RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2160
(773 letters)
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 91
Score = 146 bits (372), Expect = 6e-42
Identities = 58/91 (63%), Positives = 68/91 (74%)
Query: 349 ESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEP 408
E V+I+KNLF P F++D TLI E + DLREEC K G VKKVV+ D+HP+GVA + FKEP
Sbjct: 1 EKVVILKNLFSPEEFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEP 60
Query: 409 EAADACRELLNGRWFGQRQITAETWDGKTRY 439
E AD C E LNGRWF RQ+ AE WDGKT Y
Sbjct: 61 EEADRCIEALNGRWFAGRQLEAERWDGKTDY 91
Score = 146 bits (372), Expect = 6e-42
Identities = 58/91 (63%), Positives = 68/91 (74%)
Query: 634 ESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEP 693
E V+I+KNLF P F++D TLI E + DLREEC K G VKKVV+ D+HP+GVA + FKEP
Sbjct: 1 EKVVILKNLFSPEEFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEP 60
Query: 694 EAADACRELLNGRWFGQRQITAETWDGKTRY 724
E AD C E LNGRWF RQ+ AE WDGKT Y
Sbjct: 61 EEADRCIEALNGRWFAGRQLEAERWDGKTDY 91
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 141 bits (359), Expect = 5e-40
Identities = 58/93 (62%), Positives = 71/93 (76%), Gaps = 2/93 (2%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
NT VYVS LPLD+T EEFVEV KCG++ +D +T + KIKLY D KGDALC Y+K
Sbjct: 1 NTNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGN-LKGDALCCYLK 59
Query: 560 KESVDLALSILDGYEI-RGKKIKVERAKFTMKG 591
+ESV+LA+ +LDG EI RG K+KVERAKF +KG
Sbjct: 60 EESVELAIQLLDGTEIGRGYKMKVERAKFQLKG 92
Score = 139 bits (352), Expect = 5e-39
Identities = 57/92 (61%), Positives = 70/92 (76%), Gaps = 2/92 (2%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T VYVS LPLD+T EEFVEV KCG++ +D +T + KIKLY D KGDALC Y+K+
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGN-LKGDALCCYLKE 60
Query: 276 ESVDLALSILDGYEI-RGKKIKVERAKFTMKG 306
ESV+LA+ +LDG EI RG K+KVERAKF +KG
Sbjct: 61 ESVELAIQLLDGTEIGRGYKMKVERAKFQLKG 92
Score = 30.6 bits (70), Expect = 0.57
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 456 ETFLGKKIKVERAKFTMKG 474
E G K+KVERAKF +KG
Sbjct: 74 EIGRGYKMKVERAKFQLKG 92
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 100 bits (251), Expect = 2e-25
Identities = 40/84 (47%), Positives = 52/84 (61%), Gaps = 1/84 (1%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEA 410
+I+KN+FDPA +D E ++D+ EECSK G V+ + + PEGV + FK EA
Sbjct: 3 CVILKNMFDPAEETED-EWDDEIKEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEA 61
Query: 411 ADACRELLNGRWFGQRQITAETWD 434
A C + LNGRWF RQITAE D
Sbjct: 62 AQKCIQALNGRWFDGRQITAEYVD 85
Score = 100 bits (251), Expect = 2e-25
Identities = 40/84 (47%), Positives = 52/84 (61%), Gaps = 1/84 (1%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEA 695
+I+KN+FDPA +D E ++D+ EECSK G V+ + + PEGV + FK EA
Sbjct: 3 CVILKNMFDPAEETED-EWDDEIKEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEA 61
Query: 696 ADACRELLNGRWFGQRQITAETWD 719
A C + LNGRWF RQITAE D
Sbjct: 62 AQKCIQALNGRWFDGRQITAEYVD 85
>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 = 70.4 bits (173), Expect = 4e-15
Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+Y+S LP D+T++ E+ G++ +D T IK+YTD T+ KG+A TY +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKGEATVTYDDPSA 59
Query: 278 VDLALSILDGYEIRGKKIKVE 298
A+ +GYE RG KIKV
Sbjct: 60 AQAAIEWFNGYEFRGNKIKVS 80
Score = 70.4 bits (173), Expect = 4e-15
Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+Y+S LP D+T++ E+ G++ +D T IK+YTD T+ KG+A TY +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKGEATVTYDDPSA 59
Query: 563 VDLALSILDGYEIRGKKIKVE 583
A+ +GYE RG KIKV
Sbjct: 60 AQAAIEWFNGYEFRGNKIKVS 80
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 61.5 bits (150), Expect = 8e-12
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 11/89 (12%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH---PEGVAQIF--F 405
+++++N+ P D+D+ + ++ EEC K G V V++H+ + +IF F
Sbjct: 3 ILVLRNMVTPGEIDEDL------KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEF 56
Query: 406 KEPEAADACRELLNGRWFGQRQITAETWD 434
+ + A LNGR+FG R++TA +D
Sbjct: 57 SDADEAIKAVRALNGRFFGGRKVTARFYD 85
Score = 61.5 bits (150), Expect = 8e-12
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 11/89 (12%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH---PEGVAQIF--F 690
+++++N+ P D+D+ + ++ EEC K G V V++H+ + +IF F
Sbjct: 3 ILVLRNMVTPGEIDEDL------KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEF 56
Query: 691 KEPEAADACRELLNGRWFGQRQITAETWD 719
+ + A LNGR+FG R++TA +D
Sbjct: 57 SDADEAIKAVRALNGRFFGGRKVTARFYD 85
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 60.3 bits (147), Expect = 1e-11
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++V NLP D T+EE E+ K G V ++L D T KG A + +E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVES--------VRLVRDKETGKSKGFAFVEFESEE 52
Query: 277 SVDLALSILDGYEIRGKKIKV 297
+ AL L+G E+ G+ +KV
Sbjct: 53 DAEKALEALNGKELDGRPLKV 73
Score = 60.3 bits (147), Expect = 1e-11
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++V NLP D T+EE E+ K G V ++L D T KG A + +E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVES--------VRLVRDKETGKSKGFAFVEFESEE 52
Query: 562 SVDLALSILDGYEIRGKKIKV 582
+ AL L+G E+ G+ +KV
Sbjct: 53 DAEKALEALNGKELDGRPLKV 73
Score = 46.8 bits (112), Expect = 8e-07
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFK 406
+ V NL D T +++LRE SK G V+ V ++ DK +G A + F+
Sbjct: 1 TLFVGNL------PPDTT-----EEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFE 49
Query: 407 EPEAADACRELLNGRWFGQRQIT 429
E A+ E LNG+ R +
Sbjct: 50 SEEDAEKALEALNGKELDGRPLK 72
Score = 46.8 bits (112), Expect = 8e-07
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFK 691
+ V NL D T +++LRE SK G V+ V ++ DK +G A + F+
Sbjct: 1 TLFVGNL------PPDTT-----EEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFE 49
Query: 692 EPEAADACRELLNGRWFGQRQIT 714
E A+ E LNG+ R +
Sbjct: 50 SEEDAEKALEALNGKELDGRPLK 72
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 61.3 bits (149), Expect = 1e-11
Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 14/92 (15%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIF 404
V++++N+ P D D+ + ++ EEC K G V +V+++ ++ E + +IF
Sbjct: 3 VMVLRNMVGPEDLDDDL------EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIF 56
Query: 405 --FKEPEAADACRELLNGRWFGQRQITAETWD 434
F P A+ + LNGRWFG R++ AE +D
Sbjct: 57 VEFSLPSEAEKAIQALNGRWFGGRKVKAELYD 88
Score = 61.3 bits (149), Expect = 1e-11
Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 14/92 (15%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIF 689
V++++N+ P D D+ + ++ EEC K G V +V+++ ++ E + +IF
Sbjct: 3 VMVLRNMVGPEDLDDDL------EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIF 56
Query: 690 --FKEPEAADACRELLNGRWFGQRQITAETWD 719
F P A+ + LNGRWFG R++ AE +D
Sbjct: 57 VEFSLPSEAEKAIQALNGRWFGGRKVKAELYD 88
>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 = 57.7 bits (140), Expect = 1e-10
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NLP D T+E+ E+ K G + +++ D K KG A + E
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIES--------VRIVRDKDGK-SKGFAFVEFESPED 51
Query: 278 VDLALSILDGYEIRGKKIKVE 298
+ AL L+G E+ G+K+KV
Sbjct: 52 AEKALEALNGKELDGRKLKVS 72
Score = 57.7 bits (140), Expect = 1e-10
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NLP D T+E+ E+ K G + +++ D K KG A + E
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIES--------VRIVRDKDGK-SKGFAFVEFESPED 51
Query: 563 VDLALSILDGYEIRGKKIKVE 583
+ AL L+G E+ G+K+KV
Sbjct: 52 AEKALEALNGKELDGRKLKVS 72
Score = 50.4 bits (121), Expect = 5e-08
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 14/83 (16%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEP 408
+ V NL D T ++DLRE SK G ++ V + D +G A + F+ P
Sbjct: 1 LFVGNL------PPDTT-----EEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESP 49
Query: 409 EAADACRELLNGRWFGQRQITAE 431
E A+ E LNG+ R++
Sbjct: 50 EDAEKALEALNGKELDGRKLKVS 72
Score = 50.4 bits (121), Expect = 5e-08
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 14/83 (16%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEP 693
+ V NL D T ++DLRE SK G ++ V + D +G A + F+ P
Sbjct: 1 LFVGNL------PPDTT-----EEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESP 49
Query: 694 EAADACRELLNGRWFGQRQITAE 716
E A+ E LNG+ R++
Sbjct: 50 EDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 56.0 bits (136), Expect = 6e-10
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 12/90 (13%)
Query: 351 VIIVKNLFDPALF--DKDVTLILEYQQDLREECSKCGHVKKVVL-----HDKHPEGVAQI 403
V+ + N+ P D++ ILE D++EEC K G V VV+ GV ++
Sbjct: 3 VLCLLNMVTPEELEDDEEYEEILE---DVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKV 59
Query: 404 F--FKEPEAADACRELLNGRWFGQRQITAE 431
F F + E A + L GR F R + A
Sbjct: 60 FVEFADVEDAQKAQLALAGRKFDGRTVVAS 89
Score = 56.0 bits (136), Expect = 6e-10
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 12/90 (13%)
Query: 636 VIIVKNLFDPALF--DKDVTLILEYQQDLREECSKCGHVKKVVL-----HDKHPEGVAQI 688
V+ + N+ P D++ ILE D++EEC K G V VV+ GV ++
Sbjct: 3 VLCLLNMVTPEELEDDEEYEEILE---DVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKV 59
Query: 689 F--FKEPEAADACRELLNGRWFGQRQITAE 716
F F + E A + L GR F R + A
Sbjct: 60 FVEFADVEDAQKAQLALAGRKFDGRTVVAS 89
>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 = 55.3 bits (134), Expect = 8e-10
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+V N+P D T+E+ +E+ + G V+ +L TD T KG C + E+
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVS--------FRLVTDRDTGKPKGYGFCEFEDIET 52
Query: 278 VDLALSILDGYEIRGKKIKVERA 300
A+ L+GYE G+ ++V+ A
Sbjct: 53 AASAIRNLNGYEFNGRALRVDFA 75
Score = 55.3 bits (134), Expect = 8e-10
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+V N+P D T+E+ +E+ + G V+ +L TD T KG C + E+
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVS--------FRLVTDRDTGKPKGYGFCEFEDIET 52
Query: 563 VDLALSILDGYEIRGKKIKVERA 585
A+ L+GYE G+ ++V+ A
Sbjct: 53 AASAIRNLNGYEFNGRALRVDFA 75
Score = 35.7 bits (83), Expect = 0.008
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPE-AADACRELLNGRWFGQRQI 428
++ L E S+ G V ++ D+ P+G F++ E AA A R LNG F R +
Sbjct: 12 EEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN-LNGYEFNGRAL 70
Score = 35.7 bits (83), Expect = 0.008
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPE-AADACRELLNGRWFGQRQI 713
++ L E S+ G V ++ D+ P+G F++ E AA A R LNG F R +
Sbjct: 12 EEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN-LNGYEFNGRAL 70
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 60.7 bits (146), Expect = 8e-10
Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 8/172 (4%)
Query: 151 SYGFIEQPNTVDEKKPSADLVQSKVEEKSVDATAPMENPKAEEKVVPGQKRKPEPPKWFD 210
+ IE + KK + + E+ ++ E +E + P
Sbjct: 51 NSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQK 110
Query: 211 IGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 270
EE+ ++V NLP D+T+E+ E+ +K G V +++L D T +G A
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPV--------KRVRLVRDRETGKSRGFAFV 162
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKD 322
+ +ES + A+ L+G E+ G+ ++V++A+ + + KK
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKL 214
Score = 53.8 bits (128), Expect = 1e-07
Identities = 30/128 (23%), Positives = 61/128 (47%), Gaps = 8/128 (6%)
Query: 480 KLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIK 539
+ + + + + K +EN ++V NLP D+T+E+ E+ +K G V + ++
Sbjct: 95 EEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKR--------VR 146
Query: 540 LYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLK 599
L D T +G A + +ES + A+ L+G E+ G+ ++V++A+ + +
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNL 206
Query: 600 PKKKRKKD 607
KK
Sbjct: 207 DASFAKKL 214
Score = 39.2 bits (90), Expect = 0.005
Identities = 41/192 (21%), Positives = 72/192 (37%), Gaps = 23/192 (11%)
Query: 315 PKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ 374
++ + + +E K R + + + + V NL DVT +
Sbjct: 81 EEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNL------PYDVT-----E 129
Query: 375 QDLREECSKCGHVKKVVLH----DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
+DLRE K G VK+V L G A + F+ E+A+ E LNG+ R +
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRV 189
Query: 431 ETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKD 490
+ K Q ++ R + KK+ +A K + P K +++
Sbjct: 190 Q--------KAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEE 241
Query: 491 LEKLKKAQENTK 502
L L K++ +
Sbjct: 242 LADLFKSRGDIV 253
Score = 36.8 bits (84), Expect = 0.034
Identities = 29/118 (24%), Positives = 47/118 (39%), Gaps = 15/118 (12%)
Query: 600 PKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ 659
++ + + +E K R + + + + V NL DVT +
Sbjct: 81 EEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNL------PYDVT-----E 129
Query: 660 QDLREECSKCGHVKKVVLH----DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+DLRE K G VK+V L G A + F+ E+A+ E LNG+ R +
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPL 187
>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 = 61.1 bits (148), Expect = 1e-09
Identities = 50/228 (21%), Positives = 93/228 (40%), Gaps = 34/228 (14%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ ++Y+ NLPL L +++ E+++ G + L D T KG A C Y
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFG--------DLKAFNLIKDIATGLSKGYAFCEY 344
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
D+A++ L+G + K+ V+RA + K +
Sbjct: 345 KDPSVTDVAIAALNGKDTGDNKLHVQRACVGAN----QATIDTSNGMAPVTLLAKALSQS 400
Query: 333 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ---QDLREECSKCGHVKK 389
+ ++ G+ +K V+ + NL + D+ EY+ +D++ E SK G +
Sbjct: 401 IL-----QIGGKPTK---VVQLTNL----VTGDDLMDDEEYEEIYEDVKTEFSKYGPLIN 448
Query: 390 VVLHDKHP-----EGVAQIFFKEPEAADA--CRELLNGRWFGQRQITA 430
+V+ + GV ++F + + A E +NGR F R + A
Sbjct: 449 IVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVA 496
Score = 59.5 bits (144), Expect = 3e-09
Identities = 50/224 (22%), Positives = 92/224 (41%), Gaps = 34/224 (15%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++Y+ NLPL L +++ E+++ G + L D T KG A C Y
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFG--------DLKAFNLIKDIATGLSKGYAFCEYKDPS 348
Query: 562 SVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDW 621
D+A++ L+G + K+ V+RA + K + +
Sbjct: 349 VTDVAIAALNGKDTGDNKLHVQRACVGAN----QATIDTSNGMAPVTLLAKALSQSIL-- 402
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ---QDLREECSKCGHVKKVVLH 678
++ G+ +K V+ + NL + D+ EY+ +D++ E SK G + +V+
Sbjct: 403 ---QIGGKPTK---VVQLTNL----VTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP 452
Query: 679 DKHP-----EGVAQIFFKEPEAADA--CRELLNGRWFGQRQITA 715
+ GV ++F + + A E +NGR F R + A
Sbjct: 453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVA 496
>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 = 53.8 bits (130), Expect = 2e-09
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NLP D T+E+ ++ K G + I++ D T KG A + +E
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIES--------IRIVRDE-TGRSKGFAFVEFEDEED 51
Query: 278 VDLALSILDGYEIRGKKIK 296
+ AL L+G E+ G++++
Sbjct: 52 AEKALEALNGKELGGRELR 70
Score = 53.8 bits (130), Expect = 2e-09
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NLP D T+E+ ++ K G + I++ D T KG A + +E
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIES--------IRIVRDE-TGRSKGFAFVEFEDEED 51
