RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1185
(131 letters)
>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 = 112 bits (282), Expect = 3e-30
Identities = 40/80 (50%), Positives = 60/80 (75%), Gaps = 1/80 (1%)
Query: 49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
+E VT G+ VI+Y S D KKNRGF F+EY+SH++A++A+++L GR+++WG I V
Sbjct: 157 EEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV 216
Query: 108 DWADPQEEPDTETMSKVLML 127
DWA+P+EE D + M+KV +L
Sbjct: 217 DWAEPEEEVDEDVMAKVKIL 236
Score = 79.3 bits (195), Expect = 2e-18
Identities = 32/54 (59%), Positives = 46/54 (85%), Gaps = 2/54 (3%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
M+KVK+LYVRNL TEE ++++F ++ G+VERVK+I+DYAFVHFEDR++A+
Sbjct: 230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAV 283
>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 = 94.7 bits (236), Expect = 1e-26
Identities = 29/57 (50%), Positives = 44/57 (77%)
Query: 54 VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
G+ VI+Y SPDD KNRGF F+EY+SH++A++A+++L GR+ +WG ++ VDWA
Sbjct: 26 TEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRKLVPGRILLWGHEVAVDWA 82
>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 = 90.8 bits (226), Expect = 2e-25
Identities = 34/50 (68%), Positives = 41/50 (82%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT 53
VKVLYVRNL TEE+L+E F +YG VERVK+IKDYAFVHFE+R +A+
Sbjct: 1 VKVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVK 50
>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 = 83.2 bits (205), Expect = 4e-22
Identities = 36/57 (63%), Positives = 46/57 (80%)
Query: 56 GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
GL VI+Y PDD KKNRGFCFLEY+ HKSA+ A++RL +G++KVWG + V+WADP
Sbjct: 29 GLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADP 85
>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 = 81.7 bits (201), Expect = 2e-21
Identities = 35/57 (61%), Positives = 47/57 (82%)
Query: 56 GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
GL+ VI+Y PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG + V+WADP
Sbjct: 29 GLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVVTVEWADP 85
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 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 = 89
Score = 74.3 bits (182), Expect = 1e-18
Identities = 30/67 (44%), Positives = 49/67 (73%)
Query: 51 AITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
+ G+ VI+Y+S D KNRGF F+EY+SH++A++A+++L GR+++WG I VDWA
Sbjct: 23 SKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA 82
Query: 111 DPQEEPD 117
+P+ + D
Sbjct: 83 EPEIDVD 89
>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM2 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 85
Score = 73.6 bits (180), Expect = 2e-18
Identities = 29/57 (50%), Positives = 44/57 (77%)
Query: 56 GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
G+ VI+Y S D KNRGF F+EY+SH++A++A+++L GR+++WG I VDWA+P
Sbjct: 29 GVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMARRKLLPGRIQLWGHPIAVDWAEP 85
>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM2 of RBM46, also termed
cancer/testis antigen 68 (CT68). It is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 85
Score = 70.4 bits (172), Expect = 3e-17
Identities = 32/68 (47%), Positives = 46/68 (67%), Gaps = 1/68 (1%)
Query: 46 EDRQEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD 104
E +E VT G+ VI+Y S D KNRGF F+EY+SH++A++A+++L G ++WG
Sbjct: 18 EILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHT 77
Query: 105 IIVDWADP 112
I VDWA P
Sbjct: 78 IQVDWACP 85
>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 = 68.1 bits (166), Expect = 2e-16
Identities = 29/49 (59%), Positives = 41/49 (83%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
VKVL+VRNL TEE L+++F ++G++ERVK++KDYAFVHFE+R A+
Sbjct: 1 VKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEERDAAV 49
>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 = 67.7 bits (165), Expect = 3e-16
Identities = 29/49 (59%), Positives = 41/49 (83%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
VKVL+VRNL TEE L++AF Q+G++ERVK++KDYAF+HF++R A+
Sbjct: 1 VKVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKDYAFIHFDERDGAV 49
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 63.5 bits (154), Expect = 2e-14
Identities = 34/69 (49%), Positives = 48/69 (69%), Gaps = 3/69 (4%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFE--QYGRVERVKRIKDYAFVHFEDRQEAI-TVTGL 57
MS VK+LYVRNL TEE +++ F + G VERVK+I+DYAFVHF +R++A+ + L
Sbjct: 5 MSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNAL 64
Query: 58 SQVIIYSSP 66
+ +I SP
Sbjct: 65 NGKVIDGSP 73
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 62.4 bits (151), Expect = 4e-14
Identities = 28/51 (54%), Positives = 39/51 (76%), Gaps = 2/51 (3%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
VK+LYVRNL +E+ +K+ F Q+ G VERVK+I+DYAFVHF R++A+
Sbjct: 1 VKILYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAV 51
>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 = 61.8 bits (151), Expect = 6e-14
Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 28/87 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V NL TEE LK+ F ++G +E ++ +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV----------------------------R 32
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
D+ +++GF F+E++ + A A + L
Sbjct: 33 DETGRSKGFAFVEFEDEEDAEKALEAL 59
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 61.2 bits (148), Expect = 1e-13
Identities = 29/51 (56%), Positives = 39/51 (76%), Gaps = 2/51 (3%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
VKVLYVRNL TEE +K F ++ G VERVK+++DYAFVHF +R++A+
Sbjct: 1 VKVLYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRDYAFVHFFNREDAV 51
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 59.9 bits (146), Expect = 4e-13
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+V NL TEE+L+E F ++G+VE V+ ++D +AFV FE ++A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDA 54
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to
the RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
TRBP-interacting domain. RBM4 is a ubiquitously
expressed splicing factor with two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may also function as a translational
regulator of stress-associated mRNAs as well as play a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RRMs, a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. This family also includes Drosophila
RNA-binding protein lark (Dlark), a homolog of human
RBM4. It plays an important role in embryonic
development and in the circadian regulation of adult
eclosion. Dlark shares high sequence similarity with
RBM4 at the N-terminal region. However, Dlark has three
proline-rich segments instead of three alanine-rich
segments within the C-terminal region. .
Length = 66
Score = 56.1 bits (136), Expect = 8e-12
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+V NL T E+L+ FE+YG V +K+Y FVH E+ ++A
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDA 46
>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 = 55.4 bits (134), Expect = 2e-11
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L+V NL TEE L+E F ++G +E V+ ++D +AFV FE ++A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDA 52
>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 = 50.3 bits (120), Expect = 1e-09
Identities = 20/45 (44%), Positives = 29/45 (64%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+V NL TE++++ FEQYG+V IK+Y FVH +D+ A
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAA 47
>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 = 48.8 bits (117), Expect = 7e-09
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAI 52
L+VRNL TEE+L+E FE +G + V KR K +AFV F + A+
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV 55
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 48.5 bits (115), Expect = 7e-09
Identities = 20/46 (43%), Positives = 31/46 (67%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
L+V N++ CT ++L+ FE+YG V +KDYAFVH E ++A+
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAV 48
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 47.5 bits (113), Expect = 2e-08
Identities = 20/45 (44%), Positives = 32/45 (71%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
++V N++ CT ++L+ FE++GRV ++KDYAFVH E +EA
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEA 47
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 47.0 bits (112), Expect = 2e-08
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
LYVR +E ++E F YG V+ VK I ++AFV FE + AI
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAI 47
>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 = 47.2 bits (113), Expect = 3e-08
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+ +++RNL TEE+LKE F Q+G V+ + +KD AFV F+ ++ A
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 46.8 bits (112), Expect = 3e-08
Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK------RIKDYAFVHFEDRQEA 51
LYVRNL TEE L+E F YG+VE V+ R + +AFV F ++A
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDA 51
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM1 of the majority of family
members that include polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. Rod1 is
a mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. In addition, this family also includes
RNA-binding motif protein 20 (RBM20) that is an
alternative splicing regulator associated with dilated
cardiomyopathy (DCM) and contains only one RRM. .
Length = 74
Score = 46.8 bits (112), Expect = 4e-08
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--AFVHFEDRQEAITVTGLSQ 59
VL++RNL TE L +G+V V ++ A V + + A ++
Sbjct: 1 VLHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYL 56
>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 = 46.4 bits (111), Expect = 6e-08
Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 30/109 (27%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
L +R L TEE + +A ++ V+ I+D +TG S
Sbjct: 3 NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRD-------------KLTGTS---- 45
Query: 63 YSSPDDNKKNRGFCFLEYDSHKSASLAKKRL-ATGRLKVWGCDIIVDWA 110
RGF F+E+ S + A+ L + G + V +A
Sbjct: 46 ----------RGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 46.0 bits (110), Expect = 1e-07
Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 33/105 (31%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NL+ Y TEE++ E F + G ++R+ + GL
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRI-------------------IMGL--------- 32
Query: 67 DDNKKNR--GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDW 109
D GFCF+EY + + A A K L +L I VDW
Sbjct: 33 -DRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLD--DRIIRVDW 74
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 32/107 (29%), Positives = 41/107 (38%), Gaps = 31/107 (28%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
+L V NL T+E+ +E +G VER F ++YS
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPFGAVER-------CF------------------LVYSE 35
Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDII-VDWAD 111
K GF EY S SA AK +L K G + VDWAD
Sbjct: 36 STGESKGYGFV--EYASKASALKAKNQLDG---KQIGGRKLQVDWAD 77
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 29/105 (27%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
L V L+ Y TE L+E F +YG +E+V+ + D++ TG S
Sbjct: 1 CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVY--------DQK-----TGRS------- 40
Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
RGF F+ ++S + A AK+RL + G I VD++
Sbjct: 41 -------RGFGFVYFESVEDAKEAKERLNGMEI--DGRRIRVDYS 76
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV NL TEE LK+ F Q+G V + I D + FV E +EA
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEA 54
>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 = 45.1 bits (107), Expect = 2e-07
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAI-TVTGLSQ 59
+Y+ NL + +EE+L+E E++G ++++K +K+ AFVHF AI VT L
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTLPC 61
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds
to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share
high sequence similarity and are expressed in a wide
variety of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains. This subfamily also
includes a yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1, termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein, which has been identified as
both a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP).
It may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. PUB1 is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it
is one of the major cellular proteins cross-linked by
UV light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there
is no strong evidence implicating PUB1 in the mechanism
of DNA replication. PUB1 contains three RRMs, and a GAR
motif (glycine and arginine rich stretch) that is
located between RRM2 and RRM3. .
