K+++ +
Sbjct: 58 AVKQLHNYE 66
>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 = 25.1 bits (55), Expect = 8.5
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL 160
RT +++ F FV ++ +D A +EM+ GD
Sbjct: 35 RTFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDT 71
>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 = 24.9 bits (55), Expect = 8.6
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 57 DKRTNKTKGFGFVSFKDPQ 75
K K+KGF +V F
Sbjct: 35 HKANGKSKGFAYVEFASEA 53
Score = 24.9 bits (55), Expect = 8.6
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 122 DKRTNKTKGFGFVSFKDPQ 140
K K+KGF +V F
Sbjct: 35 HKANGKSKGFAYVEFASEA 53
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 26.2 bits (58), Expect = 8.7
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 56 RDKRTNKTKGFGFVSFKDPQDFIRANKE 83
DK NK F + PQ +A E
Sbjct: 40 TDKSVNKATKKLFEVYPTPQALAQAGLE 67
Score = 26.2 bits (58), Expect = 8.7
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 121 RDKRTNKTKGFGFVSFKDPQDFIRANKE 148
DK NK F + PQ +A E
Sbjct: 40 TDKSVNKATKKLFEVYPTPQALAQAGLE 67
>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 = 25.2 bits (55), Expect = 9.0
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
L + F +Y +A + R KR K GF FV+ K ++ A + N
Sbjct: 16 VKLKKIFGRYGKVREATIPR-KRGGKLCGFAFVTMKKRKNAEIALENTNG 64
>gnl|CDD|132436 TIGR03395, sphingomy, sphingomyelin phosphodiesterase. Members of
this family are bacterial proteins that act as
sphingomyelin phosphodiesterase (EC 3.1.4.12), also
called sphingomyelinase. Some members of this family
have been shown to act as hemolysins [Cellular
processes, Pathogenesis].
Length = 283
Score = 26.3 bits (58), Expect = 9.8
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 71 FKDPQDFIRANKEMNDDFRLFCGDL----GNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 126
+ QDFI + D+ L GDL G++ ++ P ++ D TN
Sbjct: 162 LNEIQDFIDSKNIPKDETVLIGGDLNVNKGSNEYHDMFKTLNVSEPRYVGVPATWDATTN 221
Query: 127 KTKGFGF 133
+ +
Sbjct: 222 SIAKYYY 228
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
0.323 0.141 0.426
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,702,199
Number of extensions: 792243
Number of successful extensions: 1499
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1406
Number of HSP's successfully gapped: 556
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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 (21.9 bits)
S2: 55 (24.9 bits)