Query: 563 VDLALSILDGYEIRGKKIK 581
+ AL L+G E+ G++++
Sbjct: 52 AEKALEALNGKELGGRELR 70
Score = 41.0 bits (97), Expect = 7e-05
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH---DKHPEGVAQIFFKEP 408
+ V NL D T ++DL++ SK G ++ + + +G A + F++
Sbjct: 1 LFVGNL------PPDTT-----EEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDE 49
Query: 409 EAADACRELLNGRWFGQRQIT 429
E A+ E LNG+ G R++
Sbjct: 50 EDAEKALEALNGKELGGRELR 70
Score = 41.0 bits (97), Expect = 7e-05
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH---DKHPEGVAQIFFKEP 693
+ V NL D T ++DL++ SK G ++ + + +G A + F++
Sbjct: 1 LFVGNL------PPDTT-----EEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDE 49
Query: 694 EAADACRELLNGRWFGQRQIT 714
E A+ E LNG+ G R++
Sbjct: 50 EDAEKALEALNGKELGGRELR 70
>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 = 59.9 bits (145), Expect = 3e-09
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 411
+++ N+FDPA +++ E D++EECSK G V + + K+ G + F +AA
Sbjct: 365 LVLSNMFDPAT-EEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAA 423
Query: 412 DACRELLNGRWFGQRQITA 430
A + LNGR+FG + ITA
Sbjct: 424 LAAFQALNGRYFGGKMITA 442
Score = 59.9 bits (145), Expect = 3e-09
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 696
+++ N+FDPA +++ E D++EECSK G V + + K+ G + F +AA
Sbjct: 365 LVLSNMFDPAT-EEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAA 423
Query: 697 DACRELLNGRWFGQRQITA 715
A + LNGR+FG + ITA
Sbjct: 424 LAAFQALNGRYFGGKMITA 442
Score = 37.2 bits (86), Expect = 0.036
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
K+YV NL ++T++E ++ + G + ++L+ DP T KG + E
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIED--------VQLHRDPETGRSKGFGFIQFHDAE 239
Query: 277 SVDLALSILDGYEIRGKKIKV 297
AL +++G+E+ G+ IKV
Sbjct: 240 EAKEALEVMNGFELAGRPIKV 260
Score = 37.2 bits (86), Expect = 0.036
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
K+YV NL ++T++E ++ + G + ++L+ DP T KG + E
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIED--------VQLHRDPETGRSKGFGFIQFHDAE 239
Query: 562 SVDLALSILDGYEIRGKKIKV 582
AL +++G+E+ G+ IKV
Sbjct: 240 EAKEALEVMNGFELAGRPIKV 260
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 52.4 bits (126), Expect = 1e-08
Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+VSNLP + T+++ E G++ D T + KI LY D T + KG+A TY +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 278 VDLALSILDGYEIRGKKIKVERA 300
A+ + + G IKV A
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83
Score = 52.4 bits (126), Expect = 1e-08
Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+VSNLP + T+++ E G++ D T + KI LY D T + KG+A TY +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 563 VDLALSILDGYEIRGKKIKVERA 585
A+ + + G IKV A
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83
>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 = 57.8 bits (139), Expect = 2e-08
Identities = 38/143 (26%), Positives = 68/143 (47%), Gaps = 20/143 (13%)
Query: 305 KGEAYDPKLKPKKKRKKDLEKLKKAQEKLF----DWRPDKMRGERSKNES-VIIVKNLFD 359
K E +L+PK + L QE + R M+ N S VI+++N+
Sbjct: 466 KKEKEGEELQPKLVMNSEDASLAS-QEGMSIRGNSARHLVMQKLMRTNRSNVIVLRNMVT 524
Query: 360 PALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIFFKEPEAADA 413
P D+ + + ++REEC K G V +V+++ ++ E + +IF + ++ +
Sbjct: 525 PQDIDEFL------EGEIREECGKFGVVDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEV 578
Query: 414 CR--ELLNGRWFGQRQITAETWD 434
R L+GR+FG R + AE +D
Sbjct: 579 DRAKAALDGRFFGGRTVVAEAYD 601
Score = 57.8 bits (139), Expect = 2e-08
Identities = 38/143 (26%), Positives = 68/143 (47%), Gaps = 20/143 (13%)
Query: 590 KGEAYDPKLKPKKKRKKDLEKLKKAQEKLF----DWRPDKMRGERSKNES-VIIVKNLFD 644
K E +L+PK + L QE + R M+ N S VI+++N+
Sbjct: 466 KKEKEGEELQPKLVMNSEDASLAS-QEGMSIRGNSARHLVMQKLMRTNRSNVIVLRNMVT 524
Query: 645 PALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIFFKEPEAADA 698
P D+ + + ++REEC K G V +V+++ ++ E + +IF + ++ +
Sbjct: 525 PQDIDEFL------EGEIREECGKFGVVDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEV 578
Query: 699 CR--ELLNGRWFGQRQITAETWD 719
R L+GR+FG R + AE +D
Sbjct: 579 DRAKAALDGRFFGGRTVVAEAYD 601
Score = 33.1 bits (75), Expect = 0.67
Identities = 17/91 (18%), Positives = 46/91 (50%), Gaps = 8/91 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++A++ ++YV+++ DL++ + V + G + +K +L P + KG
Sbjct: 199 EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEI--------VKCQLARAPTGRGHKGYGF 250
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
Y +S A++ ++ +++ G+ ++V +
Sbjct: 251 IEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281
>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 = 50.3 bits (121), Expect = 5e-08
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
+V+V +P DL ++E V + +K G + +++L D + +G A TY K
Sbjct: 2 CEVFVGKIPRDLFEDELVPLFEKAGPI--------YELRLMMDFSGLN-RGYAFVTYTNK 52
Query: 276 ESVDLALSILDGYEIR-GKKIKVER 299
E+ A+ L YEIR GK++ V
Sbjct: 53 EAAQRAVKQLHNYEIRPGKRLGVCI 77
Score = 50.3 bits (121), Expect = 5e-08
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+V+V +P DL ++E V + +K G + +++L D + +G A TY K
Sbjct: 2 CEVFVGKIPRDLFEDELVPLFEKAGPI--------YELRLMMDFSGLN-RGYAFVTYTNK 52
Query: 561 ESVDLALSILDGYEIR-GKKIKVER 584
E+ A+ L YEIR GK++ V
Sbjct: 53 EAAQRAVKQLHNYEIRPGKRLGVCI 77
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 48.7 bits (116), Expect = 2e-07
Identities = 28/80 (35%), Positives = 42/80 (52%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV L ++T EE + + CG+V + T Q + +YTD T KGDA +Y S
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 278 VDLALSILDGYEIRGKKIKV 297
A+ DG + +G K+KV
Sbjct: 63 AKAAVEWFDGKDFQGSKLKV 82
Score = 48.7 bits (116), Expect = 2e-07
Identities = 28/80 (35%), Positives = 42/80 (52%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV L ++T EE + + CG+V + T Q + +YTD T KGDA +Y S
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 563 VDLALSILDGYEIRGKKIKV 582
A+ DG + +G K+KV
Sbjct: 63 AKAAVEWFDGKDFQGSKLKV 82
>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 = 47.3 bits (113), Expect = 5e-07
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V N+ T EE E + CG + +I + D +T KG A ++ K S
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTI--------NRITILCDKFTGQPKGFAYIEFLDKSS 53
Query: 278 VDLALSILDGYEIRGKKIKV 297
V+ AL L+ E RG++IKV
Sbjct: 54 VENALL-LNESEFRGRQIKV 72
Score = 47.3 bits (113), Expect = 5e-07
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V N+ T EE E + CG + +I + D +T KG A ++ K S
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTI--------NRITILCDKFTGQPKGFAYIEFLDKSS 53
Query: 563 VDLALSILDGYEIRGKKIKV 582
V+ AL L+ E RG++IKV
Sbjct: 54 VENALL-LNESEFRGRQIKV 72
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 48.0 bits (115), Expect = 6e-07
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 12/90 (13%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH----PEGVAQIF-- 404
V++++N+ P D+D+ + +++EECSK G V KV++ + + +IF
Sbjct: 4 VVLLRNMVGPGEVDEDL------EPEVKEECSKYGKVTKVLIFEIPGASPDDEAVRIFVE 57
Query: 405 FKEPEAADACRELLNGRWFGQRQITAETWD 434
F+ E+A LNGR+FG R + A +D
Sbjct: 58 FERVESAIKAVVDLNGRFFGGRTVKASFYD 87
Score = 48.0 bits (115), Expect = 6e-07
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 12/90 (13%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH----PEGVAQIF-- 689
V++++N+ P D+D+ + +++EECSK G V KV++ + + +IF
Sbjct: 4 VVLLRNMVGPGEVDEDL------EPEVKEECSKYGKVTKVLIFEIPGASPDDEAVRIFVE 57
Query: 690 FKEPEAADACRELLNGRWFGQRQITAETWD 719
F+ E+A LNGR+FG R + A +D
Sbjct: 58 FERVESAIKAVVDLNGRFFGGRTVKASFYD 87
>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 = 46.5 bits (111), Expect = 1e-06
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+YV NLP ++T+E+ ++ + G V ++ TD T +G E
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTS--------ARVITDRETGRSRGFGFVEMETAE 52
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
+ A+ L+G + G+ + V A+
Sbjct: 53 EANAAIEKLNGTDFGGRTLTVNEAR 77
Score = 46.5 bits (111), Expect = 1e-06
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+YV NLP ++T+E+ ++ + G V ++ TD T +G E
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTS--------ARVITDRETGRSRGFGFVEMETAE 52
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
+ A+ L+G + G+ + V A+
Sbjct: 53 EANAAIEKLNGTDFGGRTLTVNEAR 77
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
K++VS L T++E + K G V + MK DP T + +G T+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRV---EEVLLMK-----DPETGESRGFGFVTFESV 53
Query: 276 ESVDLALSILDGYEIRGKKIKVERAK 301
E D A+ L+G E+ G+ IKVE+AK
Sbjct: 54 EDADAAIRDLNGKELEGRVIKVEKAK 79
Score = 45.7 bits (109), Expect = 2e-06
Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
K++VS L T++E + K G V + MK DP T + +G T+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRV---EEVLLMK-----DPETGESRGFGFVTFESV 53
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
E D A+ L+G E+ G+ IKVE+AK
Sbjct: 54 EDADAAIRDLNGKELEGRVIKVEKAK 79
Score = 29.9 bits (68), Expect = 0.83
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 376 DLREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
+L SK G V++V+L K PE G + F+ E ADA LNG+ R I
Sbjct: 17 ELEALFSKFGRVEEVLLM-KDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKV 75
Query: 431 E 431
E
Sbjct: 76 E 76
Score = 29.9 bits (68), Expect = 0.83
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 661 DLREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQITA 715
+L SK G V++V+L K PE G + F+ E ADA LNG+ R I
Sbjct: 17 ELEALFSKFGRVEEVLLM-KDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKV 75
Query: 716 E 716
E
Sbjct: 76 E 76
>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 = 45.6 bits (108), Expect = 3e-06
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+V N+P + T+E+ ++ + G V+ +L D T KG C Y +E+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVS--------FRLVYDRETGKPKGYGFCEYKDQET 52
Query: 278 VDLALSILDGYEIRGKKIKVERA 300
A+ L+GYE+ G++++V+ A
Sbjct: 53 ALSAMRNLNGYELNGRQLRVDNA 75
Score = 45.6 bits (108), Expect = 3e-06
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+V N+P + T+E+ ++ + G V+ +L D T KG C Y +E+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVS--------FRLVYDRETGKPKGYGFCEYKDQET 52
Query: 563 VDLALSILDGYEIRGKKIKVERA 585
A+ L+GYE+ G++++V+ A
Sbjct: 53 ALSAMRNLNGYELNGRQLRVDNA 75
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 45.3 bits (107), Expect = 3e-06
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T+V+V +P DL ++E V + +K G + ++L DP + +G A T+ K
Sbjct: 2 TEVFVGKIPRDLYEDELVPLFEKAGPIWD--------LRLMMDPLSGQNRGYAFITFCGK 53
Query: 276 ESVDLALSILDGYEIR-GKKIKV 297
E+ A+ + D YEIR GK + V
Sbjct: 54 EAAQEAVKLCDNYEIRPGKHLGV 76
Score = 45.3 bits (107), Expect = 3e-06
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T+V+V +P DL ++E V + +K G + ++L DP + +G A T+ K
Sbjct: 2 TEVFVGKIPRDLYEDELVPLFEKAGPIWD--------LRLMMDPLSGQNRGYAFITFCGK 53
Query: 561 ESVDLALSILDGYEIR-GKKIKV 582
E+ A+ + D YEIR GK + V
Sbjct: 54 EAAQEAVKLCDNYEIRPGKHLGV 76
>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 = 50.2 bits (120), Expect = 4e-06
Identities = 64/269 (23%), Positives = 106/269 (39%), Gaps = 80/269 (29%)
Query: 488 KKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYT 542
KK + ++ T +YV NL + +++ E+ K G VMKD
Sbjct: 166 KKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRS------- 218
Query: 543 DPYTKDFKGDALCTYIKKESVDLALSILDGYEI----RGKKIKVERAKFTMKGEAYDPKL 598
+G A + K E A+ ++G +I GKK+ V RA
Sbjct: 219 -------RGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRA------------- 258
Query: 599 KPKKKRKKDLEKL--KKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLIL 656
+ + +R+ +L + + QE R +++ + VKN D + D
Sbjct: 259 QKRAEREAELRRKFEELQQE----------RKMKAQG-VNLYVKN-LDDTVTD------- 299
Query: 657 EYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIF----FKEPEAADACRELLNGRWFGQ 710
+ LRE S+CG + KV+L +K GV++ F F PE A+ ++GR G
Sbjct: 300 ---EKLRELFSECGEITSAKVMLDEK---GVSRGFGFVCFSNPEEANRAVTEMHGRMLG- 352
Query: 711 RQITAETWDGKTRY-KIQETAEEREARLK 738
GK Y + + E+R A L+
Sbjct: 353 ---------GKPLYVALAQRKEQRRAHLQ 372
Score = 48.6 bits (116), Expect = 8e-06
Identities = 66/279 (23%), Positives = 109/279 (39%), Gaps = 86/279 (30%)
Query: 193 EKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVD 247
+ + +R+ P K F T +YV NL + +++ E+ K G VMKD
Sbjct: 162 GRFIKKHEREAAPLKKF------TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS 215
Query: 248 TNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI----RGKKIKVERAKFT 303
+G A + K E A+ ++G +I GKK+ V RA
Sbjct: 216 GRS--------------RGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRA--- 258
Query: 304 MKGEAYDPKLKPKKKRKKDLEKL--KKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPA 361
+ + +R+ +L + + QE R +++ + VKN D
Sbjct: 259 ----------QKRAEREAELRRKFEELQQE----------RKMKAQG-VNLYVKN-LDDT 296
Query: 362 LFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIF----FKEPEAADACR 415
+ D + LRE S+CG + KV+L +K GV++ F F PE A+
Sbjct: 297 VTD----------EKLRELFSECGEITSAKVMLDEK---GVSRGFGFVCFSNPEEANRAV 343
Query: 416 ELLNGRWFGQRQITAETWDGKTRY-KIQETAEEREARLK 453
++GR G GK Y + + E+R A L+
Sbjct: 344 TEMHGRMLG----------GKPLYVALAQRKEQRRAHLQ 372
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 44.9 bits (107), Expect = 8e-06
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 375 QDLREECSKCGHVKKVVLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
+D+ E S+ G ++ +V+ D H G + F+ E A+A + LNGR++ R + E
Sbjct: 40 EDVFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99
Score = 44.9 bits (107), Expect = 8e-06
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 660 QDLREECSKCGHVKKVVLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
+D+ E S+ G ++ +V+ D H G + F+ E A+A + LNGR++ R + E
Sbjct: 40 EDVFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 42.5 bits (101), Expect = 2e-05
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 10/79 (12%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NLP +T+E+ E G V +++ D +G A + E
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKV------EGVRLVRNKDR----PRGFAFVEFASPED 50
Query: 278 VDLALSILDGYEIRGKKIK 296
+ AL L+G + G+ ++
Sbjct: 51 AEAALKKLNGLVLDGRTLR 69
Score = 42.5 bits (101), Expect = 2e-05
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 10/79 (12%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV NLP +T+E+ E G V +++ D +G A + E
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKV------EGVRLVRNKDR----PRGFAFVEFASPED 50
Query: 563 VDLALSILDGYEIRGKKIK 581
+ AL L+G + G+ ++
Sbjct: 51 AEAALKKLNGLVLDGRTLR 69
Score = 42.2 bits (100), Expect = 3e-05
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 13/79 (16%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL--HDKHPEGVAQIFFKEPE 409
+ V+NL VT +DLRE S G V+ V L + P G A + F PE
Sbjct: 1 LYVRNL------PPSVTE-----EDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPE 49
Query: 410 AADACRELLNGRWFGQRQI 428
A+A + LNG R +
Sbjct: 50 DAEAALKKLNGLVLDGRTL 68
Score = 42.2 bits (100), Expect = 3e-05
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 13/79 (16%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL--HDKHPEGVAQIFFKEPE 694
+ V+NL VT +DLRE S G V+ V L + P G A + F PE
Sbjct: 1 LYVRNL------PPSVTE-----EDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPE 49
Query: 695 AADACRELLNGRWFGQRQI 713