Length = 73
Score = 44.9 bits (107), Expect = 2e-07
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEAIT 53
+YV NL TEE+L+ F +G +E RV + K YAFV F+ + A T
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAAT 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 = 44.6 bits (106), Expect = 3e-07
Identities = 30/104 (28%), Positives = 38/104 (36%), Gaps = 30/104 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L VRNL CTE LK+ F +G V V I P
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVT--------------------------IPRKP 35
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
D K +GF F+++ S A K K+ G + VDWA
Sbjct: 36 D--GKKKGFAFVQFTSKADA--EKAIKGVNGKKIKGRPVAVDWA 75
>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 = 44.6 bits (106), Expect = 3e-07
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV NL TE+ L+ FE +G +E V+ +D Y F+ F D ++A
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDA 53
>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 = 44.5 bits (106), Expect = 3e-07
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV---KRIKDYAFVHFEDRQEA 51
+YV NL T+ +L++ FE+YG + V + +AFV FED ++A
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDA 49
>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 = 44.2 bits (105), Expect = 3e-07
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
LYV NL + TE+ L E F Q G ++ K I++ YAFV + D + A
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSA 50
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 44.5 bits (105), Expect = 4e-07
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 10/81 (12%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEAITVTGLSQV 60
KVL++RNL CTEE+L E + +G++ K ++ AFV F D +AI + V
Sbjct: 3 KVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAI-----AMV 57
Query: 61 IIYSSPDDNKKNRG-FCFLEY 80
Y+S + + RG +L+Y
Sbjct: 58 SYYASSSEPAQVRGKTVYLQY 78
>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 = 44.1 bits (105), Expect = 4e-07
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 27/92 (29%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V LT+ ++ LKE F YG V+ V D
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPID--------------------------- 33
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRL 98
+ RG+ ++E++S + A A K + G++
Sbjct: 34 REVNLPRGYAYVEFESPEDAEKAIKHMDGGQI 65
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 44.1 bits (104), Expect = 5e-07
Identities = 34/108 (31%), Positives = 49/108 (45%), Gaps = 31/108 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V L + TE++++E F YGRVE IY
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVED----------------------------IYMMR 33
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADP 112
D+ K++RG F++Y S + A A K L G + GCD +IV +ADP
Sbjct: 34 DEMKQSRGCAFVKYSSKEMAQAAIKAL-NGVYTMRGCDQPLIVRFADP 80
>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 = 44.2 bits (105), Expect = 7e-07
Identities = 28/104 (26%), Positives = 46/104 (44%), Gaps = 29/104 (27%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
L+V L+ TEE L+E F +YG + R++ ++D VTG S
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRD-------------IVTGFS------ 44
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVD 108
+G+ F+EY+ + A A + +L + G +I VD
Sbjct: 45 --------KGYAFVEYEHERDALRAYR--DAHKLVIDGSEIFVD 78
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.2 bits (102), Expect = 1e-06
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHF 45
L++RNL CTEE L++ F +YG + V K+ K +AFV +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>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 = 43.3 bits (103), Expect = 1e-06
Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+YV+NL + +EKLKE F +YG++ K +KD + FV+FE+ + A
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAA 55
>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 = 42.9 bits (102), Expect = 1e-06
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
V+Y+ +L E +L++ F Q+G V R++ + K YAFV FE + A
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 54
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 42.6 bits (101), Expect = 1e-06
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
++V NL T ++E L+E F +YG++ + K Y FV F++ ++A
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDA 48
>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 = 42.2 bits (100), Expect = 2e-06
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAI-TVTGLS 58
LYV+NL +E+L+E F +G + K + D + FV F +EA VT ++
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63
Query: 59 QVIIYSSP 66
II P
Sbjct: 64 GRIIGGKP 71
>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 = 42.1 bits (99), Expect = 3e-06
Identities = 31/104 (29%), Positives = 43/104 (41%), Gaps = 30/104 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NL TE+ LK+ F+ G V+ VK I P
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKII----------------------------P 32
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
D N K + F+EY A +A + L GR ++ +I V+WA
Sbjct: 33 DKNNKGVNYGFVEYHQSHDAEIALQTL-NGR-QIENNEIRVNWA 74
>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 = 42.1 bits (100), Expect = 3e-06
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
L+V L + TEE ++ FE+YG +E V I+D AFV F R+EA
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEA 54
>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 = 41.8 bits (99), Expect = 4e-06
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 9 VRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
V NL++ E+ L+E F +G + RV KD +AFV F R++A
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDA 54
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 43.8 bits (102), Expect = 5e-06
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITV 54
L+V NL TEE L+E F+++G V+RV + + +AFV FE + A
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173
>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 = 41.5 bits (98), Expect = 5e-06
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
K L+V L TE KL+ FE+YG ++R++ ++D YAF+ FE
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEH 52
>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 = 41.2 bits (97), Expect = 6e-06
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAI 52
L+VRNL C E+ L++ F ++G + V + K +A+V F D ++A+
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV 58
>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 = 41.1 bits (97), Expect = 7e-06
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+V + TEE+L++ F ++G V+ VK I D Y FV FE +++A
Sbjct: 6 FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDA 56
>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 = 41.0 bits (97), Expect = 7e-06
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+ V+NL +Y TE++L+E FE G V VK ++ + FV F+ ++A
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDA 54
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 40.8 bits (96), Expect = 9e-06
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITVTGLSQ 59
V++VR L TE L EA ++G + V + K A V FED +A +Q
Sbjct: 4 VVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQ 59
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM4 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 40.9 bits (96), Expect = 9e-06
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 52
+Y+ N+ TEEKL+ F QYG +E V R K+ AFV+F + AI
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAI 53
>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 = 40.7 bits (96), Expect = 1e-05
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQEA 51
+YVRNL E+ L+ F ++G VE ++ K +AFV F+D A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSA 58
>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 = 42.5 bits (100), Expect = 1e-05
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEAI-T 53
++ LYV+NL T+EKL+E F + G + K + + FV F + +EA
Sbjct: 283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRA 342
Query: 54 VTGLSQVIIYSSP 66
VT + ++ P
Sbjct: 343 VTEMHGRMLGGKP 355
Score = 39.8 bits (93), Expect = 1e-04
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
LYV+NL E+KL+E F ++G + +KD +AFV+FE ++A
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDA 232
Score = 35.2 bits (81), Expect = 0.006
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEAI 52
S V ++V+NL + + L + F ++G + K + + Y FVHFE + A
Sbjct: 86 SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAK 143
Score = 31.3 bits (71), Expect = 0.13
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV +L TE KL + F+ +G V V+ +D Y +V+F++ +A
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADA 55
>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 = 40.0 bits (94), Expect = 2e-05
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
L+V NL TEE+ KE F +YG V V + K + F+ + R A
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNA 50
>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 = 39.8 bits (93), Expect = 2e-05
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
++V N+ + ++E+L+ FE YG V ++ +AFVH A
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAA 47
>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 = 39.4 bits (93), Expect = 2e-05
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 21 LKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAIT-VTGLSQVIIY 63
L + F +G VE++K +K +AFV F + A V L+ V+
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFG 47
>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 = 39.9 bits (94), Expect = 2e-05
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+V L+ TE++L+ F ++GRVE V +KD + FV FE ++A
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDA 56
>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 = 39.5 bits (93), Expect = 2e-05
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V L + T++ L++ F Q+G +E I D Y FV F+D++ A
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESA 55
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in
vertebrate. It has been reported to be involved in
pre-splicesome assembly and to interact with the
Ca2+-signaling protein ALG-2. It also plays an
important role in embryogenesis. RBM22 contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a zinc finger of the unusual type
C-x8-C-x5-C-x3-H, and a C-terminus that is unusually
rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 39.6 bits (93), Expect = 2e-05
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
+ LYV L + TE+ L++ F Q+G + + + + AFV F R+ A
Sbjct: 1 ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAA 50
>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 = 39.1 bits (92), Expect = 3e-05
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQY-GRVE-RVKRIKDYAFVHFED 47
K+L+++NL + T+E L+ F Q+ G E R+ + AFV FE
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFET 47
>gnl|CDD|240937 cd12493, RRM2_DND1, RNA recognition motif 2 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM2 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4. It is an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. Moreover, DND1 interacts
specifically with apolipoprotein B editing complex 3
(APOBEC3), a multi-functional protein inhibiting
retroviral replication. The DND1-APOBEC3 interaction may
play a role in maintaining viability of germ cells and
for preventing germ cell tumor development. DND1
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 83
Score = 39.0 bits (91), Expect = 5e-05
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 56 GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
G+ V+++ SP K ++Y SH++A++AKK L G ++G + V+W P
Sbjct: 29 GVEDVLLHPSP--GKGKGVVALVKYSSHRAAAMAKKALVEGFRNLYGISVTVEWLKP 83
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 38.9 bits (91), Expect = 5e-05
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
L++ +L++ TEE LK FE+YG ++ + I + A+V E RQ+A
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDA 51
>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 = 39.1 bits (92), Expect = 5e-05
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 18/83 (21%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEAITVTGLSQVIIY 63
L +RNL + E+KLKE F + K +IK + R
Sbjct: 3 LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKR--------------- 47
Query: 64 SSPDDNKKNRGFCFLEYDSHKSA 86
P+ K++G+ F+E+ +H+ A
Sbjct: 48 VDPNGKGKSKGYGFVEFTNHEHA 70
>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 = 38.4 bits (90), Expect = 6e-05
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY---AFVHFEDRQEAITVTGLSQVI 61
++V LT+ TEE L++ F Q+G V V K + AFV F D + A ++ G +I
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCGEDHII 60
>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 = 38.5 bits (90), Expect = 7e-05
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEA 51
L+V L T+E+L++ F+++G V+ V+ + K A+V +E+ A
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSA 56
>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 = 38.4 bits (90), Expect = 7e-05
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
L V+NL+ + + E L++AF Q+G VER I D
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD 34
>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 = 38.0 bits (89), Expect = 8e-05
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 13/71 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAITVT 55
+YV NL + TEE L E F Q G V V KD Y FV F ED AI +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI- 59
Query: 56 GLSQVIIYSSP 66
++ + +Y P
Sbjct: 60 -MNMIKLYGKP 69
>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 = 38.4 bits (90), Expect = 8e-05
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
VL+V L T+E L+ F ++G+++ + I+D YAF+ FE +++
Sbjct: 5 VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDC 58
>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 = 38.5 bits (90), Expect = 8e-05
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
LYVRN+ + L+ F +YG + V +R + +A+V FED ++A
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDA 55
>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 = 38.0 bits (89), Expect = 9e-05
Identities = 11/48 (22%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 52
L+V L + + +L+ F+++G + R+ ++YA++ +E + A
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQ 48
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 37.8 bits (88), Expect = 1e-04
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+V EE +++ FE +G + R K +AFV FED ++A
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDA 47
>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 = 38.0 bits (89), Expect = 1e-04
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----------RIKDYAFVHFEDRQEA 51
LYV NL TEE L + F ++G + VK R ++ FV F +R +A
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADA 59
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract
binding protein ) and hnRNP-L. These proteins contain
four RNA recognition motifs (rrm: pfam00067).
Length = 481
Score = 39.8 bits (93), Expect = 1e-04
Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT-VTGLSQVI 61
V++VRNL Q E L EA +G V V + K A V FED + A V + V
Sbjct: 3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVP 62
Query: 62 IY 63
IY
Sbjct: 63 IY 64
Score = 28.6 bits (64), Expect = 0.99
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 6 VLYVRNLTQ-YCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
VL V L Q ++L F YG VERVK K+ A + D +A
Sbjct: 277 VLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQA 326
Score = 28.2 bits (63), Expect = 1.3
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 10/61 (16%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY---------AFVHFEDRQEAITVTG 56
L++ N+ +EE LKE F + G V +VK+ K + + +E ++A+
Sbjct: 396 TLHLSNIPLSVSEEDLKELFAENG-VHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALI 454
Query: 57 L 57
Sbjct: 455 A 455
>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 = 38.0 bits (88), Expect = 1e-04
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 9/64 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
LYV NL + TE++L++ FE YG + + ++D AFV ++ R+EA ++ L
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 58 SQVI 61
+ I
Sbjct: 63 NGTI 66
>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 = 37.2 bits (87), Expect = 1e-04
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA-ITVTGL 57
+Y+R L T+E L++ + +G++ K I K Y FV F+ + A + GL
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62
>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 = 37.3 bits (87), Expect = 2e-04
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFED 47
L+V NL TEE L E F Q G +E VK + K +AFV F+
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKH 51
>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 = 37.3 bits (87), Expect = 2e-04
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 25/87 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NLT + T+E L+ A + G V+ +K F FE +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVD----VKSIKF--FEHKA----------------- 37
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
N K++GF ++E+ S +A+ K++L
Sbjct: 38 --NGKSKGFAYVEFASEAAAAAVKEKL 62
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 11/58 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAIT 53
L+VRNL T+E+L+E F + G ++R +KD + +V F ED + A+
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ +L + E + AF + G V VK I++ Y FV F + A
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAA 54
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 75
Score = 37.0 bits (86), Expect = 2e-04
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY-------AFVHFEDRQEA 51
L+V NL + EE++ E F++YGRVE VK + AFV F D + A
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSA 53
>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 = 36.7 bits (85), Expect = 3e-04
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+ ++ N + +++ F +YGRV+RV +AFV+ ED ++A
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDA 47
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 36.8 bits (86), Expect = 3e-04
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
V+ V+NL TEE+L+E FE++G + R+ + A V F + +A
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDA 49
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 36.9 bits (86), Expect = 3e-04
Identities = 24/80 (30%), Positives = 32/80 (40%), Gaps = 27/80 (33%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V L + TEE L+E F QYG VE V+ + D TG
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE-------------TG---------- 38
Query: 67 DDNKKNRGFCFLEYDSHKSA 86
K RGF F+ +D +
Sbjct: 39 ----KKRGFAFVTFDDYDPV 54
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
L V+NL + E+KL++ FE +G + V+ + + + FV ++ +EA
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEA 54
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to
the RRM domain in the G3BP family of RNA-binding and
SH3 domain-binding proteins. G3BP acts at the level of
RNA metabolism in response to cell signaling, possibly
as RNA transcript stabilizing factors or an RNase.
Members include G3BP1, G3BP2 and similar proteins.
These proteins associate directly with the SH3 domain
of GTPase-activating protein (GAP), which functions as
an inhibitor of Ras. They all contain an N-terminal
nuclear transfer factor 2 (NTF2)-like domain, an acidic
domain, a domain containing PXXP motif(s), an RNA
recognition motif (RRM), and an Arg-Gly-rich region
(RGG-rich region, or arginine methylation motif).
Length = 81
Score = 37.0 bits (86), Expect = 3e-04
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFED 47
L+V NL TE++LKE F+++G V V R+ ++ FV F+D
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 27/83 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+YV ++ +E+ +K FE +G+++ D TG
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPD-------------PETG---------- 39
Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
K++G+ F+EY++ +SA A
Sbjct: 40 ----KHKGYGFIEYENPQSAQDA 58
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 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. 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). Moreover, 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. 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 = 80
Score = 36.6 bits (84), Expect = 3e-04
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
L VRNL+ Y + E L+EAF Q+G VER I D
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVD 34
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal Rrp7 domain. .
Length = 102
Score = 36.9 bits (86), Expect = 3e-04
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV 34
+ L+V N+ YCTEE LK F + G+VE V
Sbjct: 1 RTLFVLNVPPYCTEESLKRLFSRCGKVESV 30
>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 = 36.4 bits (84), Expect = 4e-04
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ L+ E+ L++ F +YG++ V +KD + FV FE+ +A
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDA 55
>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 = 36.5 bits (85), Expect = 4e-04
Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 26/104 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L++ NL TE L + F +YG++++ + + S
Sbjct: 2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFL------------------------FHKSG 37
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
+ RG+CF+ +++ + A A K L G+ G ++V WA
Sbjct: 38 PLKGQPRGYCFVTFETKEEAEKALKSL-NGKT-ALGKKLVVRWA 79
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 36.5 bits (84), Expect = 4e-04
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
L V+NL Q+ + E L+EAF +G+VER I D
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVD 34
>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 = 36.1 bits (84), Expect = 4e-04
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
L V NLT T + L+ FE+YG V V + + +AFV F D+++A
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDA 53
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 36.1 bits (84), Expect = 5e-04
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITVTGLSQ 59
++V NL E++L++ F + G + V+ +K+ YA+V FE+ + L +
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDR 61
Query: 60 VIIYSSP 66
+I P
Sbjct: 62 ELIKGRP 68
>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 = 36.0 bits (84), Expect = 5e-04
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV +L TE L E F G V ++ +D YA+V+F++ +A
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADA 54
>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 = 36.2 bits (84), Expect = 5e-04
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L Q T+++++ F G +E K I+D Y FV++ D ++A
Sbjct: 4 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDA 56
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 36.0 bits (84), Expect = 5e-04
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEA 51
L VRN+ + KL E F ++G + +V + A V F +EA
Sbjct: 4 LEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEA 51
>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 = 36.1 bits (84), Expect = 6e-04
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 17 TEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNK 70
+ E+L FE+YG VE + K Y FV + ++A P NK
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNK 71
>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 = 38.1 bits (88), Expect = 6e-04
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 9/64 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
LYV NL + T+++L F +YG++ + ++D AFV F R+EA ++ L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255
Query: 58 SQVI 61
+ VI
Sbjct: 256 NNVI 259
>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 = 36.2 bits (84), Expect = 6e-04
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
++V L+ T+E+L E F ++G++ V IK +AF+ FE Q A
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAA 56
>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 = 35.8 bits (83), Expect = 7e-04
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V +L+ E L+ AF +G + + +KD Y FV F +++A
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDA 54
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 37.6 bits (87), Expect = 7e-04
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAI 52
LYV NL TE++L++ FE +G +E V+ R K + F+ F D +EA
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242
Score = 28.3 bits (63), Expect = 1.3
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR---QEAITVT 55
++V L E L E F + G+V V+ IKD A+V F D +A+ +T
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151
Query: 56 G--LSQVIIYSSPDDNKKNR 73
G L I +KNR
Sbjct: 152 GQMLLGRPIIVQSSQAEKNR 171
>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 = 35.5 bits (82), Expect = 8e-04
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITVTG 56
V+Y+ +L E++LK+ F Q+G V+ V+ K Y F+ F + + A
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK 59
>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 = 35.2 bits (82), Expect = 8e-04
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+V NL EE+L++ FE G VE V+ ++D + +V F+ +
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSV 54
>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 = 35.8 bits (82), Expect = 8e-04
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
L V L+ Y TE L+E F +YG + V +R + +AFV+FE+ +A
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64
>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 = 35.4 bits (82), Expect = 9e-04
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITV 54
+YV L + T E LK F +YG V V IK +AF+ FE +EA
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
Score = 30.0 bits (68), Expect = 0.093
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 68 DNKKNRGFCFLEYDSHKSASLAKKRLA 94
+GF F+E+++ + A A K L
Sbjct: 36 HTGDIKGFAFIEFETPEEAQKACKHLN 62
>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 = 35.7 bits (83), Expect = 0.001
Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 22/89 (24%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
L+V+NL TEE LK+ FE+ G V V K
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKD----------------------P 38
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
+ G+ F+E+ S ++A A KRL
Sbjct: 39 KGPGKLLSMGYGFVEFKSKEAAQKALKRL 67
>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 = 35.3 bits (82), Expect = 0.001
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYG-----RVERVKRIKDYAFVHFEDRQEA 51
++LYVRNL + E+L + F +YG R+ K + AFV +ED +A
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDA 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 = 35.5 bits (82), Expect = 0.001
Identities = 23/49 (46%), Positives = 28/49 (57%), Gaps = 9/49 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK--------DYAFVHFED 47
L+V NL TEE+L+ AFE+YG VE V IK YAFV F +
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVD-IKRPPRGQGNAYAFVKFLN 52
>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 = 35.4 bits (82), Expect = 0.001
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L Q T+E+L+ FE G +E K ++D Y FV + D +A
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDA 55
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins from plants. This
subgroup corresponds to the RRM2 in a family that
represents a novel group of arginine/serine (RS) or
serine/arginine (SR) splicing factors existing in
plants, such as A. thaliana RSp31, RSp35, RSp41 and
similar proteins. Like vertebrate RS splicing factors,
these proteins function as plant splicing factors and
play crucial roles in constitutive and alternative
splicing in plants. They all contain two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
at their N-terminus, and an RS domain at their
C-terminus.
Length = 70
Score = 34.8 bits (80), Expect = 0.001
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 7 LYVRNLTQYCTEEK-LKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+V N T + L+ FE YG++ V+ +++AFV +E +++A
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQEDA 47
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 34.9 bits (81), Expect = 0.001
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
L VRN+ T+++L+E F +G+V+ V+ + +AFV F +QEA
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEA 54
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 35.1 bits (81), Expect = 0.001
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 5 KVLYVRNLTQYCTE-EKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
+ +N+ + + L+ F ++G+V RV K A VHF D A
Sbjct: 1 TTIQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASA 50
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are highly conserved
proteins that bind to the poly(A) tail present at the
3' ends of most eukaryotic mRNAs. They have been
implicated in the regulation of poly(A) tail length
during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 35.0 bits (81), Expect = 0.001
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
+V N+ T E+L+E F+ G + R+ + D +A++ F D
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLD 50
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 34.9 bits (80), Expect = 0.001
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRV---ERVKRIKDYAFVHF---EDRQEAI 52
KVL V NL+ +E+ L+E FE+ + + R K YAFV F ED +EA+
Sbjct: 2 KVLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 34.9 bits (81), Expect = 0.002
Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEA 51
+++V + + EE + + F ++G ++ R +K YA + +E ++EA
Sbjct: 8 IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEA 61
>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 = 34.6 bits (80), Expect = 0.002
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEA 51
++V L TE++L+ F +G + VK I K FV F R A
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAA 50
>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 = 34.9 bits (81), Expect = 0.002
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
++V +L T+E L AF +Y ++ K ++D Y FV F D
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57
>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 = 34.6 bits (80), Expect = 0.002
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+YV NL T L + F +YG+V +V +KD AF+ F DR++A
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDA 56
>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 = 34.6 bits (80), Expect = 0.002
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 27/83 (32%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
+ K ++V L TE L++ F Q+G V V V++
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEV-------------------------VVM 35
Query: 63 YSSPDDNKKNRGFCFLEYDSHKS 85
Y + K+ RGF F+ ++S S
Sbjct: 36 YDH--EKKRPRGFGFITFESEDS 56
>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 = 34.5 bits (80), Expect = 0.002
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
LYV L + E+ L AF +G ++ ++ DY AFV FE+ ++A
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDA 53
>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 = 34.3 bits (79), Expect = 0.002
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
+YV NL E +++ F +YG ++ + +K+ +AFV FED ++A
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAID-LKNRRRGPPFAFVEFEDPRDA 51
>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 = 34.3 bits (79), Expect = 0.002
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
L+V NL+ TE++L+ F + GR+ RV+ + K +AFV FE+ + A
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFA 53
>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 = 34.6 bits (79), Expect = 0.002
Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 32/109 (29%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K L+V+ L++ TEE LKE+F+ V DR
Sbjct: 1 KTLFVKGLSEDTTEETLKESFDGSIAARIVT-----------DR---------------- 33
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
D ++GF F+++ S + A AK+ + G + G + +D+A P+
Sbjct: 34 ---DTGSSKGFGFVDFSSEEDAKAAKEAMEDGEID--GNKVTLDFAKPK 77
>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 = 34.5 bits (79), Expect = 0.002
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 9/64 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
LYV L + T+++L++ F QYGR+ + ++D F+ F+ R EA + GL
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 58 SQVI 61
+
Sbjct: 63 NGQK 66
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 34.6 bits (80), Expect = 0.003
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVE------RVKRIKDYAFVHFEDRQEAITV 54
+V+YV + T +L++ F+ +G +E R Y FV + +A
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN-YGFVTYRYACDAFRA 57
>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 = 33.8 bits (78), Expect = 0.003
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+Y+ L E ++ F+ YGR+ + + FV FED ++A
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDA 46
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 34.0 bits (78), Expect = 0.003
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 33/82 (40%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPD 67
YV N+ Y T+ L F+ +G E R +
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGY-------------ILEFRHQP---------------- 34
Query: 68 DNKKNRGFCFLEYDSHKSASLA 89
+RGF F++ D+H+ A++A
Sbjct: 35 ----DRGFAFVKLDTHEQAAMA 52
>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 = 34.2 bits (78), Expect = 0.003
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 31/104 (29%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NL++ TE + + F Q G + K I D A
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTA------------------------- 36
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
N +CF+E+ H+ A+ + + GR K+ G ++ V+WA
Sbjct: 37 ----GNDPYCFVEFFEHRHAAASLAAM-NGR-KIMGKEVKVNWA 74
>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage
factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar
proteins. This subgroup corresponds to the RRM of
CFIm68. 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. The family includes CFIm68,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF6), or cleavage and
polyadenylation specificity factor 68 kDa subunit
(CPSF68), or protein HPBRII-4/7. CFIm68 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. The N-terminal RRM of CFIm68 mediates the
interaction with CFIm25. It also serves to enhance RNA
binding and facilitate RNA looping. .