A+A + LNG R +
Sbjct: 50 DAEAALKKLNGLVLDGRTL 68
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 43.0 bits (101), Expect = 3e-05
Identities = 27/84 (32%), Positives = 41/84 (48%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+N ++V L D+T E + ++ G++ + T Q I LYTD T KG+A ++
Sbjct: 1 DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60
Query: 559 KKESVDLALSILDGYEIRGKKIKV 582
S A+ DG E G IKV
Sbjct: 61 DPPSAKAAIDWFDGKEFSGNPIKV 84
Score = 40.7 bits (95), Expect = 2e-04
Identities = 26/84 (30%), Positives = 41/84 (48%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
++ ++V L D+T E + ++ G++ + T Q I LYTD T KG+A ++
Sbjct: 1 DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60
Query: 274 KKESVDLALSILDGYEIRGKKIKV 297
S A+ DG E G IKV
Sbjct: 61 DPPSAKAAIDWFDGKEFSGNPIKV 84
>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 = 42.3 bits (100), Expect = 3e-05
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NLP D T E+ + + G ++L TD T KG A + E+
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPS--------VRLLTDKKTGKSKGCAFVEFDTAEA 54
Query: 278 VDLALSILDGYEIRGKKIKVE 298
+ AL L ++G+KI VE
Sbjct: 55 MTKALK-LHHTLLKGRKINVE 74
Score = 42.3 bits (100), Expect = 3e-05
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NLP D T E+ + + G ++L TD T KG A + E+
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPS--------VRLLTDKKTGKSKGCAFVEFDTAEA 54
Query: 563 VDLALSILDGYEIRGKKIKVE 583
+ AL L ++G+KI VE
Sbjct: 55 MTKALK-LHHTLLKGRKINVE 74
>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 = 41.9 bits (99), Expect = 5e-05
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 219 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 278
YV NL ++T+++ + + G + ++L DP T KG + E
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEF--------VQLQRDPETGRSKGYGFIQFADAEDA 53
Query: 279 DLALSILDGYEIRGKKIKV 297
AL L+G+E+ G+ IKV
Sbjct: 54 KKALEQLNGFELAGRPIKV 72
Score = 41.9 bits (99), Expect = 5e-05
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 504 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 563
YV NL ++T+++ + + G + ++L DP T KG + E
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEF--------VQLQRDPETGRSKGYGFIQFADAEDA 53
Query: 564 DLALSILDGYEIRGKKIKV 582
AL L+G+E+ G+ IKV
Sbjct: 54 KKALEQLNGFELAGRPIKV 72
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 41.9 bits (98), Expect = 5e-05
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T+++V +P DL ++E V + +K G + ++L DP T +G A T+ K
Sbjct: 2 TEIFVGKIPRDLFEDELVPLFEKAGPIWD--------LRLMMDPLTGLNRGYAFVTFCTK 53
Query: 276 ESVDLALSILDGYEIR-GKKIKV 297
E+ A+ + + +EIR GK I V
Sbjct: 54 EAAQEAVKLYNNHEIRPGKHIGV 76
Score = 41.9 bits (98), Expect = 5e-05
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T+++V +P DL ++E V + +K G + ++L DP T +G A T+ K
Sbjct: 2 TEIFVGKIPRDLFEDELVPLFEKAGPIWD--------LRLMMDPLTGLNRGYAFVTFCTK 53
Query: 561 ESVDLALSILDGYEIR-GKKIKV 582
E+ A+ + + +EIR GK I V
Sbjct: 54 EAAQEAVKLYNNHEIRPGKHIGV 76
>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 = 41.5 bits (98), Expect = 6e-05
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 219 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 278
V NLPL+ T E+F E++ G V + L T + KG Y K S
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAV--------ERCFLVYSESTGESKGYGFVEYASKASA 54
Query: 279 DLALSILDGYEIRGKKIKVERA 300
A + LDG +I G+K++V+ A
Sbjct: 55 LKAKNQLDGKQIGGRKLQVDWA 76
Score = 41.5 bits (98), Expect = 6e-05
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 504 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 563
V NLPL+ T E+F E++ G V + L T + KG Y K S
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAV--------ERCFLVYSESTGESKGYGFVEYASKASA 54
Query: 564 DLALSILDGYEIRGKKIKVERA 585
A + LDG +I G+K++V+ A
Sbjct: 55 LKAKNQLDGKQIGGRKLQVDWA 76
Score = 30.7 bits (70), Expect = 0.46
Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 374 QQDLREECSKCGHVKK--VVLHDK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ RE S G V++ +V + +G + + +A + L+G+ G R++
Sbjct: 13 DEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
Score = 30.7 bits (70), Expect = 0.46
Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 659 QQDLREECSKCGHVKK--VVLHDK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+ RE S G V++ +V + +G + + +A + L+G+ G R++
Sbjct: 13 DEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
>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 = 41.1 bits (97), Expect = 1e-04
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 10/83 (12%)
Query: 216 TKVYVSNLPLDLTQEEFVE-VMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
T V+V N+P ++ ++F+ +++KCG V+ K DP T K C +
Sbjct: 1 TTVFVGNIPEGVS-DDFIRKLLEKCGKVLS--------WKRVKDPSTGKLKAFGFCEFED 51
Query: 275 KESVDLALSILDGYEIRGKKIKV 297
E AL +L+G E+ GKK+ V
Sbjct: 52 PEGALRALRLLNGLELGGKKLLV 74
Score = 41.1 bits (97), Expect = 1e-04
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 10/83 (12%)
Query: 501 TKVYVSNLPLDLTQEEFVE-VMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
T V+V N+P ++ ++F+ +++KCG V+ K DP T K C +
Sbjct: 1 TTVFVGNIPEGVS-DDFIRKLLEKCGKVLS--------WKRVKDPSTGKLKAFGFCEFED 51
Query: 560 KESVDLALSILDGYEIRGKKIKV 582
E AL +L+G E+ GKK+ V
Sbjct: 52 PEGALRALRLLNGLELGGKKLLV 74
>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 = 40.2 bits (95), Expect = 1e-04
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 377 LREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
L + S G+V+K+ L K P G A + F EAA+ + LNG FG R +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKP-GFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
Score = 40.2 bits (95), Expect = 1e-04
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 662 LREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
L + S G+V+K+ L K P G A + F EAA+ + LNG FG R +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKP-GFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
>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 = 40.8 bits (96), Expect = 1e-04
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VYVSNLP LT + ++ K G V+K + + D T+ KG A ++ +E
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVK--------VTIVKDKETRKSKGVAFILFLDRED 55
Query: 278 VDLALSILDGYEIRGKKIKVERA 300
+ L+ E+ G+ +K A
Sbjct: 56 AHKCVKALNNKELFGRTLKCSIA 78
Score = 40.8 bits (96), Expect = 1e-04
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VYVSNLP LT + ++ K G V+K + + D T+ KG A ++ +E
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVK--------VTIVKDKETRKSKGVAFILFLDRED 55
Query: 563 VDLALSILDGYEIRGKKIKVERA 585
+ L+ E+ G+ +K A
Sbjct: 56 AHKCVKALNNKELFGRTLKCSIA 78
Score = 31.5 bits (72), Expect = 0.27
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 376 DLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
DL + SK G V KV ++ DK +GVA I F + E A C + LN + R +
Sbjct: 17 DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKC 75
Score = 31.5 bits (72), Expect = 0.27
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 661 DLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 715
DL + SK G V KV ++ DK +GVA I F + E A C + LN + R +
Sbjct: 17 DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKC 75
>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 = 40.7 bits (96), Expect = 1e-04
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 14/87 (16%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIK---LYTDPYTKDFKGDALCTYI 273
K+++ LP L++++ E+++ G K+K L D T KG A C Y+
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFG-----------KLKAFNLVKDSATGLSKGYAFCEYL 50
Query: 274 KKESVDLALSILDGYEIRGKKIKVERA 300
D A++ L+G ++ KK+ V+RA
Sbjct: 51 DPSVTDQAIAGLNGMQLGDKKLTVQRA 77
Score = 40.7 bits (96), Expect = 1e-04
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 14/87 (16%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIK---LYTDPYTKDFKGDALCTYI 558
K+++ LP L++++ E+++ G K+K L D T KG A C Y+
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFG-----------KLKAFNLVKDSATGLSKGYAFCEYL 50
Query: 559 KKESVDLALSILDGYEIRGKKIKVERA 585
D A++ L+G ++ KK+ V+RA
Sbjct: 51 DPSVTDQAIAGLNGMQLGDKKLTVQRA 77
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 40.1 bits (94), Expect = 2e-04
Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 12/82 (14%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VY P + + + CG V K T + A T+ E+
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRK-----------VTMLSRT-VQPHAFITFENLEA 49
Query: 278 VDLALSILDGYEIRGKKIKVER 299
LA+ L+G + G IKV+R
Sbjct: 50 AQLAIETLNGASVDGNCIKVQR 71
Score = 40.1 bits (94), Expect = 2e-04
Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 12/82 (14%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VY P + + + CG V K T + A T+ E+
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRK-----------VTMLSRT-VQPHAFITFENLEA 49
Query: 563 VDLALSILDGYEIRGKKIKVER 584
LA+ L+G + G IKV+R
Sbjct: 50 AQLAIETLNGASVDGNCIKVQR 71
Score = 32.0 bits (73), Expect = 0.14
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
D++ CG V+KV + + + A I F+ EAA E LNG I +
Sbjct: 14 SDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70
Score = 32.0 bits (73), Expect = 0.14
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
D++ CG V+KV + + + A I F+ EAA E LNG I +
Sbjct: 14 SDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDF-KGDALCTYIKK 275
++YV NL L +++ + K G +V+ ++I D G A T+
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFG----EVE--SIRIPKKQDEKQGRLNNGFAFVTFKDA 55
Query: 276 ESVDLALSILDGYEIRGKKIKVER 299
S + AL L+G E+ G+KI V
Sbjct: 56 SSAENALQ-LNGTELGGRKISVSL 78
Score = 39.9 bits (94), Expect = 2e-04
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDF-KGDALCTYIKK 560
++YV NL L +++ + K G +V+ ++I D G A T+
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFG----EVE--SIRIPKKQDEKQGRLNNGFAFVTFKDA 55
Query: 561 ESVDLALSILDGYEIRGKKIKVER 584
S + AL L+G E+ G+KI V
Sbjct: 56 SSAENALQ-LNGTELGGRKISVSL 78
Score = 34.2 bits (79), Expect = 0.029
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 19/87 (21%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-------HDKHPEGVAQIF 404
I V+NL D + + DLR SK G V+ + + + G A +
Sbjct: 3 IYVRNL------DFKLD-----EDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVT 51
Query: 405 FKEPEAADACRELLNGRWFGQRQITAE 431
FK+ +A+ + LNG G R+I+
Sbjct: 52 FKDASSAENALQ-LNGTELGGRKISVS 77
Score = 34.2 bits (79), Expect = 0.029
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 19/87 (21%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-------HDKHPEGVAQIF 689
I V+NL D + + DLR SK G V+ + + + G A +
Sbjct: 3 IYVRNL------DFKLD-----EDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVT 51
Query: 690 FKEPEAADACRELLNGRWFGQRQITAE 716
FK+ +A+ + LNG G R+I+
Sbjct: 52 FKDASSAENALQ-LNGTELGGRKISVS 77
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 43.8 bits (103), Expect = 3e-04
Identities = 40/150 (26%), Positives = 63/150 (42%), Gaps = 32/150 (21%)
Query: 198 GQKRKPEPPKWFDIG--EESTKVYVSNLPLDLTQEEFVEVMQKCGLV-----MKDVDTNQ 250
GQ++ PP + +V+V +P DL ++E V + +K G + M D
Sbjct: 39 GQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQN 98
Query: 251 MKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIR-----GKKIKVERAKFTMK 305
+G A T+ KE A+ +L+ YEIR G I V+ + +
Sbjct: 99 --------------RGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVG 144
Query: 306 GEAYDPKLKPKKKRKKDLEKLKKAQEKLFD 335
G PK KKR++ LE+ K E + D
Sbjct: 145 G---IPKN---KKREEILEEFSKVTEGVVD 168
Score = 41.5 bits (97), Expect = 0.001
Identities = 36/133 (27%), Positives = 56/133 (42%), Gaps = 30/133 (22%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLV-----MKDVDTNQMKIKLYTDPYTKDFKGD 552
+V+V +P DL ++E V + +K G + M D +G
Sbjct: 56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQN--------------RGY 101
Query: 553 ALCTYIKKESVDLALSILDGYEIR-----GKKIKVERAKFTMKGEAYDPKLKPKKKRKKD 607
A T+ KE A+ +L+ YEIR G I V+ + + G PK KKR++
Sbjct: 102 AFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGG---IPKN---KKREEI 155
Query: 608 LEKLKKAQEKLFD 620
LE+ K E + D
Sbjct: 156 LEEFSKVTEGVVD 168
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 40.0 bits (94), Expect = 4e-04
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 377 LREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
L++ C K G V++V ++ HP+ G+A++ F ++A C E LN + I
Sbjct: 19 LKDMCKKYGEVEEVKIY-FHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVF 77
Query: 432 -TWDGKTRYKIQETAE 446
G+ R ++ E E
Sbjct: 78 LDPKGEIRKRLYEDLE 93
Score = 40.0 bits (94), Expect = 4e-04
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 662 LREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
L++ C K G V++V ++ HP+ G+A++ F ++A C E LN + I
Sbjct: 19 LKDMCKKYGEVEEVKIY-FHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVF 77
Query: 717 -TWDGKTRYKIQETAE 731
G+ R ++ E E
Sbjct: 78 LDPKGEIRKRLYEDLE 93
>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 = 39.1 bits (92), Expect = 4e-04
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 9/81 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+V NLP D+ +EE + + CG V +++ D T KG + K+S
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDV--------EAVRIVRDRKTGIGKGFGYVLFKTKDS 53
Query: 278 VDLALSILDGYEIRGKKIKVE 298
V LAL L+G +++G+KI+V+
Sbjct: 54 VALALK-LNGIKLKGRKIRVK 73
Score = 39.1 bits (92), Expect = 4e-04
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 9/81 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+V NLP D+ +EE + + CG V +++ D T KG + K+S
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDV--------EAVRIVRDRKTGIGKGFGYVLFKTKDS 53
Query: 563 VDLALSILDGYEIRGKKIKVE 583
V LAL L+G +++G+KI+V+
Sbjct: 54 VALALK-LNGIKLKGRKIRVK 73
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 38.7 bits (90), Expect = 6e-04
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 10/82 (12%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+V+V +P D+ ++E V + ++ G + + +L + ++ + +G A Y KE
Sbjct: 3 EVFVGKIPRDMYEDELVPLFERAGKIYE--------FRLMME-FSGENRGYAFVMYTTKE 53
Query: 277 SVDLALSILDGYEIR-GKKIKV 297
LA+ IL+ YEIR GK I V
Sbjct: 54 EAQLAIRILNNYEIRPGKFIGV 75
Score = 38.7 bits (90), Expect = 6e-04
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 10/82 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+V+V +P D+ ++E V + ++ G + + +L + ++ + +G A Y KE
Sbjct: 3 EVFVGKIPRDMYEDELVPLFERAGKIYE--------FRLMME-FSGENRGYAFVMYTTKE 53
Query: 562 SVDLALSILDGYEIR-GKKIKV 582
LA+ IL+ YEIR GK I V
Sbjct: 54 EAQLAIRILNNYEIRPGKFIGV 75
>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 = 39.2 bits (92), Expect = 7e-04
Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 8/94 (8%)
Query: 208 WFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 267
W D ++S +Y+ LP +LT+ + + V + G + VD I L D T KG
Sbjct: 2 WHDQYKDSAYIYIGGLPYELTEGDILCVFSQYGEI---VD-----INLVRDKKTGKSKGF 53
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
A Y + S LA+ L+G ++ G+ I+V+ +
Sbjct: 54 AFLAYEDQRSTILAVDNLNGIKLLGRTIRVDHVR 87
Score = 37.2 bits (87), Expect = 0.003
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+Y+ LP +LT+ + + V + G + VD I L D T KG A Y + S
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEI---VD-----INLVRDKKTGKSKGFAFLAYEDQRS 63
Query: 563 VDLALSILDGYEIRGKKIKVERAK 586
LA+ L+G ++ G+ I+V+ +
Sbjct: 64 TILAVDNLNGIKLLGRTIRVDHVR 87