Length = 77
Score = 33.9 bits (78), Expect = 0.004
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 25/89 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NLT + T++ L EA + G V + + F FE+R
Sbjct: 2 LYVGNLTWWTTDQDLTEAIQSIG----VNDLLEIKF--FENRA----------------- 38
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLAT 95
N +++GF + S S+ +L
Sbjct: 39 --NGQSKGFALIVLGSESSSRKLMDKLPK 65
>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 = 33.9 bits (78), Expect = 0.004
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
L+V NL+ +E LK FE++G V + R + + +V FE ++A
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDA 54
>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 = 34.1 bits (78), Expect = 0.004
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+VRNL TEE L F ++G V + D FV F+D+
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY 56
>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 = 33.8 bits (78), Expect = 0.004
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI 52
+V N+ TEE+L E F + G V + + D Y F FED + A
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAA 54
>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 = 33.4 bits (77), Expect = 0.005
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQE 50
L+V NL ++LKE F Q+G+V+ K Y FV F R
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDG 53
>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 = 33.7 bits (77), Expect = 0.005
Identities = 20/107 (18%), Positives = 39/107 (36%), Gaps = 29/107 (27%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+VRNL T+E L + F ++ + D
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTD--------------------------- 34
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
+ ++RG+ F+ + + A A +L +L G + +D A+ +
Sbjct: 35 PETGESRGYGFVTFAMLEDAQEALAKLKNKKLH--GRILRLDIAERR 79
>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 = 33.7 bits (78), Expect = 0.005
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 62 IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
IY D+ K +G+ F+E+ + + A A K L
Sbjct: 39 IYMPVDETGKTKGYAFVEFATPEEAKEAVKAL 70
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 33.5 bits (77), Expect = 0.005
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITVTGLS 58
+V + +E+ LKE F G V RV+ D +AFV F D + A++ LS
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLS 60
>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 = 33.1 bits (76), Expect = 0.005
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
L+V NL+ E+ + EAF +YG + V+ R K + +V F ++ A
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAA 53
>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 = 33.1 bits (76), Expect = 0.006
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 31/78 (39%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V L+ TEEK++E F ++G + ++ P
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIEL-----------------------------P 32
Query: 67 DDNKKN--RGFCFLEYDS 82
D K N RGFCF+ +DS
Sbjct: 33 MDKKTNKRRGFCFITFDS 50
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 32.9 bits (76), Expect = 0.006
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKD-------YAFVHFEDRQEA 51
V+ +R L TEE +++ F + + + D A+V F ++A
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDA 54
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in
RNA-binding protein MRN1 and similar proteins. This
subgroup corresponds to the RRM2 and RRM4 of MRN1, also
termed multicopy suppressor of RSC-NHP6 synthetic
lethality protein 1, or post-transcriptional regulator
of 69 kDa, and is an RNA-binding protein found in
yeast. Although its specific biological role remains
unclear, MRN1 might be involved in translational
regulation. Members in this family contain four copies
of conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 82
Score = 33.3 bits (76), Expect = 0.006
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 7 LYVRNLT-----QYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
+Y+ N++ + E++L++ E+YG +E ++ R K AF++F + AI
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAA 59
>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 = 33.2 bits (76), Expect = 0.007
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 12/58 (20%)
Query: 7 LYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKD-----YAFVHF---EDRQEAI 52
++V +L ++++L+ A F +YG + VK ++D YAFV F +D + A+
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNAL 62
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif
2 in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized
to the nuclear and cytoplasmic compartments. In
addition to PARP activity, PARP-10 is also involved in
the control of cell proliferation by inhibiting c-Myc-
and E1A-mediated cotransformation of primary cells.
PARP-10 may also play a role in nuclear processes
including the regulation of chromatin, gene
transcription, and nuclear/cytoplasmic transport.
PARP-10 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two overlapping C-terminal
domains composed of a glycine-rich region and a region
with homology to catalytic domains of PARP enzymes
(PARP domain). In addition, PARP-10 contains two
ubiquitin-interacting motifs (UIM). PARP-14, also
termed aggressive lymphoma protein 2, is a member of
the B aggressive lymphoma (BAL) family of
macrodomain-containing PARPs. Like PARP-10, PARP-14
also includes two RRMs at the N-terminus. Nmi, also
termed N-myc and STAT interactor, is an interferon
inducible protein that interacts with c-Myc, N-Myc, Max
and c-Fos, and other transcription factors containing
bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc
proteins, Nmi also associates with all the Stat family
of transcription factors except Stat2. In response to
cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can
enhance Stat-mediated transcriptional activity through
recruiting the Stat1 and Stat5 transcriptional
coactivators, CREB-binding protein (CBP) and p300. IFP
35 is an interferon-induced leucine zipper protein that
can specifically form homodimers. Distinct from known
bZIP proteins, IFP 35 lacks a basic domain critical for
DNA binding. In addition, IFP 35 may negatively
regulate other bZIP transcription factors by
protein-protein interaction. For instance, it can form
heterodimers with B-ATF, a member of the AP1
transcription factor family. Both Nmi and IFP35 harbor
one RRM. RBM43 is a putative RNA-binding protein
containing one RRM, but its biological function remains
unclear. .
Length = 74
Score = 33.0 bits (76), Expect = 0.007
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRI--KDYAFVHFEDRQEAITVTGLSQ 59
+ V L + +++KL+ FE G V RV+ + K A V F D + A V +
Sbjct: 3 VLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREKGSALVTFADFKVAERVVKQKK 62
Query: 60 VIIYSSP 66
+ +
Sbjct: 63 HPLNGTQ 69
>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 = 33.2 bits (76), Expect = 0.007
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY-------AFVHFEDRQEAITVT 55
L+V L++ C E ++ F +G +E ++D AFV F RQ A+
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAI 59
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 32.9 bits (76), Expect = 0.007
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK-------DYAFVHFEDRQEA 51
L+V NL TEE+L++ F R +R+K FV FED A
Sbjct: 5 LFVANLGPNTTEEELRQLF---SRQPGFRRLKMHNKGGGPVCFVEFEDVSFA 53
>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 = 32.8 bits (75), Expect = 0.008
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
++V L+ TE+ +K+ F Q+G+VE R + + FV FE
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of
RBM23 remains unclear, it shows high sequence homology
to RBM39 and contains two RRMs. It may possibly
function as a pre-mRNA splicing factor. .
Length = 73
Score = 32.6 bits (75), Expect = 0.008
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVTGLS 58
+V L+ E L E F + G+V V+ I+D A+V F D + GL+
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLT 61
>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 = 33.1 bits (76), Expect = 0.008
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKD--------YAFVHFEDRQEA 51
L++ +L Y E +K AF G V VK I++ Y FV F D A
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATA 55
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM1 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 75
Score = 33.0 bits (75), Expect = 0.008
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
KVL+VRN+ +E L + + +G V ++ R K+ A + +D AI+
Sbjct: 1 KVLHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQALLQMQDVSSAISA 52
>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 = 32.7 bits (75), Expect = 0.009
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V NL E L + F +G V VK I+D Y FV + +EA
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEA 56
>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 = 32.7 bits (74), Expect = 0.012
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
L V+NL+ + E L++AF Q+G VER I D
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVD 34
>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 = 32.2 bits (73), Expect = 0.015
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFE 46
+ L+V NL TEE + E F Q G V +VK KD +AFV+F+
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFK 50
>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 = 32.2 bits (73), Expect = 0.015
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 11/55 (20%)
Query: 9 VRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKDYAFVHFE---DRQEAI 52
V L+ Y TE L+E F +YG + +R R + +AFV+FE D +EA+
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAM 58
>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 = 32.2 bits (73), Expect = 0.015
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+V L E L E F Q+G VE+ + I D + FV+F++ A
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSA 54
>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 = 31.8 bits (73), Expect = 0.017
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV-------ERVKRIKDYAFVHFEDRQEAI 52
L V NL +++ +KE F ++G + +R R A V FE R +A+
Sbjct: 3 LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADAL 55
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and
similar proteins. This subfamily corresponds to the
RRM of Acinus, a caspase-3-activated nuclear factor
that induces apoptotic chromatin condensation after
cleavage by caspase-3 without inducing DNA
fragmentation. It is essential for apoptotic chromatin
condensation and may also participate in nuclear
structural changes occurring in normal cells. Acinus
contains a P-loop motif and an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which indicates Acinus
might have ATPase and DNA/RNA-binding activity. .
Length = 90
Score = 32.2 bits (74), Expect = 0.018
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEAI 52
L++ NL + T +LKE + G +IK + +V + +EA+
Sbjct: 3 ALHIDNLVRPFTLNQLKELLSETGTGVIEGFWMDKIKSHCYVTYSTVEEAV 53
>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 = 31.7 bits (72), Expect = 0.018
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 7/51 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
+YV NL E+ L++ F +YGR+ ++ +K+ +AFV FED ++A
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIE-LKNRRGLVPFAFVRFEDPRDA 51
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 32.0 bits (73), Expect = 0.019
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVE--RV----KRIKDYAFVHFEDRQEAITVTGLS 58
+ +YV ++ Q TEE+L F G+V RV + +AF+ F D + A LS
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALSLS 62
Query: 59 QVIIYSSP 66
++ P
Sbjct: 63 GTMLGFYP 70
>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 = 31.8 bits (72), Expect = 0.019
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA-ITVTGLSQVIIY 63
L+V NL TEE K+ FE+YG V R + + F+ E R A I L I+
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 63
Query: 64 SSP 66
+ P
Sbjct: 64 NRP 66
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the
RRM of Star-PAP, also termed RNA-binding motif protein
21 (RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs
to the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both,
the poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione
S-transferase (GST)-PIPKIalpha. Star-PAP preferentially
uses ATP as a nucleotide substrate and possesses PAP
activity that is stimulated by PtdIns4,5P2. It contains
an N-terminal C2H2-type zinc finger motif followed by
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
split PAP domain linked by a proline-rich region, a PAP
catalytic and core domain, a PAP-associated domain, an
RS repeat, and a nuclear localization signal (NLS). .