>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 = 38.4 bits (90), Expect = 7e-04
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+++ +LP + T ++ ++ G N + K++ D T K +Y ES
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFG--------NVISAKVFVDKNTGQSKCFGFVSYDNPES 52
Query: 278 VDLALSILDGYEIRGKKIKVE 298
A+ ++G+++ GK++KV+
Sbjct: 53 AQAAIKAMNGFQVGGKRLKVQ 73
Score = 38.4 bits (90), Expect = 7e-04
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+++ +LP + T ++ ++ G N + K++ D T K +Y ES
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFG--------NVISAKVFVDKNTGQSKCFGFVSYDNPES 52
Query: 563 VDLALSILDGYEIRGKKIKVE 583
A+ ++G+++ GK++KV+
Sbjct: 53 AQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 37.4 bits (87), Expect = 0.002
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 10/80 (12%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VY+ NL D+T+++ E + C + ++L TD T +FKG + +ES
Sbjct: 2 VYIGNLAWDITEDDVREFFKGCEIT---------SVRLATDKETGEFKGFGHVDFADEES 52
Query: 278 VDLALSILDGYEIRGKKIKV 297
+D AL LDG + G+ I++
Sbjct: 53 LDAALK-LDGTVLCGRPIRI 71
Score = 37.4 bits (87), Expect = 0.002
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 10/80 (12%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VY+ NL D+T+++ E + C + ++L TD T +FKG + +ES
Sbjct: 2 VYIGNLAWDITEDDVREFFKGCEIT---------SVRLATDKETGEFKGFGHVDFADEES 52
Query: 563 VDLALSILDGYEIRGKKIKV 582
+D AL LDG + G+ I++
Sbjct: 53 LDAALK-LDGTVLCGRPIRI 71
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 37.6 bits (88), Expect = 0.002
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 13/88 (14%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V++ NLP D T+EE E+ + G V ++ D T KG A + KES
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEV--------KYARIVKDKLTGHSKGTAFVKFKTKES 54
Query: 278 VDLALSILD-----GYEIRGKKIKVERA 300
L D G + G+++ V A
Sbjct: 55 AQKCLEAADNAEDSGLSLDGRRLIVTLA 82
Score = 37.6 bits (88), Expect = 0.002
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 13/88 (14%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V++ NLP D T+EE E+ + G V ++ D T KG A + KES
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEV--------KYARIVKDKLTGHSKGTAFVKFKTKES 54
Query: 563 VDLALSILD-----GYEIRGKKIKVERA 585
L D G + G+++ V A
Sbjct: 55 AQKCLEAADNAEDSGLSLDGRRLIVTLA 82
Score = 37.2 bits (87), Expect = 0.002
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 374 QQDLREECSKCGHVK--KVVLHD--KHPEGVAQIFFKEPEAADAC 414
+++L+E S+ G VK ++V H +G A + FK E+A C
Sbjct: 14 EEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKC 58
Score = 37.2 bits (87), Expect = 0.002
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 659 QQDLREECSKCGHVK--KVVLHD--KHPEGVAQIFFKEPEAADAC 699
+++L+E S+ G VK ++V H +G A + FK E+A C
Sbjct: 14 EEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKC 58
>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 = 37.3 bits (87), Expect = 0.002
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T + V+ LP D+TQEE + + G + K+ D T G Y+ +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIES--------CKIVRDRITGQSLGYGFVDYVDE 52
Query: 276 ESVDLALSILDGYEIRGKKIKVERA 300
A++ L+G+EIR K++KV A
Sbjct: 53 NDAQKAINTLNGFEIRNKRLKVSYA 77
Score = 37.3 bits (87), Expect = 0.002
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP D+TQEE + + G + K+ D T G Y+ +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIES--------CKIVRDRITGQSLGYGFVDYVDE 52
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
A++ L+G+EIR K++KV A
Sbjct: 53 NDAQKAINTLNGFEIRNKRLKVSYA 77
>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 = 36.8 bits (86), Expect = 0.003
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+V L L + + + E K G V +DV ++ D ++ KG A + +ES
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKV-RDV-------RIIRDRNSRRSKGVAYVEFYDEES 53
Query: 278 VDLALSILDGYEIRGKKIKV 297
V LAL L G + G+ I V
Sbjct: 54 VPLALG-LTGQRLLGQPIMV 72
Score = 36.8 bits (86), Expect = 0.003
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+V L L + + + E K G V +DV ++ D ++ KG A + +ES
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKV-RDV-------RIIRDRNSRRSKGVAYVEFYDEES 53
Query: 563 VDLALSILDGYEIRGKKIKV 582
V LAL L G + G+ I V
Sbjct: 54 VPLALG-LTGQRLLGQPIMV 72
>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 = 36.8 bits (86), Expect = 0.003
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 411
+ VKNL KD T + +R+ CG +++V + + VA I F+ + A
Sbjct: 3 VKVKNL------PKDTT-----ENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEA 51
Score = 36.8 bits (86), Expect = 0.003
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 696
+ VKNL KD T + +R+ CG +++V + + VA I F+ + A
Sbjct: 3 VKVKNL------PKDTT-----ENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEA 51
>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 = 36.4 bits (85), Expect = 0.003
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 18/83 (21%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
K++V NLP T EE + +K G V + DV +K Y ++
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDV------VKNY-----------GFVHMEEE 43
Query: 276 ESVDLALSILDGYEIRGKKIKVE 298
E + A+ L+GYE GK+I VE
Sbjct: 44 EDAEDAIKALNGYEFMGKRINVE 66
Score = 36.4 bits (85), Expect = 0.003
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 18/83 (21%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
K++V NLP T EE + +K G V + DV +K Y ++
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDV------VKNY-----------GFVHMEEE 43
Query: 561 ESVDLALSILDGYEIRGKKIKVE 583
E + A+ L+GYE GK+I VE
Sbjct: 44 EDAEDAIKALNGYEFMGKRINVE 66
>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 = 36.8 bits (85), Expect = 0.003
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T +YV+NLP LT++E ++ + G + V N ++ K P +G A Y K+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNI---VQCNLLRDKSTGLP-----RGVAFVRYDKR 52
Query: 276 ESVDLALSILDG 287
E A+S L+G
Sbjct: 53 EEAQAAISSLNG 64
Score = 36.8 bits (85), Expect = 0.003
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T +YV+NLP LT++E ++ + G + V N ++ K P +G A Y K+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNI---VQCNLLRDKSTGLP-----RGVAFVRYDKR 52
Query: 561 ESVDLALSILDG 572
E A+S L+G
Sbjct: 53 EEAQAAISSLNG 64
>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 = 36.8 bits (86), Expect = 0.003
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 14/75 (18%)
Query: 350 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKH--PEGVAQIFFK 406
+ + V NL DVT ++DL E + G VKKV ++ D+ EG A + F+
Sbjct: 1 TRLRVSNL------HYDVT-----EEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFE 49
Query: 407 EPEAADACRELLNGR 421
+ E A+ + NG
Sbjct: 50 KREDAERAIKQFNGV 64
Score = 36.8 bits (86), Expect = 0.003
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 14/75 (18%)
Query: 635 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKH--PEGVAQIFFK 691
+ + V NL DVT ++DL E + G VKKV ++ D+ EG A + F+
Sbjct: 1 TRLRVSNL------HYDVT-----EEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFE 49
Query: 692 EPEAADACRELLNGR 706
+ E A+ + NG
Sbjct: 50 KREDAERAIKQFNGV 64
Score = 34.5 bits (80), Expect = 0.017
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T++ VSNL D+T+E+ E+ + G V K KI D + +G A + K+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKV------KINY--DR-SGRSEGTADVVFEKR 51
Query: 276 ESVDLALSILDGYEIRGKKIKVE 298
E + A+ +G + G+ ++VE
Sbjct: 52 EDAERAIKQFNGVLLDGQPMQVE 74
Score = 34.5 bits (80), Expect = 0.017
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T++ VSNL D+T+E+ E+ + G V K KI D + +G A + K+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKV------KINY--DR-SGRSEGTADVVFEKR 51
Query: 561 ESVDLALSILDGYEIRGKKIKVE 583
E + A+ +G + G+ ++VE
Sbjct: 52 EDAERAIKQFNGVLLDGQPMQVE 74
>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 = 36.6 bits (85), Expect = 0.003
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+VYV ++ +L ++ + G + I + DP T KG A Y E
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKS--------IDMSWDPVTMKHKGFAFVEYEVPE 53
Query: 277 SVDLALSILDGYEIRGKKIKVER 299
+ LAL ++G + G+ IKV R
Sbjct: 54 AAQLALEQMNGVMLGGRNIKVGR 76
Score = 36.6 bits (85), Expect = 0.003
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+VYV ++ +L ++ + G + I + DP T KG A Y E
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKS--------IDMSWDPVTMKHKGFAFVEYEVPE 53
Query: 562 SVDLALSILDGYEIRGKKIKVER 584
+ LAL ++G + G+ IKV R
Sbjct: 54 AAQLALEQMNGVMLGGRNIKVGR 76
>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 = 36.4 bits (85), Expect = 0.004
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T VYV NL D+ E+ E+ K G + K+ D K KG +
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKI--------TSAKVMKDDEGKS-KGFGFVNFENH 52
Query: 276 ESVDLALSILDGYEIRGKKIKVERA 300
E+ A+ L+G E+ GKK+ V RA
Sbjct: 53 EAAQKAVEELNGKEVNGKKLYVGRA 77
Score = 36.4 bits (85), Expect = 0.004
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T VYV NL D+ E+ E+ K G + K+ D K KG +
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKI--------TSAKVMKDDEGKS-KGFGFVNFENH 52
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
E+ A+ L+G E+ GKK+ V RA
Sbjct: 53 EAAQKAVEELNGKEVNGKKLYVGRA 77
>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 = 36.5 bits (85), Expect = 0.004
Identities = 18/85 (21%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
++YV+++ DL++++ V + G + L DP T KG Y
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKI--------KSCSLAPDPETGKHKGYGFIEYENP 52
Query: 276 ESVDLALSILDGYEIRGKKIKVERA 300
+S A++ ++ +++ G++++V +A
Sbjct: 53 QSAQDAIASMNLFDLGGQQLRVGKA 77
Score = 36.5 bits (85), Expect = 0.004
Identities = 18/85 (21%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
++YV+++ DL++++ V + G + L DP T KG Y
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKI--------KSCSLAPDPETGKHKGYGFIEYENP 52
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
+S A++ ++ +++ G++++V +A
Sbjct: 53 QSAQDAIASMNLFDLGGQQLRVGKA 77
>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 = 36.6 bits (85), Expect = 0.004
Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 9/84 (10%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
E K++VS LP +T+EE ++ +K G V+K V +L T+ K KG A Y
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHG-VVKSV-------RLVTNRSGKP-KGLAYVEYE 51
Query: 274 KKESVDLALSILDGYEIRGKKIKV 297
+ S A+ +DG EI+ K I V
Sbjct: 52 NESSASQAVLKMDGTEIKEKTISV 75
Score = 36.6 bits (85), Expect = 0.004
Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 9/84 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
E K++VS LP +T+EE ++ +K G V+K V +L T+ K KG A Y
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHG-VVKSV-------RLVTNRSGKP-KGLAYVEYE 51
Query: 559 KKESVDLALSILDGYEIRGKKIKV 582
+ S A+ +DG EI+ K I V
Sbjct: 52 NESSASQAVLKMDGTEIKEKTISV 75
>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 = 36.1 bits (84), Expect = 0.005
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++++ NL LT+ +++ K G + K D K + P +G T+ KE
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKI-KKFDFLFHK----SGPLKGQPRGYCFVTFETKE 55
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
+ AL L+G GKK+ V A
Sbjct: 56 EAEKALKSLNGKTALGKKLVVRWAH 80
Score = 36.1 bits (84), Expect = 0.005
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++++ NL LT+ +++ K G + K D K + P +G T+ KE
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKI-KKFDFLFHK----SGPLKGQPRGYCFVTFETKE 55
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
+ AL L+G GKK+ V A
Sbjct: 56 EAEKALKSLNGKTALGKKLVVRWAH 80
Score = 30.3 bits (69), Expect = 0.61
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 382 SKCGHVKKV--VLHD-----KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
SK G +KK + H P G + F+ E A+ + LNG+ +++
Sbjct: 21 SKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVV 76
Score = 30.3 bits (69), Expect = 0.61
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 667 SKCGHVKKV--VLHD-----KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 715
SK G +KK + H P G + F+ E A+ + LNG+ +++
Sbjct: 21 SKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVV 76
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 35.9 bits (83), Expect = 0.007
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 14/89 (15%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD---FKGDALCTY 272
T + + N+P L +E+ +++++ G+ + Y Y D F+G A +
Sbjct: 2 TAIVIKNIPFSLRKEQLLDIIEDLGIPLP-----------YAFNYHFDNGVFRGLAFANF 50
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
E + L+GYEI G++++VE +
Sbjct: 51 RSPEEAQTVVEALNGYEISGRRLRVEYKR 79
Score = 35.9 bits (83), Expect = 0.007
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 14/89 (15%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD---FKGDALCTY 557
T + + N+P L +E+ +++++ G+ + Y Y D F+G A +
Sbjct: 2 TAIVIKNIPFSLRKEQLLDIIEDLGIPLP-----------YAFNYHFDNGVFRGLAFANF 50
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
E + L+GYEI G++++VE +
Sbjct: 51 RSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>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 = 35.7 bits (83), Expect = 0.008
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 375 QDLREECSKCGH--VKKVVLHDKHP----EGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+DL ++ G VK + + +G A + F AA A +E L GR F ++
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKC 72
Query: 429 TA 430
Sbjct: 73 VV 74
Score = 35.7 bits (83), Expect = 0.008
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 660 QDLREECSKCGH--VKKVVLHDKHP----EGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+DL ++ G VK + + +G A + F AA A +E L GR F ++
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKC 72
Query: 714 TA 715
Sbjct: 73 VV 74
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 38.8 bits (90), Expect = 0.009
Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 11/117 (9%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E T + V+ LP +TQEE + G + KL D T G Y
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIES--------CKLVRDKVTGQSLGYGFVNY 52
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFT---MKGEAYDPKLKPKKKRKKDLEKL 326
++ E + A++ L+G ++ K IKV A+ + +KG PK + +LE +
Sbjct: 53 VRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESI 109
Score = 37.6 bits (87), Expect = 0.019
Identities = 30/114 (26%), Positives = 49/114 (42%), Gaps = 11/114 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP +TQEE + G + KL D T G Y++
Sbjct: 4 TNLIVNYLPQTMTQEEIRSLFTSIGEIES--------CKLVRDKVTGQSLGYGFVNYVRP 55
Query: 561 ESVDLALSILDGYEIRGKKIKVERAKFT---MKGEAYDPKLKPKKKRKKDLEKL 611
E + A++ L+G ++ K IKV A+ + +KG PK + +LE +
Sbjct: 56 EDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESI 109
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 34.9 bits (81), Expect = 0.014
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NLP D T E+ E + G + + + D +K +G T+ +E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCF--------VVKDKGSKKCRGFGYVTFALEED 53
Query: 278 VDLALSILDGYEIRGKKIKVERAK 301
AL + G+KI VE AK
Sbjct: 54 AKRALEEKKKTKFGGRKIHVEFAK 77
Score = 34.9 bits (81), Expect = 0.014
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NLP D T E+ E + G + + + D +K +G T+ +E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCF--------VVKDKGSKKCRGFGYVTFALEED 53
Query: 563 VDLALSILDGYEIRGKKIKVERAK 586
AL + G+KI VE AK
Sbjct: 54 AKRALEEKKKTKFGGRKIHVEFAK 77
>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 = 34.8 bits (81), Expect = 0.014
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 220 VSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVD 279
V+NL D +++ E+ + G + + + L D T +G A T+ +E +
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISR--------VYLAKDKETGQSRGFAFVTFHTREDAE 55
Query: 280 LALSILDGYEIRGKKIKVERAK 301
A+ L+G+ + VE AK
Sbjct: 56 RAIEKLNGFGYDNLILSVEWAK 77
Score = 34.8 bits (81), Expect = 0.014
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 505 VSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVD 564
V+NL D +++ E+ + G + + + L D T +G A T+ +E +
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISR--------VYLAKDKETGQSRGFAFVTFHTREDAE 55
Query: 565 LALSILDGYEIRGKKIKVERAK 586
A+ L+G+ + VE AK
Sbjct: 56 RAIEKLNGFGYDNLILSVEWAK 77
Score = 31.4 bits (72), Expect = 0.27
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 374 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGR 421
+ DLRE G + +V L DK G A + F E A+ E LNG
Sbjct: 13 EDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
Score = 31.4 bits (72), Expect = 0.27
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 659 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGR 706
+ DLRE G + +V L DK G A + F E A+ E LNG
Sbjct: 13 EDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
>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 = 34.8 bits (81), Expect = 0.016
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 382 SKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWD 434
S+CG +K++++ K P G + + E A+ + LNG R I + WD
Sbjct: 20 SRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRVD-WD 75
Score = 34.8 bits (81), Expect = 0.016
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 667 SKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWD 719
S+CG +K++++ K P G + + E A+ + LNG R I + WD
Sbjct: 20 SRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRVD-WD 75
Score = 34.1 bits (79), Expect = 0.025
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NL T+E+ E+ +CG + + + M + D +TK G Y +E
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRII----MGL----DRFTKTPCGFCFVEYYTRED 52
Query: 278 VDLALSILDGYEIRGKKIKVE 298
+ A+ L+G ++ + I+V+
Sbjct: 53 AENAVKYLNGTKLDDRIIRVD 73
Score = 34.1 bits (79), Expect = 0.025
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV NL T+E+ E+ +CG + + + M + D +TK G Y +E
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRII----MGL----DRFTKTPCGFCFVEYYTRED 52
Query: 563 VDLALSILDGYEIRGKKIKVE 583
+ A+ L+G ++ + I+V+
Sbjct: 53 AENAVKYLNGTKLDDRIIRVD 73
>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 = 35.1 bits (80), Expect = 0.017
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T + V+ LP ++TQEEF + G + KL D T G YI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNYIDP 54
Query: 276 ESVDLALSILDGYEIRGKKIKVERAK 301
+ + A++ L+G ++ K IKV A+
Sbjct: 55 KDAEKAINTLNGLRLQTKTIKVSYAR 80
Score = 35.1 bits (80), Expect = 0.017
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP ++TQEEF + G + KL D T G YI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNYIDP 54
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+ + A++ L+G ++ K IKV A+
Sbjct: 55 KDAEKAINTLNGLRLQTKTIKVSYAR 80
>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 = 34.3 bits (79), Expect = 0.020
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NL D ++ E + G + ++L TDP + KG + +E+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISS--------VRLPTDPDSGRPKGFGYVEFSSQEA 52
Query: 278 VDLALSILDGYEIRGKKIKVE 298
AL L G ++ G+ ++++
Sbjct: 53 AQAALDALGGTDLLGRPVRLD 73
Score = 34.3 bits (79), Expect = 0.020
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NL D ++ E + G + ++L TDP + KG + +E+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISS--------VRLPTDPDSGRPKGFGYVEFSSQEA 52
Query: 563 VDLALSILDGYEIRGKKIKVE 583
AL L G ++ G+ ++++
Sbjct: 53 AQAALDALGGTDLLGRPVRLD 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 = 34.3 bits (79), Expect = 0.020
Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VYV +P T++E CG + ++ L T P T F+G A T+ K E
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEI--------EELDLMTFPDTGRFRGIAFITF-KTEE 51
Query: 278 VDLALSILDGYEIRGKKIKVE 298
LDG ++ G+ +KVE
Sbjct: 52 AAKRALALDGEDMGGRFLKVE 72
Score = 34.3 bits (79), Expect = 0.020
Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VYV +P T++E CG + ++ L T P T F+G A T+ K E
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEI--------EELDLMTFPDTGRFRGIAFITF-KTEE 51
Query: 563 VDLALSILDGYEIRGKKIKVE 583
LDG ++ G+ +KVE
Sbjct: 52 AAKRALALDGEDMGGRFLKVE 72
>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 = 34.1 bits (79), Expect = 0.022
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 22/86 (25%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+++ NLP D+T+ + + ++ G V TN + ++ K AL ++ +S
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKV-----TNVLLLR---------GKNQAL---VEMDS 44
Query: 278 VDLALSILDGYE-----IRGKKIKVE 298
V+ A S++D Y IRG+++ ++
Sbjct: 45 VESAKSMVDYYLTVPALIRGRRVYIQ 70
Score = 34.1 bits (79), Expect = 0.022
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 22/86 (25%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+++ NLP D+T+ + + ++ G V TN + ++ K AL ++ +S
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKV-----TNVLLLR---------GKNQAL---VEMDS 44
Query: 563 VDLALSILDGYE-----IRGKKIKVE 583
V+ A S++D Y IRG+++ ++
Sbjct: 45 VESAKSMVDYYLTVPALIRGRRVYIQ 70
>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 = 33.9 bits (78), Expect = 0.030
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T + V+ LP ++TQ+E + G ++++ KL D T G Y+
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIG----EIES----CKLIRDKVTGQSLGYGFVNYVDP 53
Query: 276 ESVDLALSILDGYEIRGKKIKVERA 300
E + A++ L+G ++ K IKV A
Sbjct: 54 EDAEKAINTLNGLRLQNKTIKVSYA 78
Score = 33.9 bits (78), Expect = 0.030
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP ++TQ+E + G ++++ KL D T G Y+
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIG----EIES----CKLIRDKVTGQSLGYGFVNYVDP 53
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
E + A++ L+G ++ K IKV A
Sbjct: 54 EDAEKAINTLNGLRLQNKTIKVSYA 78
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 33.9 bits (77), Expect = 0.035
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ T + V+ LP ++TQEEF + G ++++ KL D T G Y
Sbjct: 1 DSKTNLIVNYLPQNMTQEEFKSLFGSIG----EIES----CKLVRDKITGQSLGYGFVNY 52
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ D A++ L+G +++ K IKV A+
Sbjct: 53 VDPNDADKAINTLNGLKLQTKTIKVSYAR 81
Score = 33.6 bits (76), Expect = 0.050
Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP ++TQEEF + G ++++ KL D T G Y+
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIG----EIES----CKLVRDKITGQSLGYGFVNYVDP 55
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
D A++ L+G +++ K IKV A+
Sbjct: 56 NDADKAINTLNGLKLQTKTIKVSYAR 81
>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 = 33.7 bits (78), Expect = 0.036
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
TK++V LP T + + + G + + V + TD T +G T+ K
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAV--------VITDRQTGKSRGYGFVTFKDK 52
Query: 276 ESVDLALS----ILDGYEIRGKKIKVERA 300
ES + A I+D G+K V A
Sbjct: 53 ESAERACKDPNPIID-----GRKANVNLA 76
Score = 33.7 bits (78), Expect = 0.036
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
TK++V LP T + + + G + + V + TD T +G T+ K
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAV--------VITDRQTGKSRGYGFVTFKDK 52
Query: 561 ESVDLALS----ILDGYEIRGKKIKVERA 585
ES + A I+D G+K V A
Sbjct: 53 ESAERACKDPNPIID-----GRKANVNLA 76
>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 = 33.4 bits (77), Expect = 0.038
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 218 VYVSNLPLDLTQEEFVEV-MQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++V NL +T+E E+ +Q L +K+ DP K K A T+ +
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLE---------GVKIPKDPNGKP-KSFAFVTFKHEV 53
Query: 277 SVDLALSILDGYEIRGKKIKVE 298
SV A+ +L+G + G++++++
Sbjct: 54 SVPYAIQLLNGIRLFGRELRIK 75
Score = 33.4 bits (77), Expect = 0.038
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 503 VYVSNLPLDLTQEEFVEV-MQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++V NL +T+E E+ +Q L +K+ DP K K A T+ +
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLE---------GVKIPKDPNGKP-KSFAFVTFKHEV 53
Query: 562 SVDLALSILDGYEIRGKKIKVE 583
SV A+ +L+G + G++++++
Sbjct: 54 SVPYAIQLLNGIRLFGRELRIK 75
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 34.1 bits (79), Expect = 0.042
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 371 LEYQQDLREECSKCGHVK--KVVL-HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQ 427
E+ D+ E K G V KV ++ H G + ++ E A A ++ NGRW+ +Q
Sbjct: 39 EEFYDDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQ 98
Query: 428 ITAE 431
+T E
Sbjct: 99 LTCE 102
Score = 34.1 bits (79), Expect = 0.042
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 656 LEYQQDLREECSKCGHVK--KVVL-HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQ 712
E+ D+ E K G V KV ++ H G + ++ E A A ++ NGRW+ +Q
Sbjct: 39 EEFYDDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQ 98
Query: 713 ITAE 716
+T E
Sbjct: 99 LTCE 102
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 33.4 bits (77), Expect = 0.046
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 220 VSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVD 279
V NL T ++ V +K G V + + D YT++ +G A + K +
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGD--------VYIPRDRYTRESRGFAFVRFYDKRDAE 54
Query: 280 LALSILDGYEIRGKKIKV 297
A+ +DG E+ G++++V
Sbjct: 55 DAMDAMDGKELDGRELRV 72
Score = 33.4 bits (77), Expect = 0.046
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 505 VSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVD 564
V NL T ++ V +K G V + + D YT++ +G A + K +
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGD--------VYIPRDRYTRESRGFAFVRFYDKRDAE 54
Query: 565 LALSILDGYEIRGKKIKV 582
A+ +DG E+ G++++V
Sbjct: 55 DAMDAMDGKELDGRELRV 72
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 33.0 bits (75), Expect = 0.064
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 17/83 (20%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD----ALCTY 272
++++ LP DL ++E + + +K G K+Y DF G+ A T+
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIG-------------KIYEMRMMMDFNGNNRGYAFVTF 49
Query: 273 IKKESVDLALSILDGYEIRGKKI 295
K+ A+ L+ YEIR ++
Sbjct: 50 SNKQEAKNAIKQLNNYEIRNGRL 72
Score = 33.0 bits (75), Expect = 0.064
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 17/83 (20%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD----ALCTY 557
++++ LP DL ++E + + +K G K+Y DF G+ A T+
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIG-------------KIYEMRMMMDFNGNNRGYAFVTF 49
Query: 558 IKKESVDLALSILDGYEIRGKKI 580
K+ A+ L+ YEIR ++
Sbjct: 50 SNKQEAKNAIKQLNNYEIRNGRL 72
>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 = 33.1 bits (76), Expect = 0.068
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
ES ++++ NL T+E+ ++ K G + + + L D TK KG A TY+
Sbjct: 1 ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSE--------VHLPIDKLTKKPKGFAFVTYM 52
Query: 274 KKESVDLALSILDGYEIRGK 293
E A + LDG +G+
Sbjct: 53 IPEHAVKAFAELDGTVFQGR 72
Score = 30.8 bits (70), Expect = 0.38
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
E+ ++++ NL T+E+ ++ K G + + + L D TK KG A TY+
Sbjct: 1 ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSE--------VHLPIDKLTKKPKGFAFVTYM 52
Query: 559 KKESVDLALSILDGYEIRGK 578
E A + LDG +G+
Sbjct: 53 IPEHAVKAFAELDGTVFQGR 72
>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 = 32.6 bits (75), Expect = 0.085
Identities = 25/85 (29%), Positives = 33/85 (38%), Gaps = 8/85 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
+++ V NLP LT+ E E K G + DV KL K + A Y +
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDV-------KLLRTEDGK-SRRIAFIGYKTE 52
Query: 276 ESVDLALSILDGYEIRGKKIKVERA 300
E A + I KI VE A
Sbjct: 53 EEAQKAKDYFNNTYINTSKISVEFA 77
Score = 32.6 bits (75), Expect = 0.085
Identities = 25/85 (29%), Positives = 33/85 (38%), Gaps = 8/85 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+++ V NLP LT+ E E K G + DV KL K + A Y +
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDV-------KLLRTEDGK-SRRIAFIGYKTE 52
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
E A + I KI VE A
Sbjct: 53 EEAQKAKDYFNNTYINTSKISVEFA 77
>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 = 32.7 bits (75), Expect = 0.10
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 375 QDLREECSKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLN 419
+ L+ SK G V V L H +G A I F+ PE A + LN
Sbjct: 14 EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLN 62
Score = 32.7 bits (75), Expect = 0.10
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 660 QDLREECSKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLN 704
+ L+ SK G V V L H +G A I F+ PE A + LN
Sbjct: 14 EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLN 62
>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 = 32.7 bits (74), Expect = 0.10
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+++V NLP DLT ++ E +CG VM +IK+ KG + E
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVM------FAEIKMENGKS----KGCGTVRFDSPE 50
Query: 277 SVDLALSILDGYEIRGKKIKV 297
S + A +++G +I G++I V
Sbjct: 51 SAEKACRLMNGIKINGREIDV 71
Score = 32.7 bits (74), Expect = 0.10
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+++V NLP DLT ++ E +CG VM +IK+ KG + E
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVM------FAEIKMENGKS----KGCGTVRFDSPE 50
Query: 562 SVDLALSILDGYEIRGKKIKV 582
S + A +++G +I G++I V
Sbjct: 51 SAEKACRLMNGIKINGREIDV 71
Score = 31.9 bits (72), Expect = 0.18
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 362 LFDKDVTLILEYQQDLREECSKCGHV--KKVVLHDKHPEGVAQIFFKEPEAADACRELLN 419
+F +++ L +Q+ L+E+ S+CGHV ++ + + +G + F PE+A+ L+N
Sbjct: 2 IFVRNLPFDLTWQK-LKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMN 60
Query: 420 GRWFGQRQI 428
G R+I
Sbjct: 61 GIKINGREI 69
Score = 31.9 bits (72), Expect = 0.18
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 647 LFDKDVTLILEYQQDLREECSKCGHV--KKVVLHDKHPEGVAQIFFKEPEAADACRELLN 704
+F +++ L +Q+ L+E+ S+CGHV ++ + + +G + F PE+A+ L+N
Sbjct: 2 IFVRNLPFDLTWQK-LKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMN 60
Query: 705 GRWFGQRQI 713
G R+I
Sbjct: 61 GIKINGREI 69
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or P-CIP2,
is a serine/threonine protein kinase functionally
related to RNA metabolism and neurite outgrowth. It
contains an N-terminal kinase domain and a C-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), with
high homology to the corresponding motif of the
mammalian U2 small nuclear ribonucleoprotein auxiliary
factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1
targets two key regulators of cell proliferation and
migration, the cyclin-dependent kinase (CDK) inhibitor
p27Kip1 and the microtubule-destabilizing protein
stathmin. It plays a critical role during vascular wound
repair by preventing excessive vascular smooth muscle
cell (VSMC) migration into the vascular lesion.