Length = 74
Score = 31.6 bits (72), Expect = 0.020
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQ 49
+ ++V + +EE+L + F +G V V KD YA V F+ ++
Sbjct: 2 ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKE 50
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
family also includes polypyrimidine tract binding
protein homolog 3 (PTBPH3) found in plant. Although its
biological roles remain unclear, PTBPH3 shows
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 31.8 bits (73), Expect = 0.020
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 6 VLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIK---DYAFVHFEDRQEA-ITVTGLSQV 60
VL V L + +KL F YG V R+K +K A V D Q A + L+ V
Sbjct: 1 VLMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGV 60
Query: 61 IIY 63
+++
Sbjct: 61 VLF 63
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins.
This subgroup corresponds to the RRM1 of SF2, also
termed SR1 protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal domain rich in proline, serine
and lysine residues (PSK domain), a composition
reminiscent of histones. This PSK domain harbors a
putative phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 31.7 bits (72), Expect = 0.020
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
+YV NL E ++++ F +YG + + R YAF+ FED ++A
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDA 51
>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 = 31.9 bits (73), Expect = 0.020
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV L + T+++L+ F YGR+ + + D F+ F+ R EA
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEA 55
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 31.5 bits (72), Expect = 0.022
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
L+V NL+ ++ L+E F++ G V V+ R K + V F + A
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGA 53
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 31.5 bits (71), Expect = 0.029
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKD-----YAFVHFED 47
L++ NL +E +L+ AF++YG +E V KR YAF+ F++
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQN 58
>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 = 31.2 bits (71), Expect = 0.030
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 43 VHFEDRQEAITVT----GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLA 89
+ FE ++ I G + I S K++GF F+EY+ ++A LA
Sbjct: 8 ISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLA 58
>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 = 31.4 bits (72), Expect = 0.032
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAIT 53
++V N+ + +++ +++ E+ G+V KR+KD + F FED + A+
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALR 57
>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 = 33.0 bits (75), Expect = 0.034
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L Q T+E+++ F G +E K ++D Y FV++ ++A
Sbjct: 6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDA 58
Score = 29.9 bits (67), Expect = 0.34
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V NL+ E L + F +G V+ VK I+D Y FV + EA
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEA 324
Score = 29.5 bits (66), Expect = 0.46
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------KDYAFVHFEDRQEA 51
LYV L + T+ +L+ F +G++ RI K F+ F+ R EA
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQI-ITSRILSDNVTGLSKGVGFIRFDKRDEA 144
>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 = 31.2 bits (71), Expect = 0.034
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKDYAFVHFEDRQEA 51
++V L TEE+ KE F Q+G+V R + + FV F+
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAV 54
>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 = 31.2 bits (71), Expect = 0.035
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRV-----ERVKRIKDYAFVHFED 47
+ L++ NL + T L+EAFE++G + ++ YAF+ + D
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYAD 50
>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 = 31.0 bits (70), Expect = 0.036
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+Y+ L+ + E+ ++ F YG++ + Y FV FED ++A
Sbjct: 2 VYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDA 46
>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 = 31.2 bits (71), Expect = 0.038
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAI 52
L+V + + E+ L+ FEQ+G++ + +KD AF+ + R+ A+
Sbjct: 8 LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61
>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 = 31.2 bits (70), Expect = 0.041
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 8/51 (15%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
K L+V + + E L++ FE+YG+++ ++ I D + FV F+D
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51
>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 = 31.1 bits (70), Expect = 0.042
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
K ++V + + E L++ FEQYG++E ++ + D +AFV F+D
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51
>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 = 31.1 bits (70), Expect = 0.045
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
L+V ++ + TE++++ FE++G V V IKD FV + R EA
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEA 54
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 30.9 bits (70), Expect = 0.045
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEA 51
+YV NL + +++ F +YG + + +R +AFV FED ++A
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDA 50
>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 = 31.3 bits (70), Expect = 0.045
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGR-------VERVKRI-KDYAFVHFEDRQEA 51
LYV L + T+++L++ F QYGR V++V + + F+ F+ R EA
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 60
>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 = 30.8 bits (70), Expect = 0.049
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAI 52
K L+V N+ + L++ F Q+G + V+ I K + FV F + +A
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADAD 54
>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 = 30.6 bits (70), Expect = 0.050
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
L++ L+ TEE L+E F +YG V +KD + FV F D
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFAD 49
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM4 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 30.7 bits (70), Expect = 0.051
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQ-YGRVERVKRI-KD--YAFVHFEDRQEAIT 53
L++ N+ TEE LKE F Q G V+ K KD A + +EAI
Sbjct: 1 TLHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIE 52
>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 = 30.7 bits (70), Expect = 0.055
Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 36/101 (35%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--ERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
L++ +L T++ L + F +G V +V F D+ TG S
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKV----------FVDKN-----TGQS------ 39
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL-----ATGRLKV 100
+ F F+ YD+ +SA A K + RLKV
Sbjct: 40 --------KCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72
>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 = 30.9 bits (69), Expect = 0.058
Identities = 26/104 (25%), Positives = 43/104 (41%), Gaps = 31/104 (29%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NL++ TE + + F Q G + K I ++
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT------------------------- 36
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
N +CF+E+ H+ A+ A + GR K+ G ++ V+WA
Sbjct: 37 ----SNDPYCFVEFYEHRDAAAALAAM-NGR-KILGKEVKVNWA 74
>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 = 30.7 bits (70), Expect = 0.058
Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 27/83 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+Y+ L TE + F QYG + + ++D TG
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRD-------------KKTG---------- 48
Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
K++GF FL Y+ +S LA
Sbjct: 49 ----KSKGFAFLAYEDQRSTILA 67
>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 = 30.8 bits (70), Expect = 0.060
Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 27/76 (35%)
Query: 14 QYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNR 73
+ TE+ L+EAF +G ++ + +KD K+++
Sbjct: 12 KSVTEDDLREAFAPFGEIQDIWVVKD---------------------------KQTKESK 44
Query: 74 GFCFLEYDSHKSASLA 89
G ++++ SA+ A
Sbjct: 45 GVAYVKFAKASSAARA 60
>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 = 32.2 bits (73), Expect = 0.060
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 27/83 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+Y+ NL Y E+++KE E +G ++ IKD A TGLS
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIA-------------TGLS-------- 336
Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
+G+ F EY +A
Sbjct: 337 ------KGYAFCEYKDPSVTDVA 353
>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 = 0.062
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV---KRIKDYAFVHFEDRQEA-ITVTGLSQVII 62
+YV NL + +L+ AF YG + V + +AFV FED ++A V GL +I
Sbjct: 2 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61
Query: 63 YSS 65
S
Sbjct: 62 CGS 64
>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 = 30.4 bits (69), Expect = 0.064
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVTGLS 58
L V L TE+ LK+ F +G + V+ KD + FV F D ++ + V
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQR 61
Query: 59 QVI 61
+I
Sbjct: 62 HMI 64
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM1 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single-
and double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. It forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manneras well as with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 30.2 bits (68), Expect = 0.071
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
L+V NL TEE++++ FE+YG+ + KD + F+ E R A
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLA 50
>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 = 30.5 bits (68), Expect = 0.076
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV L + T+++L++ F QYGR+ + + D F+ F+ R EA
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 57
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 30.2 bits (69), Expect = 0.082
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 9/55 (16%)
Query: 7 LYVRNLTQYCTEEKLKEA----FEQYGRVERV---KRIKDY--AFVHFEDRQEAI 52
LY+ NL + +++LK + F Q+G V + K +K AFV F+D + A
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESAT 56
>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 = 30.3 bits (68), Expect = 0.084
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
L+VRN+ E L+ F +YG + V +R + +A+V FED ++A
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDA 55
>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 = 30.0 bits (68), Expect = 0.10
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKDYAFVHFEDRQEA 51
L++ L+ T++ LK F Q+G + KR + + FV F E
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEV 54
>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 = 29.7 bits (67), Expect = 0.10
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 17 TEEKLKEAFEQYGRVERVKRIKD 39
TEE L+E F+++G +E V +KD
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKD 35
>gnl|CDD|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM1 of hnRNP-L, a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-L shows significant sequence homology
to polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 30.0 bits (67), Expect = 0.10
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQ---EAITVTGLSQV 60
V++VR L E L EA +++G + V + K A V FED A+ +Q+
Sbjct: 4 VVHVRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQALVEFEDMNGACNAVNYAADNQI 63
Query: 61 IIYSSP 66
I P
Sbjct: 64 YIAGHP 69
>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 = 29.9 bits (67), Expect = 0.11
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFED 47
L+V NL + +LKE F+QYG V ++ ++ ++ FV F+D
Sbjct: 6 LFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDD 51
>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 = 29.8 bits (67), Expect = 0.11
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 18 EEKLKEAFEQYGRVERVKRIKD-------YAFVHFED 47
E +++ F +YG V+ VK I D Y FV F D
Sbjct: 19 ETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYD 55
>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 = 29.8 bits (67), Expect = 0.11
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 17 TEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITV 54
E L++ F QYG V+ VK + D Y FV FE +++A +
Sbjct: 15 NENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKI 59
>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 = 30.1 bits (67), Expect = 0.12
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L Q T+E+LK F G +E K ++D Y FV++ D ++A
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 59
>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 = 29.9 bits (68), Expect = 0.13
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 29/90 (32%)
Query: 5 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIY 63
+ L+V L + L++ F Q G+ + Q+
Sbjct: 3 RCLFVDRLPKTFRDVSILRKLFSQVGKP-------TFC-----------------QL--- 35
Query: 64 SSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
+ N + RGF F+EY + + A A++ L
Sbjct: 36 -AIAPNGQPRGFAFVEYATAEDAEEAQQAL 64
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 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 = 72
Score = 29.7 bits (67), Expect = 0.13
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
+ V+N T E+L++ FE +G++ RV A V F + Q+A
Sbjct: 1 TTILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQA 49
>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 = 29.6 bits (66), Expect = 0.14
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 27/81 (33%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K ++V + + E L++ FE+YG++E ++ + EDRQ
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVM--------EDRQSG------------- 39
Query: 65 SPDDNKKNRGFCFLEYDSHKS 85
K RGF F+ +D H +
Sbjct: 40 ------KKRGFAFVTFDDHDT 54
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 29.5 bits (67), Expect = 0.15
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 12/60 (20%)
Query: 5 KVLYVRNLTQYCTEEKLKE---AFEQYGRVERVK---------RIKDYAFVHFEDRQEAI 52
K LYV+NL++ TEE L F E+ R+K AFV F + A
Sbjct: 2 KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61
>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 = 29.2 bits (66), Expect = 0.16
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 17 TEEKLKEAFEQYGRVERV--KRIKDYAFVHFE 46
TEE LK+AF +G + + ++ K+ FV FE
Sbjct: 15 TEEILKKAFSPFGNIINISMEKEKNCGFVTFE 46
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell
surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or
ENOX) proteins. This subgroup corresponds to the
conserved RNA recognition motif (RRM) in ECTO-NOX
proteins (also termed ENOX), comprising a family of
plant and animal NAD(P)H oxidases exhibiting both,
oxidative and protein disulfide isomerase-like,
activities. They are growth-related and drive cell
enlargement, and may play roles in aging and
neurodegenerative diseases. ENOX proteins function as
terminal oxidases of plasma membrane electron transport
(PMET) through catalyzing electron transport from
plasma membrane quinones to extracellular oxygen,
forming water as a product. They are also hydroquinone
oxidases that oxidize externally supplied NADH, hence
NOX. ENOX proteins harbor a di-copper center that lack
flavin. ENOX proteins display protein disulfide
interchange activity that is also possessed by protein
disulfide isomerase. In contrast to the classic protein
disulfide isomerases, ENOX proteins lack the double
CXXC motif. This family includes two ENOX proteins,
ENOX1 and ENOX2. ENOX1, also termed candidate
growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous
and refractory to drugs. ENOX2, also termed APK1
antigen, or cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role
in cell proliferation and tumor progression. In
contrast to ENOX1, ENOX2 is drug-responsive and harbors
a drug binding site to which the cancer-specific
S-peptide tagged pan-ENOX2 recombinant (scFv) is
directed. Moreover, ENOX2 is specifically inhibited by
a variety of quinone site inhibitors that have
anticancer activity and is unique to the surface of
cancer cells. ENOX proteins contain many functional
motifs.