Moreover, UHMK1 may control cell migration and neurite
outgrowth by interacting with and phosphorylating the
splicing factor SF1, thereby probably contributing to
the control of protein expression. Furthermore, UHMK1
may be functionally related to microtubule dynamics and
axon development. It localizes to RNA granules,
interacts with three proteins found in RNA granules
(KIF3A, NonO, and eEF1A), and further enhances the local
translation. UHMK1 is highly expressed in regions of the
brain implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 32.7 bits (74), Expect = 0.12
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAAD--ACRELLNGRWFGQRQITA 430
+D++EEC K G V +++ ++P G Q+F + A D A ++LL GR F + + A
Sbjct: 28 EDIKEECQKYGPVVSLLIPKENP-GKGQVFVEYANAGDSKAAQKLLTGRIFDGKFVVA 84
Score = 32.7 bits (74), Expect = 0.12
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAAD--ACRELLNGRWFGQRQITA 715
+D++EEC K G V +++ ++P G Q+F + A D A ++LL GR F + + A
Sbjct: 28 EDIKEECQKYGPVVSLLIPKENP-GKGQVFVEYANAGDSKAAQKLLTGRIFDGKFVVA 84
>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 = 32.1 bits (74), Expect = 0.13
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V L ++ ++ E+ G V KDVD L D +G A + E
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTV-KDVD-------LPIDREVNLPRGYAYVEFESPED 52
Query: 278 VDLALSILDGYEIRGKKIKVE 298
+ A+ +DG +I G+++ VE
Sbjct: 53 AEKAIKHMDGGQIDGQEVTVE 73
Score = 32.1 bits (74), Expect = 0.13
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V L ++ ++ E+ G V KDVD L D +G A + E
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTV-KDVD-------LPIDREVNLPRGYAYVEFESPED 52
Query: 563 VDLALSILDGYEIRGKKIKVE 583
+ A+ +DG +I G+++ VE
Sbjct: 53 AEKAIKHMDGGQIDGQEVTVE 73
>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 = 32.2 bits (74), Expect = 0.13
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++V NLP +T ++ ++ ++CG V++ DV T+ KG + E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRS----------KGFGTVLFESPE 50
Query: 277 SVDLALSILDGYEIRGKKIKV 297
A+ + +GY++ G++++V
Sbjct: 51 DAQRAIEMFNGYDLEGRELEV 71
Score = 32.2 bits (74), Expect = 0.13
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++V NLP +T ++ ++ ++CG V++ DV T+ KG + E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRS----------KGFGTVLFESPE 50
Query: 562 SVDLALSILDGYEIRGKKIKV 582
A+ + +GY++ G++++V
Sbjct: 51 DAQRAIEMFNGYDLEGRELEV 71
>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 = 32.2 bits (74), Expect = 0.13
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEP-EAADACRELLNGRWFGQR 426
++L +E K G ++ V + ++P G A + F++P +A DA R L R G R
Sbjct: 14 RELEDEFEKYGPLRSVWVA-RNPPGFAFVEFEDPRDAEDAVRALDGRRICGNR 65
Score = 32.2 bits (74), Expect = 0.13
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEP-EAADACRELLNGRWFGQR 711
++L +E K G ++ V + ++P G A + F++P +A DA R L R G R
Sbjct: 14 RELEDEFEKYGPLRSVWVA-RNPPGFAFVEFEDPRDAEDAVRALDGRRICGNR 65
>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 = 31.3 bits (71), Expect = 0.20
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMK 244
K++V N+ D +QEE + + G V+
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLS 29
Score = 31.3 bits (71), Expect = 0.20
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMK 529
K++V N+ D +QEE + + G V+
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLS 29
>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 = 31.6 bits (72), Expect = 0.20
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 18/91 (19%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFK-----GDALC 270
T + ++ LP LT EEF + G V KI +D + G
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPV------KNCKI-------VRDKRTGYSYGFGFV 47
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAK 301
Y E A+ L+G +++ K+IKV A+
Sbjct: 48 DYQSAEDAQRAIRTLNGLQLQNKRIKVAYAR 78
Score = 31.6 bits (72), Expect = 0.20
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 18/91 (19%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFK-----GDALC 555
T + ++ LP LT EEF + G V KI +D + G
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPV------KNCKI-------VRDKRTGYSYGFGFV 47
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y E A+ L+G +++ K+IKV A+
Sbjct: 48 DYQSAEDAQRAIRTLNGLQLQNKRIKVAYAR 78
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.6 bits (72), Expect = 0.22
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 10/82 (12%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQ-KCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
+V++SN+P DL ++ ++ + K G V ++L+ D K +G + + K
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTY--------VELFKDEEGK-SRGCGVVEFKDK 51
Query: 276 ESVDLALSILDGYEIRGKKIKV 297
ESV AL ++ YE++G+K+ V
Sbjct: 52 ESVQKALETMNRYELKGRKLVV 73
Score = 31.6 bits (72), Expect = 0.22
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 10/82 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQ-KCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+V++SN+P DL ++ ++ + K G V ++L+ D K +G + + K
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTY--------VELFKDEEGK-SRGCGVVEFKDK 51
Query: 561 ESVDLALSILDGYEIRGKKIKV 582
ESV AL ++ YE++G+K+ V
Sbjct: 52 ESVQKALETMNRYELKGRKLVV 73
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 32.3 bits (74), Expect = 0.22
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 359 DPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDK---HPEGVAQIFFKEPEAADACR 415
DP + ++ +D+ EE SK G V+ + + D H G + F++ E A A
Sbjct: 28 DPRELQEH---FEDFYEDIFEELSKFGEVEALNVCDNLGDHMVGNVYVKFRDEEHAAAAL 84
Query: 416 ELLNGRWFGQRQITAE 431
+ L GR++ R I E
Sbjct: 85 KALQGRFYDGRPIIVE 100
Score = 32.3 bits (74), Expect = 0.22
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 644 DPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDK---HPEGVAQIFFKEPEAADACR 700
DP + ++ +D+ EE SK G V+ + + D H G + F++ E A A
Sbjct: 28 DPRELQEH---FEDFYEDIFEELSKFGEVEALNVCDNLGDHMVGNVYVKFRDEEHAAAAL 84
Query: 701 ELLNGRWFGQRQITAE 716
+ L GR++ R I E
Sbjct: 85 KALQGRFYDGRPIIVE 100
>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 = 31.6 bits (71), Expect = 0.23
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T + V+ LP ++TQ+E + G V KL D G Y+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVES--------AKLIRDKVAGHSLGYGFVNYVNA 53
Query: 276 ESVDLALSILDGYEIRGKKIKVERAK 301
+ + A++ L+G ++ K IKV A+
Sbjct: 54 KDAERAINTLNGLRLQSKTIKVSYAR 79
Score = 31.6 bits (71), Expect = 0.23
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP ++TQ+E + G V KL D G Y+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVES--------AKLIRDKVAGHSLGYGFVNYVNA 53
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+ + A++ L+G ++ K IKV A+
Sbjct: 54 KDAERAINTLNGLRLQSKTIKVSYAR 79
>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 = 31.6 bits (72), Expect = 0.24
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 19/89 (21%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
K++V LP D+T+EEF E + G +M+D DT + +G T
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRS-------------RGFGFVT 47
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERA 300
+ + +V+ S E+ GK+++V+RA
Sbjct: 48 FDSESAVERVFS-AGMLELGGKQVEVKRA 75
Score = 31.6 bits (72), Expect = 0.24
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 19/89 (21%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
K++V LP D+T+EEF E + G +M+D DT + +G T
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRS-------------RGFGFVT 47
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERA 585
+ + +V+ S E+ GK+++V+RA
Sbjct: 48 FDSESAVERVFS-AGMLELGGKQVEVKRA 75
>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 = 31.4 bits (72), Expect = 0.24
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQR 426
+L E + G ++++ +D A I ++ EAA A +E L G G
Sbjct: 13 AELEREFDRFGAIRRID-YDPG-RNYAYIEYESIEAAQAAKEALRGFPLGGP 62
Score = 31.4 bits (72), Expect = 0.24
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQR 711
+L E + G ++++ +D A I ++ EAA A +E L G G
Sbjct: 13 AELEREFDRFGAIRRID-YDPG-RNYAYIEYESIEAAQAAKEALRGFPLGGP 62
>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 = 31.5 bits (72), Expect = 0.28
Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG-DALC--- 270
+T +YV NL +T+E + + G +KI ++ P T++ + + C
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFG------PLASVKI-MW--PRTEEERRRNRNCGFV 51
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAK 301
++ + + AL LDG ++ G ++K+ K
Sbjct: 52 AFMNRADAERALDELDGKDVMGYELKLGWGK 82
Score = 30.7 bits (70), Expect = 0.59
Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 13/90 (14%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG-DALC---T 556
T +YV NL +T+E + + G +KI ++ P T++ + + C
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFG------PLASVKI-MW--PRTEEERRRNRNCGFVA 52
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
++ + + AL LDG ++ G ++K+ K
Sbjct: 53 FMNRADAERALDELDGKDVMGYELKLGWGK 82
>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 = 31.1 bits (71), Expect = 0.28
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 15/83 (18%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T++ VSNL +T+++ VE+ G + K + G A Y++K
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGAL-KRARLVR--------------PGVAEVVYVRK 45
Query: 276 ESVDLALSILDGYEIRGKKIKVE 298
+ A+ + E+ G+ +K +
Sbjct: 46 DDALTAIDKYNNRELDGQPMKCK 68
Score = 31.1 bits (71), Expect = 0.28
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 15/83 (18%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T++ VSNL +T+++ VE+ G + K + G A Y++K
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGAL-KRARLVR--------------PGVAEVVYVRK 45
Query: 561 ESVDLALSILDGYEIRGKKIKVE 583
+ A+ + E+ G+ +K +
Sbjct: 46 DDALTAIDKYNNRELDGQPMKCK 68
>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 = 33.8 bits (77), Expect = 0.28
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
++T +YV+NLP +T ++ + K G + V N ++ KL P +G A +
Sbjct: 192 KDTNLYVTNLPRTITDDQLDTIFGKYGQI---VQKNILRDKLTGTP-----RGVAFVRFN 243
Query: 559 KKESVDLALSILD 571
K+E A+S L+
Sbjct: 244 KREEAQEAISALN 256
Score = 33.5 bits (76), Expect = 0.41
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T +YV+NLP +T ++ + K G + V N ++ KL P +G A + K+
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQI---VQKNILRDKLTGTP-----RGVAFVRFNKR 245
Query: 276 ESVDLALSILD 286
E A+S L+
Sbjct: 246 EEAQEAISALN 256
>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 = 31.0 bits (71), Expect = 0.32
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VYV NL +T+E E+ + G V+ + + D T+ +G ++ +E
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVN--------VHIPKDRVTQAHQGYGFVEFLSEED 52
Query: 278 VDLALSILDGYEIRGKKIKVER 299
D A+ I++ ++ GK I+V +
Sbjct: 53 ADYAIKIMNMIKLYGKPIRVNK 74
Score = 31.0 bits (71), Expect = 0.32
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VYV NL +T+E E+ + G V+ + + D T+ +G ++ +E
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVN--------VHIPKDRVTQAHQGYGFVEFLSEED 52
Query: 563 VDLALSILDGYEIRGKKIKVER 584
D A+ I++ ++ GK I+V +
Sbjct: 53 ADYAIKIMNMIKLYGKPIRVNK 74
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 31.1 bits (70), Expect = 0.35
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+V+V +P D+ ++E V V + G + +++L D K+ +G A Y +K
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRI--------YEMRLMMDFDGKN-RGYAFVMYTQKH 53
Query: 277 SVDLALSILDGYEIR 291
A+ L+ YEIR
Sbjct: 54 EAKRAVRELNNYEIR 68
Score = 31.1 bits (70), Expect = 0.35
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+V+V +P D+ ++E V V + G + +++L D K+ +G A Y +K
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRI--------YEMRLMMDFDGKN-RGYAFVMYTQKH 53
Query: 562 SVDLALSILDGYEIR 576
A+ L+ YEIR
Sbjct: 54 EAKRAVRELNNYEIR 68
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 31.1 bits (70), Expect = 0.36
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD--FKGDALCTYIK 274
+++V NLP D T + + +CG V LY D ++ KG + +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHV------------LYADIKMENGKSKGCGVVRFES 48
Query: 275 KESVDLALSILDGYEIRGKKIKV 297
E + A +++GY++ G++I V
Sbjct: 49 PEVAERACRMMNGYKLNGREIDV 71
Score = 31.1 bits (70), Expect = 0.36
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD--FKGDALCTYIK 559
+++V NLP D T + + +CG V LY D ++ KG + +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHV------------LYADIKMENGKSKGCGVVRFES 48
Query: 560 KESVDLALSILDGYEIRGKKIKV 582
E + A +++GY++ G++I V
Sbjct: 49 PEVAERACRMMNGYKLNGREIDV 71
Score = 28.8 bits (64), Expect = 2.3
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 377 LREECSKCGHV--KKVVLHDKHPEGVAQIFFKEPEAAD-ACRELLNGRWFGQRQI 428
L+++ ++CGHV + + + +G + F+ PE A+ ACR ++NG R+I
Sbjct: 16 LKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACR-MMNGYKLNGREI 69
Score = 28.8 bits (64), Expect = 2.3
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 662 LREECSKCGHV--KKVVLHDKHPEGVAQIFFKEPEAAD-ACRELLNGRWFGQRQI 713
L+++ ++CGHV + + + +G + F+ PE A+ ACR ++NG R+I
Sbjct: 16 LKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACR-MMNGYKLNGREI 69
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 30.9 bits (69), Expect = 0.40
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ T + V+ LP ++TQEE + G + KL D T G Y
Sbjct: 2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNY 53
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
I + + A++ L+G ++ K IKV A+
Sbjct: 54 IDPKDAEKAINTLNGLRLQTKTIKVSYAR 82
Score = 30.5 bits (68), Expect = 0.58
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T + V+ LP ++TQEE + G + KL D T G YI
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNYIDP 56
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+ + A++ L+G ++ K IKV A+
Sbjct: 57 KDAEKAINTLNGLRLQTKTIKVSYAR 82
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 30.5 bits (69), Expect = 0.40
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 373 YQQDLREECSKCGHVKKV-------VLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQ 425
++++L+EE G V K+ V ++ H G I F+ E A LNGR+F
Sbjct: 5 FERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDG 64
Query: 426 RQITAE 431
R + AE
Sbjct: 65 RLVKAE 70
Score = 30.5 bits (69), Expect = 0.40
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 658 YQQDLREECSKCGHVKKV-------VLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQ 710
++++L+EE G V K+ V ++ H G I F+ E A LNGR+F
Sbjct: 5 FERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDG 64
Query: 711 RQITAE 716
R + AE
Sbjct: 65 RLVKAE 70
>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 = 30.6 bits (69), Expect = 0.42
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V NL +T+E E+ + G V+K +KI D K F A + + S
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIK------VKIPKDKDGKPKQF---AFVNFKHEVS 54
Query: 278 VDLALSILDGYEIRGKKIKVE 298
V A+++L+G ++ G+ + ++
Sbjct: 55 VPYAMNLLNGIKLYGRPLNIQ 75
Score = 30.6 bits (69), Expect = 0.42
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
++V NL +T+E E+ + G V+K +KI D K F A + + S
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIK------VKIPKDKDGKPKQF---AFVNFKHEVS 54
Query: 563 VDLALSILDGYEIRGKKIKVE 583
V A+++L+G ++ G+ + ++
Sbjct: 55 VPYAMNLLNGIKLYGRPLNIQ 75
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 30.3 bits (69), Expect = 0.45
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
V+VSNL + ++E ++ KCG + DV +L + Y KG A + +ES
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEI-TDV-------RLVKN-YKGKSKGYAYVEFENEES 52
Query: 278 VDLALSILDGYEIRGKKIKV 297
V AL LD I+G+ + V
Sbjct: 53 VQEALK-LDRELIKGRPMFV 71
Score = 30.3 bits (69), Expect = 0.45
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+VSNL + ++E ++ KCG + DV +L + Y KG A + +ES
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEI-TDV-------RLVKN-YKGKSKGYAYVEFENEES 52
Query: 563 VDLALSILDGYEIRGKKIKV 582
V AL LD I+G+ + V
Sbjct: 53 VQEALK-LDRELIKGRPMFV 71
>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 = 30.3 bits (69), Expect = 0.52
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 17/86 (19%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYT-KDFKGDALCTYIK 274
KV+V L D+T+E+ + + G V TD Y K F+ A T+
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEV--------------TDVYIPKPFRAFAFVTFAD 46
Query: 275 KESVDLALSILDGYEIRGKKIKVERA 300
E + + I+G + V A
Sbjct: 47 PEVAQSLCG--EDHIIKGVSVHVSNA 70
Score = 30.3 bits (69), Expect = 0.52
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 17/86 (19%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYT-KDFKGDALCTYIK 559
KV+V L D+T+E+ + + G V TD Y K F+ A T+
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEV--------------TDVYIPKPFRAFAFVTFAD 46
Query: 560 KESVDLALSILDGYEIRGKKIKVERA 585
E + + I+G + V A
Sbjct: 47 PEVAQSLCG--EDHIIKGVSVHVSNA 70
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 30.4 bits (69), Expect = 0.56
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 219 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 278
+V NLP + Q + + + L +K V +L D T FKG + ES+
Sbjct: 5 FVGNLPFNTVQGDLDAIFK--DLSVKSV-------RLVRDKETDKFKGFCYVEFEDVESL 55
Query: 279 DLALSILDGYEIRGKKIKVERA 300
AL DG + ++V+ A
Sbjct: 56 KEALE-YDGALFDDRSLRVDIA 76
Score = 30.4 bits (69), Expect = 0.56
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 504 YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESV 563
+V NLP + Q + + + L +K V +L D T FKG + ES+
Sbjct: 5 FVGNLPFNTVQGDLDAIFK--DLSVKSV-------RLVRDKETDKFKGFCYVEFEDVESL 55
Query: 564 DLALSILDGYEIRGKKIKVERA 585
AL DG + ++V+ A
Sbjct: 56 KEALE-YDGALFDDRSLRVDIA 76
>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 = 30.3 bits (69), Expect = 0.59
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMK 252
+YVS LP +TQ+E + G ++ D T +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSR 42
Score = 30.3 bits (69), Expect = 0.59
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMK 537
+YVS LP +TQ+E + G ++ D T +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSR 42
>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 = 30.1 bits (68), Expect = 0.60
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T VYV N+P TQ + + + Q G + ++ + D +G A
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYI--------LEFRHQPD------RGFAFVKLDTH 46
Query: 276 ESVDLALSILDGYEIRGKKIK 296
E +A+ L G+ + G+ ++
Sbjct: 47 EQAAMAIVQLQGFPVHGRPLR 67
Score = 30.1 bits (68), Expect = 0.60
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T VYV N+P TQ + + + Q G + ++ + D +G A
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYI--------LEFRHQPD------RGFAFVKLDTH 46
Query: 561 ESVDLALSILDGYEIRGKKIK 581
E +A+ L G+ + G+ ++
Sbjct: 47 EQAAMAIVQLQGFPVHGRPLR 67
>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 = 29.9 bits (68), Expect = 0.71
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 14/82 (17%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T VYV NLP LT+EE G + +++++ D KG A +
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAI--------EEVRVFKD------KGYAFVRFDTH 46
Query: 276 ESVDLALSILDGYEIRGKKIKV 297
E+ A+ ++G I G+ +K
Sbjct: 47 EAAATAIVAVNGTSINGQTVKC 68
Score = 29.9 bits (68), Expect = 0.71
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 14/82 (17%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
T VYV NLP LT+EE G + +++++ D KG A +
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAI--------EEVRVFKD------KGYAFVRFDTH 46
Query: 561 ESVDLALSILDGYEIRGKKIKV 582
E+ A+ ++G I G+ +K
Sbjct: 47 EAAATAIVAVNGTSINGQTVKC 68
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 30.2 bits (68), Expect = 0.75
Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G E +++ +LP + E +++ G N + K++ D T K +
Sbjct: 1 GPEGCNLFIYHLPQEFGDAELMQMFLPFG--------NVISAKVFVDRATNQSKCFGFVS 52
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVE 298
+ S A+ ++G++I K++KV+
Sbjct: 53 FDNPASAQAAIQAMNGFQIGMKRLKVQ 79
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 30.0 bits (67), Expect = 0.81
Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G E +++ +LP + T + + G N + K++ D T K +
Sbjct: 1 GPEGCNLFIYHLPQEFTDTDLAQTFLPFG--------NVISAKVFIDKQTNLSKCFGFVS 52
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVE 298
Y +S A+ ++G++I K++KV+
Sbjct: 53 YDNPDSAQAAIQAMNGFQIGTKRLKVQ 79
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 29.6 bits (67), Expect = 0.83
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKV 297
Y +ES + A++ L G E+ G K+KV
Sbjct: 41 KYADRESAERAITTLHGKEVNGVKLKV 67
Score = 29.6 bits (67), Expect = 0.83
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKV 582
Y +ES + A++ L G E+ G K+KV
Sbjct: 41 KYADRESAERAITTLHGKEVNGVKLKV 67
>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 = 29.6 bits (67), Expect = 0.84
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 22/85 (25%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMK----IKLYTDPYTKDFKGDALCTY 272
+++V NLP D+T+EEF E+ K G V +V N+ K I+L T
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEV-SEVFLNKEKGFGFIRLDT--------------- 46
Query: 273 IKKESVDLALSILDGYEIRGKKIKV 297
+ + + A + LDG +G++++V
Sbjct: 47 --RTNAEKAKAELDGIMRKGRQLRV 69
Score = 29.6 bits (67), Expect = 0.84
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 22/85 (25%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMK----IKLYTDPYTKDFKGDALCTY 557
+++V NLP D+T+EEF E+ K G V +V N+ K I+L T
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEV-SEVFLNKEKGFGFIRLDT--------------- 46
Query: 558 IKKESVDLALSILDGYEIRGKKIKV 582
+ + + A + LDG +G++++V
Sbjct: 47 --RTNAEKAKAELDGIMRKGRQLRV 69
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 32.5 bits (74), Expect = 0.89
Identities = 44/212 (20%), Positives = 77/212 (36%), Gaps = 63/212 (29%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
S V+V NLP D+ + + VE + G V + M + K AL ++
Sbjct: 2 SPVVHVRNLPQDVVEADLVEALIPFGPV-----SYVMMLP---------GKRQAL---VE 44
Query: 275 KESVDLALSILDGY-----EIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKA 329
E + A + ++ IRG+ + T + ++K+
Sbjct: 45 FEDEESAKACVNFATSVPIYIRGQPAFFNYS--TSQ-------------------EIKRD 83
Query: 330 QEKLFDWR-PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK 388
FD P+K+ +IV+N P +TL + YQ + G V
Sbjct: 84 GNSDFDSAGPNKVL--------RVIVENPMYP------ITLDVLYQI-----FNPYGKVL 124
Query: 389 KVVLHDKHPEGVAQIFFKEPEAADACRELLNG 420
++V K+ A + F+ +A + LNG
Sbjct: 125 RIVTFTKNNVFQALVEFESVNSAQHAKAALNG 156
Score = 32.5 bits (74), Expect = 0.94
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEA 695
+IV+N P +TL + YQ + G V ++V K+ A + F+ +
Sbjct: 98 RVIVENPMYP------ITLDVLYQI-----FNPYGKVLRIVTFTKNNVFQALVEFESVNS 146
Query: 696 ADACRELLNG 705
A + LNG
Sbjct: 147 AQHAKAALNG 156
Score = 30.2 bits (68), Expect = 5.4
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 249 NQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
N ++K K K AL LAL+ L+G ++ GK ++V +K
Sbjct: 302 NVERVKFM---KNK--KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK 349
Score = 30.2 bits (68), Expect = 5.4
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 534 NQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
N ++K K K AL LAL+ L+G ++ GK ++V +K
Sbjct: 302 NVERVKFM---KNK--KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK 349
>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 = 29.6 bits (67), Expect = 0.93
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+++V NLP T+EE E+ + G + ++ L D TK KG A +++ E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEI--------SEVHLPLDKETKRSKGFAFVSFMFPE 52
Query: 277 SVDLALSILDGYEIRGKKIKV 297
A S LDG +G+ + V
Sbjct: 53 HAVKAYSELDGSIFQGRLLHV 73
Score = 29.6 bits (67), Expect = 0.93
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+++V NLP T+EE E+ + G + ++ L D TK KG A +++ E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEI--------SEVHLPLDKETKRSKGFAFVSFMFPE 52
Query: 562 SVDLALSILDGYEIRGKKIKV 582
A S LDG +G+ + V
Sbjct: 53 HAVKAYSELDGSIFQGRLLHV 73
Score = 28.8 bits (65), Expect = 1.7
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 376 DLREECSKCGHVKKV-VLHD---KHPEGVAQIFFKEPEAADACRELLNGRWFGQR 426
+LRE G + +V + D K +G A + F PE A L+G F R
Sbjct: 15 ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGR 69
Score = 28.8 bits (65), Expect = 1.7
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 661 DLREECSKCGHVKKV-VLHD---KHPEGVAQIFFKEPEAADACRELLNGRWFGQR 711
+LRE G + +V + D K +G A + F PE A L+G F R
Sbjct: 15 ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGR 69
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 29.6 bits (67), Expect = 0.99
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++ V NL ++ ++ + M+K G V Y D + K + + +
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVT------------YADAH-KQRPNEGVVEFATYS 48
Query: 277 SVDLALSILDGYEIRGKKIKV 297
+ A+ LDG E+ G+KIK+
Sbjct: 49 DMKRAIEKLDGTELNGRKIKL 69
Score = 29.6 bits (67), Expect = 0.99
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++ V NL ++ ++ + M+K G V Y D + K + + +
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVT------------YADAH-KQRPNEGVVEFATYS 48
Query: 562 SVDLALSILDGYEIRGKKIKV 582
+ A+ LDG E+ G+KIK+
Sbjct: 49 DMKRAIEKLDGTELNGRKIKL 69
>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 = 29.5 bits (67), Expect = 1.1
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 11/84 (13%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
N +YV NLP ++ EE ++ K G + Q++I TK+ +G A Y
Sbjct: 1 VNRILYVRNLPFKISSEELYDLFGKYGAI------RQIRIGN-----TKETRGTAFVVYE 49
Query: 559 KKESVDLALSILDGYEIRGKKIKV 582
A L G+ + + + V
Sbjct: 50 DIYDAKNACDHLSGFNVANRYLVV 73
Score = 29.1 bits (66), Expect = 1.6
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NLP ++ EE ++ K G + Q++I TK+ +G A Y
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAI------RQIRIGN-----TKETRGTAFVVYEDIYD 53
Query: 278 VDLALSILDGYEIRGKKIKV 297
A L G+ + + + V
Sbjct: 54 AKNACDHLSGFNVANRYLVV 73
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 29.6 bits (67), Expect = 1.1
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC--TYIKK 275
+YV NL +T++ E+ + G + KL + D Y
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKS--------CKLIREH-----GNDPYAFVEYYDH 47
Query: 276 ESVDLALSILDGYEIRGKKIKV 297
S AL ++G I G++IKV
Sbjct: 48 RSAAAALQTMNGRLILGQEIKV 69
Score = 29.6 bits (67), Expect = 1.1
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC--TYIKK 560
+YV NL +T++ E+ + G + KL + D Y
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKS--------CKLIREH-----GNDPYAFVEYYDH 47
Query: 561 ESVDLALSILDGYEIRGKKIKV 582
S AL ++G I G++IKV
Sbjct: 48 RSAAAALQTMNGRLILGQEIKV 69
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 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 = 29.2 bits (66), Expect = 1.2
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 411
IIVKNL L D +L + L E K G V V +H E A +FF++PE A
Sbjct: 2 IIVKNLP---LRSSDTSL----KDGLFHEFKKHGKVTSVKVHGTGSERYAIVFFRKPEDA 54
Query: 412 DACRELLNGRWF 423
+ E+ G+ F
Sbjct: 55 EKALEVSKGKLF 66
Score = 29.2 bits (66), Expect = 1.2
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 696
IIVKNL L D +L + L E K G V V +H E A +FF++PE A
Sbjct: 2 IIVKNLP---LRSSDTSL----KDGLFHEFKKHGKVTSVKVHGTGSERYAIVFFRKPEDA 54
Query: 697 DACRELLNGRWF 708
+ E+ G+ F
Sbjct: 55 EKALEVSKGKLF 66
>gnl|CDD|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane
protein Man1 (Man1) and similar proteins. This
subfamily corresponds to the RRM of Man1, also termed
LEM domain-containing protein 3 (LEMD3), an integral
protein of the inner nuclear membrane that binds to
nuclear lamins and emerin, thus playing a role in
nuclear organization. It is part of a protein complex
essential for chromatin organization and cell division.