Length = 84
Score = 29.7 bits (67), Expect = 0.16
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK-DYAFVHFEDRQ---EAITVTGLSQV 60
K ++V L + TEE ++E FEQ G + ++ K ++ + F + +AI ++G
Sbjct: 7 KTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKNFCHIRFAEEFAVDKAIYLSGYRVR 66
Query: 61 IIYSSPDDN 69
I S+ N
Sbjct: 67 IGSSTDPKN 75
>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 = 29.3 bits (65), Expect = 0.17
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA----ITVTGLS 58
+Y +T TE+ +++ F +G++ V+ D Y+FV F + A ++V G +
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTT 60
>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 = 29.3 bits (65), Expect = 0.19
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFE 46
++ K ++V L+ E +K+ FEQ+G+VE R + + FV FE
Sbjct: 1 TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53
>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 = 29.2 bits (66), Expect = 0.19
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEAIT 53
++VRNL T + LK+ F + G V R R K + V FE ++A
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQR 54
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM4 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 79
Score = 29.4 bits (66), Expect = 0.20
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEA 51
K+++V NL TEE + ++G + VK K A V F ++A
Sbjct: 8 KMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQA 58
>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 = 29.2 bits (65), Expect = 0.20
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
L+VRN+ E L+ F +YG + V +R + +A++ FED ++A
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDA 55
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-beta (PGC-1-beta) and similar proteins. This
subfamily corresponds to the RRM of PGC-1beta, also
termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta,
or PGC-1-related estrogen receptor alpha coactivator,
which is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial
oxidative energy metabolism and affects both, insulin
sensitivity and mitochondrial biogenesis, and functions
in a number of oxidative tissues. It is involved in
maintaining baseline mitochondrial function and cardiac
contractile function following pressure overload
hypertrophy by preserving glucose metabolism and
preventing oxidative stress. PGC-1beta induces
hypertriglyceridemia in response to dietary fats
through activating hepatic lipogenesis and lipoprotein
secretion. It can stimulate apolipoprotein C3 (APOC3)
expression, further mediating hypolipidemic effect of
nicotinic acid. PGC-1beta also drives nuclear
respiratory factor 1 (NRF-1) target gene expression and
NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can
be increased through binding to host cell factor (HCF),
a cellular protein involved in herpes simplex virus
(HSV) infection and cell cycle regulation. PGC-1beta is
a multi-domain protein containing an N-terminal
activation domain, an LXXLL coactivator signature, a
tetrapeptide motif (DHDY) responsible for HCF binding,
two glutamic/aspartic acid-rich acidic domains, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). In
contrast to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible
for the regulation of RNA processing. .
Length = 79
Score = 29.0 bits (65), Expect = 0.20
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK 35
+ +V+Y+RNL+ + +LK+ FE +G +E K
Sbjct: 1 EGRVIYIRNLSSSMSSTELKKRFEVFGEIEECK 33
>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 = 29.3 bits (65), Expect = 0.21
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAI-TV 54
L V L Q T+++L+ F G VE K I+D Y FV++ +D + AI T+
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63
Query: 55 TGL 57
GL
Sbjct: 64 NGL 66
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 29.2 bits (66), Expect = 0.21
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--ERVKRIKD-----YAFVHFEDRQEA 51
LY+ NL + E+ L+ + YG+V R+ R F E R++
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKC 54
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 29.0 bits (65), Expect = 0.22
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAIT 53
++V N+ TEE+LK+ F + G V + + D Y F ++D++ A++
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALS 55
>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 = 29.0 bits (65), Expect = 0.22
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYG-----RV---ERVKRIKDYAFVHFEDRQEA 51
++V +L+ T+ L AF + RV + R + Y FV F +Q+A
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDA 54
>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 = 29.1 bits (66), Expect = 0.23
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
+++ L Y +E+++KE E +G+++ +KD YAF + D
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLD 51
>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 = 29.2 bits (65), Expect = 0.23
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYA--------FVHFEDRQEA 51
LYV L + +++++++ F QYGR+ + + D F+ F+ R EA
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEA 56
>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 = 28.7 bits (65), Expect = 0.25
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEAI 52
L V NL TEE L+E F + G V++VK R + A V FE R++A
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAE 55
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 28.8 bits (65), Expect = 0.25
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 32/89 (35%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+ L+VRN+ +E+L+ FEQ+G + +Y+
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRT----------------------------LYT 33
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
+ K+RGF + Y ++A AK+ L
Sbjct: 34 A----CKHRGFIMVSYYDIRAARRAKRAL 58
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 30.0 bits (68), Expect = 0.26
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEAITVT 55
+ +V+ + V N++ TE +KE F G +E V+ + A+V F+D Q A T
Sbjct: 1 VMQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETAL 60
Query: 56 GLSQVII 62
LS I
Sbjct: 61 LLSGATI 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 = 28.7 bits (64), Expect = 0.28
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTE-EKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
L +RNL + KLK+ F +YG+V ++ +AFV + R+ A
Sbjct: 3 LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNA 55
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 28.5 bits (64), Expect = 0.28
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAI 52
++V NL +KLKE F+ G+V R +D V FE EA+
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAV 53
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 28.8 bits (64), Expect = 0.30
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LY+ L + T++ +++ F ++GR+ + + D AF+ F+ R EA
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEA 55
>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 = 28.5 bits (63), Expect = 0.33
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V +L+ T + +K AF +GR+ + +KD Y FV F ++ +A
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 56
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 28.4 bits (64), Expect = 0.36
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK----DYAFVHFEDRQEAIT 53
L V NL TE+ + E F G ++R + ++ + +V +D AI
Sbjct: 3 LVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGVAEVVYVRKDDALTAID 53
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.5 bits (64), Expect = 0.37
Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 28/106 (26%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K+L VRN+ T ++L+E F +G ++ V+ K
Sbjct: 2 KIL-VRNIPFEATVKELRELFSTFGELKTVRLPKKMT----------------------- 37
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
+RGF F+++ + + A A K L ++G ++++WA
Sbjct: 38 ---GTGSHRGFGFVDFITKQDAKRAFKALCHST-HLYGRRLVLEWA 79
>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 = 28.5 bits (64), Expect = 0.38
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 12/63 (19%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAI-TV 54
L + L Q T+E+ + F G V+ K ++D + FV + ED Q AI T+
Sbjct: 3 LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62
Query: 55 TGL 57
GL
Sbjct: 63 NGL 65
>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 = 28.3 bits (63), Expect = 0.41
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
+++ L T++ L+E F Q+G V ++D + F+ F+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49
>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 = 28.0 bits (63), Expect = 0.43
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 27/85 (31%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V+NL TE +LKE HF IT V + +
Sbjct: 3 LIVKNLPASLTEAELKE--------------------HFSKHGGEIT-----DVKLLRTE 37
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKK 91
D K+R F+ Y + + A AK
Sbjct: 38 D--GKSRRIAFIGYKTEEEAQKAKD 60
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4
is a splicing regulatory serine/arginine (SR) protein
that plays an important role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
For instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, it activates splicing of the cardiac troponin
T (cTNT) alternative exon by direct interactions with
the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between
the nucleus and cytoplasm. It contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 28.0 bits (62), Expect = 0.48
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+Y+ L+ E ++ F+ YG++ V Y FV F+D ++A
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDA 46
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 28.0 bits (63), Expect = 0.49
Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 20/83 (24%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+Y+ L TE+ L E F G ++R KR T + IY+
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKR------------------TWPPMIKIYT-- 40
Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
D + +G + YD +A A
Sbjct: 41 DKETEPKGEATVTYDDPSAAQAA 63
>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 = 28.0 bits (62), Expect = 0.49
Identities = 11/45 (24%), Positives = 25/45 (55%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+++ L E+ ++ F+ YGR+ + + + FV F+D ++A
Sbjct: 2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDA 46
>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 = 28.1 bits (63), Expect = 0.49
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 71 KNRGFCFLEYDSHKSASLAKKRL 93
K++GF ++ Y + SA AK++L
Sbjct: 39 KSKGFAYVTYSNPASAIYAKEKL 61
>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 = 27.8 bits (62), Expect = 0.50
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQE 50
L++ NL T+ ++E L F YG + ++ Y FV F+ +
Sbjct: 2 LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFVQFDSPES 46
>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 = 27.9 bits (63), Expect = 0.58
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV-------ERVKRIKDYAFVHFEDRQEA 51
L+V N + +++ FEQYG + R + + + +V F + A
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESA 54
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 27.5 bits (62), Expect = 0.65
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
+YV+ + T + ++E FE++G+V + K+ K FV F+ ++A
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDA 53
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 27.7 bits (61), Expect = 0.68
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHF-EDRQEAITVTGLSQVIIYS 64
+++ NL T + ++ F +YG++ K YAFV + +R V G + II
Sbjct: 4 VFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFVQYISERHARAAVAGENARIIAG 63
Query: 65 SPDD 68
P D
Sbjct: 64 QPLD 67
>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 = 27.6 bits (61), Expect = 0.69
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK 35
VK ++V L TEEK++E F ++G +E ++
Sbjct: 4 VKKIFVGGLNPEATEEKIREYFGEFGEIEAIE 35
>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 = 27.7 bits (61), Expect = 0.70
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 31/76 (40%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V L+ TEE++KE F +G +E ++ P
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIEL-----------------------------P 32
Query: 67 DDNKKN--RGFCFLEY 80
D K N RGFCF+ Y
Sbjct: 33 MDTKTNERRGFCFVTY 48
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the
formation of D-loops in superhelical duplex DNA, and is
involved in cell proliferation. PSF can also interact
with multiple factors. It is an RNA-binding component
of spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions,
such as DNA recombination and RNA synthesis,
processing, and transport. PSF contains two conserved
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for interactions with RNA and for
the localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 71
Score = 27.6 bits (61), Expect = 0.73
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
L+V NL TE++ K+ F +YG V + K + F+ E R A
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALA 50
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 27.7 bits (61), Expect = 0.74
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV 31
++VRNL T +KLKE F Q G V
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHV 26
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 77
Score = 27.6 bits (62), Expect = 0.77
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
+++ L + TE+ L F +YG V V R + A V F+ + A
Sbjct: 8 NCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAA 56
>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 = 27.5 bits (61), Expect = 0.79
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKD-YAFVHFEDRQEAI 52
+ L+V N+ + TE L+ FE YG V V +RI + VHF D ++A
Sbjct: 2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAK 52
>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 = 27.8 bits (61), Expect = 0.79
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L Q T+E+ + F G +E K ++D Y FV++ D ++A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 57
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 28.5 bits (63), Expect = 0.80
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ L+ + L++AF +G V K I D + FV+F D A
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAA 89
>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 = 27.7 bits (61), Expect = 0.80
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V +L+ T E +K AF +G++ + +KD Y FV F ++ +A
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 56
>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 = 27.5 bits (62), Expect = 0.83
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
++++NL + + L + F +G + K D Y FVHFE + A
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAA 56
>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 = 27.4 bits (61), Expect = 0.96
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEA 51
L+V L++ TE+ ++ FE +G +E + K AFV F EA
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEA 55
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 27.4 bits (60), Expect = 0.99
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
V++VR L + E L EA E++G + V + K A V FE + A
Sbjct: 5 VVHVRGLCESVVEADLVEALEKFGPICYVMMMPFKRQALVEFEMVESA 52
>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 = 27.0 bits (60), Expect = 1.0
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 17 TEEKLKEAFEQYGRVERV--------KRIKDYAFVHFED 47
T E L+E F ++G ++ KR + + FV F D
Sbjct: 11 TAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSD 49
>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 = 27.3 bits (60), Expect = 1.0
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 31/76 (40%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V L+ EEK++E F +G VE ++ P
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIEL-----------------------------P 32
Query: 67 DDNKKN--RGFCFLEY 80
DNK N RGFCF+ +
Sbjct: 33 MDNKTNKRRGFCFITF 48
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 27.3 bits (60), Expect = 1.1
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+++ NL T + ++ F +YGRV K YAFV + + + A
Sbjct: 4 VFIGNLNTAVVKKSDVETIFSKYGRVVGCSVHKGYAFVQYSNERHA 49
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 27.3 bits (60), Expect = 1.2
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKD-----YAFVHFEDR---QEAITVTG 56
L++ +++ C E ++ F +G++E R+ R D AFV F R Q AI
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63
Query: 57 LSQVI 61
+Q +
Sbjct: 64 QAQTM 68
>gnl|CDD|234514 TIGR04231, seadorna_VP5, seadornavirus VP5 protein. This protein
family occurs in the seadornavirus virus group, with
designations VP5 in Banna virus, and VP6 in Kadipiro
virus and Liao ning virus. The function is unassigned.
Length = 505
Score = 28.4 bits (63), Expect = 1.2
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 52 ITVTGLSQVIIYSS----PDDNKKNRGFCFLEYDSHKSAS 87
IT GLS +I Y PDD + CF+ + H S+
Sbjct: 81 ITQAGLSHLIEYCENYCLPDDAGVLKALCFIIFQIHDSSQ 120
>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 = 27.2 bits (60), Expect = 1.2
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQ 49
L+V NL E +LKE F +G V ++ ++ ++ FV F+D +
Sbjct: 8 LFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58
>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 = 27.1 bits (60), Expect = 1.2
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 7/34 (20%)
Query: 25 FEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
FE+YGR+ R + + +AFV +E ++A
Sbjct: 20 FERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDA 53
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 26.8 bits (60), Expect = 1.2
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 9 VRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----YAFVHFEDRQEA 51
V+NL + TE K+++ F+ G + VK ++ A + FE EA
Sbjct: 5 VKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEA 51
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate
nucleolin. This subfamily corresponds to the RRM2 of
ubiquitously expressed protein nucleolin, also termed
protein C23, a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines.RRM2,
together with RRM1, binds specifically to RNA
stem-loops containing the sequence (U/G)CCCG(A/G) in
the loop. .
Length = 77
Score = 26.7 bits (59), Expect = 1.3
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVE----RVKRIKDYAFVHFEDRQEA 51
+ L+V+NL T ++LKE FE + + K A++ F+ EA
Sbjct: 4 RTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKGIAYIEFKTEAEA 54
>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 = 26.9 bits (60), Expect = 1.4
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA 51
L+V L+ LK+ F +YG+V K + + + FV +EA
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEA 54
>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 = 27.0 bits (60), Expect = 1.4
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVE 32
+Y+ NL+ +EE L+E + + V
Sbjct: 2 VYISNLSYSSSEEDLEEFLKDFEPVS 27
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 26.6 bits (59), Expect = 1.4
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHF---EDRQEAI-TVTGL 57
+Y +K FE G V +V ++ +AF+ F E Q AI T+ G
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60
Query: 58 S 58
S
Sbjct: 61 S 61
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 28.0 bits (62), Expect = 1.6
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 20 KLKEAFEQYGRVERVKRIK----------DYAFVHFEDRQEAITVTGLSQVIIYSSPDDN 69
+LK A E +E ++K DY+ F RQ +TV+G QV Y+ +
Sbjct: 270 ELKIAKESLAHIEERSKLKPGLPKKDGKIDYS-KDFFGRQAFLTVSGQLQVETYACALSS 328
Query: 70 KKNRGFCFLEYDSHKSASLAK 90
G F +SH S LA+
Sbjct: 329 VYTFGPTFRAENSHTSRHLAE 349
>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 = 26.6 bits (58), Expect = 1.6
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED---RQEAITVT 55
LY+R L T++ L + + YG++ K I D Y FV F+ Q+A+T
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
Query: 56 GLSQV 60
S V
Sbjct: 64 KASGV 68
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 26.5 bits (59), Expect = 1.6
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAIT 53
+L+V NL T E L F+ G V + K AFV F D EA+T
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF-DTAEAMT 56
>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 = 26.5 bits (58), Expect = 1.7
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+++ L + E++L E+ G++ ++ + D YAFV F ++QEA
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEA 55
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form
of the carboxy-terminal domain (CTD) of the largest
subunit of RNA polymerase II (pol II). The pol II CTD
plays a role in coupling transcription and pre-mRNA
processing. SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 26.5 bits (58), Expect = 1.7
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
L+V + + T++ L FE++G++E + I + A+V RQ+A
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDA 51
>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 = 26.6 bits (58), Expect = 1.7
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQE 50
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E
Sbjct: 1 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE 56
>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 = 26.6 bits (59), Expect = 1.8
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 18/75 (24%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVK---------RIKDYAFVHFEDRQEAITVTGLS 58
Y+ NL TEE +KE F V V+ R++ + + FEDR + L
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL- 62
Query: 59 QVIIYSSPDDNKKNR 73
D++ KNR
Sbjct: 63 -------NDESLKNR 70
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of
nuclear proteins consisting of Matrin 3 (MATR3),
nuclear protein 220 (NP220) and similar proteins. MATR3
is a highly conserved inner nuclear matrix protein that
has been implicated in various biological processes.
NP220 is a large nucleoplasmic DNA-binding protein that
binds to cytidine-rich sequences, such as CCCCC (G/C),
in double-stranded DNA (dsDNA). Both, Matrin 3 and
NP220, contain two RNA recognition motif (RRM), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a Cys2-His2 zinc
finger-like motif at the C-terminal region. .
Length = 76
Score = 26.5 bits (59), Expect = 1.9
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 6 VLYVRNL-TQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEA 51
V+ + NL TE +L + E +G+V+ ++ AF+ E ++A
Sbjct: 2 VVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDA 50
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 26.4 bits (58), Expect = 1.9
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KR-----IKDYAFVHFED 47
+ L++ NL TE L+ AF+++G + V KR Y F+ FE+
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFEN 57
>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 = 26.7 bits (58), Expect = 2.0
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED---RQEAITVT 55
LY+R L T++ L + + YG++ K I D Y FV F+ Q+A++
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69
Query: 56 GLSQV 60
S V
Sbjct: 70 KASGV 74
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 26.5 bits (59), Expect = 2.1
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAI 52
YV NL T ++L E F Q G V+ V+ D YAFV F + Q ++
Sbjct: 8 YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAE-QTSV 57
>gnl|CDD|241159 cd12715, RRM2_MATR3, RNA recognition motif 2 in vertebrate
matrin-3. This subgroup corresponds to the RRM2 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated
by the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is
responsible for the activation of the
N-methyl-d-aspartic acid (NMDA) receptor. Furthermore,
MATR3 has been identified as both a Ca2+-dependent
CaM-binding protein and a downstream substrate of
caspases. Additional research indicates that matrin 3
also binds Rev/Rev responsive element (RRE)-containing
viral RNA and functions as a cofactor that mediates the
post-transcriptional regulation of HIV-1. .
Length = 80
Score = 26.4 bits (58), Expect = 2.2
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 5 KVLYVRNL--TQYCTEEKLKEAFEQYGRVER--VKRIKDYAFVHFEDRQEAITV 54
+V+++ NL + Y LK A E YG+++ + R+K+ AF+ E R++A +
Sbjct: 1 RVIHLSNLPHSGYSDSAVLKLA-EPYGKIKNYILMRMKNQAFIEMETREDAEAM 53
>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 = 26.3 bits (58), Expect = 2.4
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 10/45 (22%)
Query: 18 EEKLKEAFEQYGRVERVKRIKDYA----------FVHFEDRQEAI 52
E+ L+E FEQYG V ++ ++D + FV F R+ A+
Sbjct: 15 EKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAAL 59
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 25.9 bits (57), Expect = 2.4
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEA 51
L + NL + E L+ F+ YG V+ ++ ++ FV F D ++A
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDA 51
>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 = 26.1 bits (57), Expect = 2.6
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVER--------VKRIKDYAFVHFEDR 48
+++ L+ T+E L+E F Q+G V+ KR + + FV F D+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 26.1 bits (57), Expect = 2.7
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAF--EQYGRVERVKRIKDYAFVHFEDRQEAI 52
LY+ NL+ T E L++ F + +V YAFV + D+ AI
Sbjct: 4 LYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAI 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 = 26.0 bits (57), Expect = 2.7
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQ 49
++V NL EE L F + G +E V+ ++D +A+V F+D
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDEN 52
>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 = 27.3 bits (60), Expect = 2.9
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 11/58 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQ---EAIT 53
+YV ++ +E +K FE +G + + + + Y F+ + + Q EAI
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264
>gnl|CDD|163659 cd07416, MPP_PP2B, PP2B, metallophosphatase domain. PP2B
(calcineurin) is a unique serine/threonine protein
phosphatase in its regulation by a second messenger
(calcium and calmodulin). PP2B is involved in many
biological processes including immune responses, the
second messenger cAMP pathway, sodium/potassium ion
transport in the nephron, cell cycle progression in
lower eukaryotes, cardiac hypertrophy, and memory
formation. PP2B is highly conserved from yeast to
humans, but is absent from plants. PP2B is a
heterodimer consisting of a catalytic subunit (CnA) and
a regulatory subunit (CnB); CnB contains four Ca2+
binding motifs referred to as EF hands. The PPP
(phosphoprotein phosphatase) family, to which PP2B
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP4, PP5, PP6, PP7,
Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 305
Score = 26.9 bits (60), Expect = 3.0
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 103 CDIIVDWADPQEEPDTETMSK 123
CD++ W+DP E+ E +
Sbjct: 188 CDLL--WSDPLEDFGNEKTQE 206
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 26.0 bits (57), Expect = 3.0
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDR 48
+YV N+ T E+L+ F G + RV + K YA++ F R
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATR 51
>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 = 26.1 bits (58), Expect = 3.1
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 57 LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLA 89
L I PD ++GF F+ YDS +++ A
Sbjct: 29 LQTPKIMRDPD-TGNSKGFAFISYDSFEASDAA 60
>gnl|CDD|150955 pfam10365, DUF2436, Domain of unknown function (DUF2436). This
domain is found on peptidase C25 proteins and has no
known function.
Length = 161
Score = 26.8 bits (59), Expect = 3.2
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 34 VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH 83
V I VH ED Q+ T TG + +++ ++ + + G+ FL H
Sbjct: 4 VGGISTAYTVHAEDAQD--TRTGTATIVLVAN-CVWEDSSGYQFLLDADH 50
>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 = 25.9 bits (57), Expect = 3.3
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKDYAFVHFED 47
L+V L+ T+E L+ F QYG V + R + + FV F+D
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La
or LARP3) and similar proteins. This subgroup
corresponds to the RRM2 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition, it possesses
a short basic motif (SBM) and a nuclear localization
signal (NLS) at the C-terminus. .
Length = 76
Score = 25.7 bits (57), Expect = 3.9
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 9/41 (21%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFE 46
VL+ + + + E LKEAFE++G V A+V F
Sbjct: 3 VLHFSGVGEQTSREDLKEAFEEFGEV---------AWVDFA 34
>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 = 25.7 bits (56), Expect = 3.9
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFED 47
++V L+ T E +K+ FEQ+G+V+ R + + FV FE
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>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 = 25.8 bits (56), Expect = 4.0
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQE 50
+ + L++ L+ TEE L+ +EQ+G++ KR + + FV F E
Sbjct: 1 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNE 56
>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 = 25.6 bits (57), Expect = 4.3
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHF---EDRQEAI 52
++V + + E++L FE+ G + ++ + D YAFV + E Q A+
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAV 59
Score = 25.2 bits (56), Expect = 5.8
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
D + NRG+ F+ Y + ++A A K+L
Sbjct: 36 DFSGLNRGYAFVTYTNKEAAQRAVKQL 62
>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 = 25.5 bits (56), Expect = 4.4
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKDYAFVHFEDRQEA 51
L+V L ++ L+ F +YG++ KR + + F+ F EA
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEA 57
>gnl|CDD|241007 cd12563, RRM2_RBM6, RNA recognition motif 2 in vertebrate
RNA-binding protein 6 (RBM6). This subgroup
corresponds to the RRM2 of RBM6, also termed lung
cancer antigen NY-LU-12, or protein G16, or RNA-binding
protein DEF-3, which has been predicted to be a nuclear
factor based on its nuclear localization signal. It
shows high sequence similarity to RNA-binding protein 5
(RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5,
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. In contrast to RBM5,
RBM6 has two additional unique domains: the decamer
repeat occurring more than 20 times, and the POZ
(poxvirus and zinc finger) domain. The POZ domain may
be involved in protein-protein interactions and inhibit
binding of target sequences by zinc fingers. .
Length = 87
Score = 25.5 bits (56), Expect = 4.5
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 69 NKKNRG---FCFLEYDSHKSA 86
NK G F F++ DSH A
Sbjct: 39 NKPGPGGKTFGFIDLDSHAEA 59
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 82
Score = 25.6 bits (57), Expect = 4.5
Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 13/73 (17%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGR-----------VERVKRIKD--YAFVHFEDRQEAIT 53
LYV NL TEE+L + F Q V V+ + +AFV F +EA
Sbjct: 4 LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEATA 63
Query: 54 VTGLSQVIIYSSP 66
L +I P
Sbjct: 64 ALALDGIIFKGQP 76
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). SLT11 can facilitate the cooperative formation
of U2/U6 helix II in association with stem II in the
yeast spliceosome by utilizing its RNA-annealing and
-binding activities. .
Length = 86
Score = 25.4 bits (56), Expect = 4.6
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
+K ++ + E K+++ FEQ+G+ + V R K FV FE R+ A
Sbjct: 1 SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAK-CGFVRFETREAA 51
>gnl|CDD|215138 PLN02248, PLN02248, cellulose synthase-like protein.
Length = 1135
Score = 26.5 bits (59), Expect = 4.8
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 95 TGRLKVWGCDIIVDWADPQEEP 116
TGR + G D+ V ADP++EP
Sbjct: 361 TGRSDLPGIDVFVSTADPEKEP 382
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 25.3 bits (56), Expect = 5.1
Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 32/104 (30%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L VR+L +E+ ++ + +G A +V +S+
Sbjct: 2 LLVRHLPPELSEDDKEDLLKHFG---------------------ASSVRVMSR------- 33
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
K + F +D+ ++AS A RL +LK+ G ++V++A
Sbjct: 34 --RGKLKNTAFATFDNEQAASQALSRLH--QLKILGKRLVVEYA 73
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 25.0 bits (55), Expect = 5.6
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKD------YAFVHFEDRQEA 51
+YV + Y TE++++ F G +E + D AF+ F+ + A
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAA 53
>gnl|CDD|200430 TIGR04179, rhombo_lipo, rhombotail lipoprotein. Members of this
protein family are probable lipoproteins. Nearly every
member ends with a C-terminal region consisting of a
glycine-rich probable cleavage site, a hydrophobic
probable transmembrane helix, and a cluster of basic
residues, as described in putative protein sorting
region model TIGR03501. Furthermore, members tend to be
encoded next to a rhomboid family protease, called
rhombosortase (TIGR03902) predicted to perform a
C-terminal cleavage.
Length = 259
Score = 25.9 bits (57), Expect = 6.1
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 9 VRNLTQYCTEEKLKEAFEQYGRVERVKRI-KDY 40
V TQ EK+KE F Y V ++ I Y
Sbjct: 59 VPETTQIALLEKVKEQFRAYPYVSSIEIIPTTY 91
>gnl|CDD|241163 cd12719, RRM_SYNJ1, RNA recognition motif in synaptojanin-1 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-1, also termed synaptojanin, or
synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1,
originally identified as one of the major Grb2-binding
proteins that may participate in synaptic vesicle
endocytosis. It also acts as a Src homology 3 (SH3)
domain-binding brain-specific inositol 5-phosphatase
with a putative role in clathrin-mediated endocytosis.
Synaptojanin-1 contains an N-terminal domain homologous
to the cytoplasmic portion of the yeast protein Sac1p,
a central inositol 5-phosphatase domain followed by a
putative RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal proline-rich region mediating the
binding of synaptojanin-1 to various SH3
domain-containing proteins including amphiphysin,
SH3p4, SH3p8, SH3p13, and Grb2. Synaptojanin-1 has two
tissue-specific alternative splicing isoforms,
synaptojanin-145 expressed in brain and
synaptojanin-170 expressed in peripheral tissues.
Synaptojanin-145 is very abundant in nerve terminals
and may play an essential role in the clathrin-mediated
endocytosis of synaptic vesicles. In contrast to
synaptojanin-145, synaptojanin-170 contains three
unique asparagine-proline-phenylalanine (NPF) motifs in
the C-terminal region and may functions as a potential
binding partner for Eps15, a clathrin coat-associated
protein acting as a major substrate for the tyrosine
kinase activity of the epidermal growth factor
receptor. .
Length = 77
Score = 25.1 bits (55), Expect = 6.5
Identities = 10/39 (25%), Positives = 19/39 (48%)
Query: 21 LKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQ 59
L + F +G V ++ + D +V F + Q A+ L+
Sbjct: 26 LLQQFASFGEVILIRFVADKMWVTFLEGQSALNALSLNG 64
>gnl|CDD|222870 PHA02552, 4, head completion protein; Provisional.
Length = 151
Score = 25.8 bits (57), Expect = 6.6
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 39 DYAFVHFEDRQEAITVTGLSQVII-YSSPDDNKKNRGF 75
+ F+ + D+ ++ G +V+I Y S D K+ R F
Sbjct: 29 ERWFMKWLDKNPSVIKWGSEEVVIPYFSNADGKRRRYF 66
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 24.9 bits (54), Expect = 6.6
Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 29/106 (27%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
+L V NL T E+ +E YG +ER F+ + + VTG S
Sbjct: 1 LLCVTNLPISFTLEEFEELVRAYGNIER-------CFLVYSE------VTGHS------- 40
Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD 111
+G+ F+EY SAS A+ L +L + W D
Sbjct: 41 -------KGYGFVEYMKKDSASKARLELLGKQLGEST--LFAQWMD 77
>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 = 24.8 bits (55), Expect = 6.8
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVH 44
L+V L+ TE L+E F ++G V V+ IK
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGP 39
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 25.0 bits (54), Expect = 6.9
Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT 53
+++ NL T + ++ F +YG++ K +AFV + + + A
Sbjct: 4 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARA 51
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 24.8 bits (55), Expect = 7.1
Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 33/78 (42%)
Query: 17 TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF- 75
T + L + F YG VE++ +I+ KN G
Sbjct: 14 TVDVLHQVFSPYGAVEKI--------------------------LIFE------KNTGVQ 41
Query: 76 CFLEYDSHKSASLAKKRL 93
+++DS +SA AKK L
Sbjct: 42 ALVQFDSVESAENAKKAL 59
>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 = 25.1 bits (54), Expect = 7.5
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY 40
++V NL+ E L + F +G V VK I+D+
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDF 37
>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 = 24.9 bits (54), Expect = 7.5
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQ 49
+ L+V NL EE L E F Q G + +V KD + FV F+ +
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSE 53
>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 = 24.8 bits (54), Expect = 7.6
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVTGLS 58
+YV N+ T E+L+ F G V RV + K +A++ F D++ T L
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61
Query: 59 QVI 61
+ +
Sbjct: 62 ESL 64
>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 = 24.8 bits (53), Expect = 8.5
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFE 46
LY+R L T++ L + + YG++ K I D Y FV F+
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFD 54
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein
zinc fingers (zf-RanBP), and an asparagine-rich region.
It may possess RNA-binding and zinc ion binding
activities. Additional research had indicated that ARP
may function as a factor involved in the stress
response. .
Length = 88
Score = 24.7 bits (54), Expect = 8.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYG 29
KVLY+ NL T+ +L+ F QYG
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYG 25
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 24.6 bits (54), Expect = 8.7
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVER---VKRIKDYAFVHFED 47
LY+ NL+ E L++ FE++ VK+ YAFV D
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-GGYAFVDCPD 43
>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 = 24.7 bits (53), Expect = 9.2
Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 8/56 (14%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQE 50
+++ L++ L+ T++ L+E FE++G R + KR + + FV + +E
Sbjct: 1 QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEE 56
>gnl|CDD|193584 cd09895, NGN_SP_UpxY, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), UpxY. The
N-Utilization Substance G (NusG) proteins are involved
in transcription elongation and termination. NusG is
essential in Escherichia coli and is associated with
RNA polymerase elongation and Rho-termination. Paralogs
of eubacterial NusG, NusG SP (Specialized Paralog of
NusG), are more diverse and often found as the first
ORF in operons encoding secreted proteins and LPS
(lipopolysaccharide) biosynthesis genes. NusG SP family
members are operon-specific transcriptional
antitermination factors. UpxY proteins, UpxY proteins,
where the x is replaced by the letter designation of
the specific polysaccharide (UpaY to UphY), are a
family of NusG SP factors that act specifically in
transcriptional antitermination of operons from which
they are encoded. UpxYs are necessary and specific for
transcription regulation of the polysaccharide
biosynthesis operon. Orthologs of the NusG gene exist
in all bacteria, but their functions and requirements
are different. The NusG N-terminal (NGN) domain is
similar in all NusG orthologs, but its C-terminal
domain and the linker that separate these two domains
are different. The domain organization of NusG and its
orthologs suggests that the common properties of NusG
and its orthologs and paralogs are due to their similar
NGN domains.
Length = 95
Score = 24.8 bits (55), Expect = 9.4
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 24/78 (30%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYG----------------RVERVKR--IKDYAFVH--F 45
LY E+K+ E E+ G R +RV+ + FVH
Sbjct: 4 ALYTF----PRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITR 59
Query: 46 EDRQEAITVTGLSQVIIY 63
E+ E + G+ + + Y
Sbjct: 60 EELDEVLETPGVVRFVRY 77
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.391
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: 6,664,381
Number of extensions: 586980
Number of successful extensions: 1140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1055
Number of HSP's successfully gapped: 373
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)