It also functions as an important negative regulator for
the transforming growth factor (TGF) beta/activin/Nodal
signaling pathway by directly interacting with
chromatin-associated proteins and transcriptional
regulators, including the R-Smads, Smad1, Smad2, and
Smad3. Moreover, Man1 is a unique type of left-right
(LR) signaling regulator that acts on the inner nuclear
membrane. Man1 plays a crucial role in angiogenesis. The
vascular remodeling can be regulated at the inner
nuclear membrane through the interaction between Man1
and Smads. Man1 contains an N-terminal LEM domain, two
putative transmembrane domains, a MAN1-Src1p C-terminal
(MSC) domain, and a C-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The LEM domain interacts
with the DNA and chromatin-binding protein
Barrier-to-Autointegration Factor, and is also necessary
for efficient localization of MAN1 in the inner nuclear
membrane. Research has indicated that C-terminal
nucleoplasmic region of Man1 exhibits a DNA binding
winged helix domain and is responsible for both DNA- and
Smad-binding. .
Length = 92
Score = 29.6 bits (67), Expect = 1.4
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 354 VKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADA 413
++N+FDP + ++ + Q + E+C + + + EG I PE A
Sbjct: 4 IRNMFDPEV-ERGEDWHVRIQDAILEKCGDNNGIVHIQVDKASREGCVYIKCSSPEDAGK 62
Query: 414 CRELLNGRWFGQRQITAE 431
+ L+G WF R +T +
Sbjct: 63 AFKALHGWWFDGRLVTVK 80
Score = 29.6 bits (67), Expect = 1.4
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 639 VKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADA 698
++N+FDP + ++ + Q + E+C + + + EG I PE A
Sbjct: 4 IRNMFDPEV-ERGEDWHVRIQDAILEKCGDNNGIVHIQVDKASREGCVYIKCSSPEDAGK 62
Query: 699 CRELLNGRWFGQRQITAE 716
+ L+G WF R +T +
Sbjct: 63 AFKALHGWWFDGRLVTVK 80
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 29.4 bits (66), Expect = 1.4
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 384 CGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
CG V +V +L DK HP+G A I F + E+ L+ F RQI
Sbjct: 23 CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-ALDESLFRGRQI 70
Score = 29.4 bits (66), Expect = 1.4
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 669 CGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
CG V +V +L DK HP+G A I F + E+ L+ F RQI
Sbjct: 23 CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-ALDESLFRGRQI 70
>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 = 29.2 bits (66), Expect = 1.5
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 254 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
K+ DP T + KG A +Y E+ D A+ ++G + + I V A
Sbjct: 33 KIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYA 79
Score = 29.2 bits (66), Expect = 1.5
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 539 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
K+ DP T + KG A +Y E+ D A+ ++G + + I V A
Sbjct: 33 KIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYA 79
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 399 GVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
G A I + EA+DA E +NG++ R IT
Sbjct: 45 GFAFISYDSFEASDAAIEAMNGQYLCNRPITVS 77
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 684 GVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
G A I + EA+DA E +NG++ R IT
Sbjct: 45 GFAFISYDSFEASDAAIEAMNGQYLCNRPITVS 77
>gnl|CDD|202795 pfam03880, DbpA, DbpA RNA binding domain. This RNA binding domain
is found at the C-terminus of a number of DEAD helicase
proteins. It is sufficient to confer specificity for
hairpin 92 of 23S rRNA, which is part of the ribosomal
A-site. However, several members of this family lack
specificity for 23S rRNA. These can proteins can
generally be distinguished by a basic region that
extends beyond this domain [Karl Kossen, unpublished
data].
Length = 74
Score = 28.9 bits (66), Expect = 1.7
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
+ ++ D L L +I+G+K+K+E A
Sbjct: 47 VPEDMADKVLKALKKGKIKGRKLKIEPA 74
Score = 28.9 bits (66), Expect = 1.7
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERA 585
+ ++ D L L +I+G+K+K+E A
Sbjct: 47 VPEDMADKVLKALKKGKIKGRKLKIEPA 74
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 29.1 bits (66), Expect = 1.7
Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 13/89 (14%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E KV + NLP + ++ + ++K KIKL A T+
Sbjct: 3 SEIFKVEIKNLPKYIGFKQLKKFLKKQLFKPH-------KIKLLKRQDF------AFVTF 49
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+E AL ILDG++ +G+ + AK
Sbjct: 50 RSEEERQKALEILDGFKWKGRVLSARLAK 78
Score = 28.0 bits (63), Expect = 3.8
Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 13/88 (14%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
E KV + NLP + ++ + ++K KIKL A T+
Sbjct: 4 EIFKVEIKNLPKYIGFKQLKKFLKKQLFKPH-------KIKLLKRQDF------AFVTFR 50
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+E AL ILDG++ +G+ + AK
Sbjct: 51 SEEERQKALEILDGFKWKGRVLSARLAK 78
>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 = 29.2 bits (66), Expect = 2.0
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 11/84 (13%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NL T ++ +E + G V +++ D A + ++ S
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEV--------KYVRMAGDE--TQPTRYAFVEFAEQTS 56
Query: 278 VDLALSILDGYEIRGKKIKVERAK 301
V AL L+G G+ +KV +
Sbjct: 57 VINALK-LNGAMFGGRPLKVNHSN 79
Score = 29.2 bits (66), Expect = 2.0
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 11/84 (13%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV NL T ++ +E + G V +++ D A + ++ S
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEV--------KYVRMAGDE--TQPTRYAFVEFAEQTS 56
Query: 563 VDLALSILDGYEIRGKKIKVERAK 586
V AL L+G G+ +KV +
Sbjct: 57 VINALK-LNGAMFGGRPLKVNHSN 79
>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 = 28.8 bits (65), Expect = 2.1
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD 548
N +++V +P T+EE +E K V + V + +Y P K+
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSK---VTEGVV----DVIVYRSPDDKN 42
>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 = 28.7 bits (65), Expect = 2.2
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKHPE---GVAQIFFKEPEAADACRELLNG-RWFGQR 426
++DLRE S+ G ++KV V++D+ G ++F+ E A +E LNG G+R
Sbjct: 13 ERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70
Score = 28.7 bits (65), Expect = 2.2
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKHPE---GVAQIFFKEPEAADACRELLNG-RWFGQR 711
++DLRE S+ G ++KV V++D+ G ++F+ E A +E LNG G+R
Sbjct: 13 ERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 28.7 bits (64), Expect = 2.5
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
+YVS LP +TQ+E ++ + G ++ ++ D T +G + K+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITS--------RILRDQLTGVSRGVGFIRFDKR 52
Query: 276 ESVDLALSILDG 287
+ A+ L+G
Sbjct: 53 IEAEEAIKGLNG 64
Score = 28.7 bits (64), Expect = 2.5
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+YVS LP +TQ+E ++ + G ++ ++ D T +G + K+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITS--------RILRDQLTGVSRGVGFIRFDKR 52
Query: 561 ESVDLALSILDG 572
+ A+ L+G
Sbjct: 53 IEAEEAIKGLNG 64
>gnl|CDD|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM1 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 70
Score = 28.4 bits (63), Expect = 2.6
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
K+ + NLP D T +E ++++ L VD N K A T + E
Sbjct: 1 KILIKNLPQDSTNQEVHDLLKDYELKYCYVDRN---------------KRTAFVTLLNGE 45
Query: 277 SVDLALSILDGYEIRGKKIKVE 298
A+ +RGK I V+
Sbjct: 46 QAQDAIRTFHQTSVRGKDINVQ 67
Score = 28.4 bits (63), Expect = 2.6
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
K+ + NLP D T +E ++++ L VD N K A T + E
Sbjct: 1 KILIKNLPQDSTNQEVHDLLKDYELKYCYVDRN---------------KRTAFVTLLNGE 45
Query: 562 SVDLALSILDGYEIRGKKIKVE 583
A+ +RGK I V+
Sbjct: 46 QAQDAIRTFHQTSVRGKDINVQ 67
>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 = 28.4 bits (64), Expect = 2.7
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 16/84 (19%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NLPL T+E+ E+ + G V + KIK Y A + +++
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVK-----KIKDY-----------AFVHFEERDD 47
Query: 278 VDLALSILDGYEIRGKKIKVERAK 301
A+ ++G E+ G I+V AK
Sbjct: 48 AVKAMEEMNGKELEGSPIEVSLAK 71
Score = 28.4 bits (64), Expect = 2.7
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 16/84 (19%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV NLPL T+E+ E+ + G V + KIK Y A + +++
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVK-----KIKDY-----------AFVHFEERDD 47
Query: 563 VDLALSILDGYEIRGKKIKVERAK 586
A+ ++G E+ G I+V AK
Sbjct: 48 AVKAMEEMNGKELEGSPIEVSLAK 71
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end)
protein family. This subfamily corresponds to the RRM1
domain in the Spen (split end) 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 possesses 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 known as 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 = 28.4 bits (64), Expect = 2.7
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 358 FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACR 415
L D+D+ + L E K G V VLHD E VA + F+ PE A +
Sbjct: 9 LPSKLSDEDI------EDVLYHEFKKFGDVSVRVLHDGEDERVAYVNFRHPEDAREAK 60
Score = 28.4 bits (64), Expect = 2.7
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 643 FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACR 700
L D+D+ + L E K G V VLHD E VA + F+ PE A +
Sbjct: 9 LPSKLSDEDI------EDVLYHEFKKFGDVSVRVLHDGEDERVAYVNFRHPEDAREAK 60
>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 = 28.0 bits (63), Expect = 3.1
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLV-----MKDVDTNQMK 252
T VY+ LP + T E+ ++ Q G + + D TN+ K
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCK 42
Score = 28.0 bits (63), Expect = 3.1
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLV-----MKDVDTNQMK 537
T VY+ LP + T E+ ++ Q G + + D TN+ K
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCK 42
Score = 27.6 bits (62), Expect = 4.4
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 375 QDLREECSKCGHVK--KVVLHDKH---PEGVAQIFFKEPEAADACRELLNGR 421
+DL + C G + K +L DK +G + F PEAA E LNGR
Sbjct: 15 EDLEKLCQPFGKIISTKAIL-DKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
Score = 27.6 bits (62), Expect = 4.4
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 660 QDLREECSKCGHVK--KVVLHDKH---PEGVAQIFFKEPEAADACRELLNGR 706
+DL + C G + K +L DK +G + F PEAA E LNGR
Sbjct: 15 EDLEKLCQPFGKIISTKAIL-DKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
>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 = 27.9 bits (62), Expect = 3.2
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
K++V N+ T +E + ++ G V+ + D K A ++
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVV-ECDK---------------VKDYAFVHMERE 44
Query: 276 ESVDLALSILDGYEIRGKKIKVE 298
E A+ L+G E++G++I VE
Sbjct: 45 EEALAAIEALNGKEVKGRRINVE 67
Score = 27.9 bits (62), Expect = 3.2
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
K++V N+ T +E + ++ G V+ + D K A ++
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVV-ECDK---------------VKDYAFVHMERE 44
Query: 561 ESVDLALSILDGYEIRGKKIKVE 583
E A+ L+G E++G++I VE
Sbjct: 45 EEALAAIEALNGKEVKGRRINVE 67
>gnl|CDD|240489 cd12909, SPRY_RanBP9_10, SPRY domain in Ran binding proteins 9 and
10. This family includes SPRY domain in Ran binding
protein (RBP or RanBPM) 9 and 10, and similar proteins.
RanBP9 (also known as RanBPM), a binding partner of Ran,
is a small Ras-like GTPase that exerts multiple
functions via interactions with various proteins. RanBP9
and RanBP10 also act as androgen receptor (AR)
coactivators. Both consist of the N-terminal proline-
and glutamine-rich regions, the SPRY domain, and
LisH-CTLH and CRA motifs. SPRY domain of RanBPM forms a
complex with CD39, a prototypic member of the NTPDase
family, thus down-regulating activity substantially.
RanBP10 enhances the transcriptional activity of AR in a
ligand-dependent manner and exhibits a protein
expression pattern different from RanBPM in various cell
lines. RanBP10 is highly expressed in AR-positive
prostate cancer LNCaP cells, while RanBPM is abundant in
WI-38 and MCF-7 cells.
Length = 153
Score = 29.4 bits (67), Expect = 3.4
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 106 KGSYGYEGDT-HTYTDSTDGTVY 127
K S+GY GD H+++ S G Y
Sbjct: 70 KHSWGYHGDDGHSFSSSGTGKPY 92
>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 = 28.2 bits (63), Expect = 3.5
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
VYV NLP D+ + E ++ K G ++ D+D +KL P G A +
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIV-DID-----LKLPPRP-----PGYAFIEFEDARD 50
Query: 278 VDLALSILDGYEIRGKKIKVER 299
+ A+ DGY+ G++++VE
Sbjct: 51 AEDAIRGRDGYDFDGQRLRVEL 72
Score = 28.2 bits (63), Expect = 3.5
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
VYV NLP D+ + E ++ K G ++ D+D +KL P G A +
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIV-DID-----LKLPPRP-----PGYAFIEFEDARD 50
Query: 563 VDLALSILDGYEIRGKKIKVER 584
+ A+ DGY+ G++++VE
Sbjct: 51 AEDAIRGRDGYDFDGQRLRVEL 72
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 28.1 bits (63), Expect = 3.6
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 9/86 (10%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
+ K++V LP ++T+ + + + G V + V + D K +G T+
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVV--------VMYDHEKKRPRGFGFITFES 53
Query: 275 KESVDLALSILDGYEIRGKKIKVERA 300
++SVD ++ ++I GKK++V+RA
Sbjct: 54 EDSVDQVVNE-HFHDINGKKVEVKRA 78
>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 = 28.3 bits (64), Expect = 3.7
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 381 CSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGR 421
S G V+K+++ +K+ A + F E+A+ ++ LNGR
Sbjct: 22 FSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGR 62
Score = 28.3 bits (64), Expect = 3.7
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 666 CSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGR 706
S G V+K+++ +K+ A + F E+A+ ++ LNGR
Sbjct: 22 FSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGR 62
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 28.5 bits (64), Expect = 4.0
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 404 FFKEPEAADACRELLNGRWFGQRQITAE 431
F +E +A A +L N RWF + I AE
Sbjct: 75 FRREEDAEKAVNDL-NNRWFNGQPIYAE 101
Score = 28.5 bits (64), Expect = 4.0
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 689 FFKEPEAADACRELLNGRWFGQRQITAE 716
F +E +A A +L N RWF + I AE
Sbjct: 75 FRREEDAEKAVNDL-NNRWFNGQPIYAE 101
>gnl|CDD|237216 PRK12821, PRK12821, aspartyl/glutamyl-tRNA amidotransferase subunit
C-like protein; Provisional.
Length = 477
Score = 30.2 bits (68), Expect = 4.7
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 452 LKKWETFLGK-KIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPL 510
LK ++T L + + K + F+ PK KK++ + ++LKK + + L
Sbjct: 351 LKGFKTELSETQTKGIKKSFSDLQSPLFPKHWTSKKQQLNKDELKKLARLVMFDLDDAEL 410
Query: 511 DLTQEEFVEVMQKCGLVMKDVDTNQMK 537
+ Q EF ++ V K +DT +K
Sbjct: 411 EKLQVEFKDITSSFKQVEK-IDTTNVK 436
>gnl|CDD|224336 COG1418, COG1418, Predicted HD superfamily hydrolase [General
function prediction only].
Length = 222
Score = 29.7 bits (67), Expect = 5.1
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 285 LDGYEIRGKKIKVERAKFTMKGE-AYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRG 343
D + RG I R E AY + + +R + +KL QEKL +
Sbjct: 139 ADRLDARGA-IGEARVFLFEGVEKAYAIQAGRELRRIVEDKKLDHFQEKLLK-LKISKKT 196
Query: 344 ERSKNESVIIVKNLF 358
E +K E +K
Sbjct: 197 EEAKAEYPGKIKVTV 211
Score = 29.7 bits (67), Expect = 5.1
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 570 LDGYEIRGKKIKVERAKFTMKGE-AYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRG 628
D + RG I R E AY + + +R + +KL QEKL +
Sbjct: 139 ADRLDARGA-IGEARVFLFEGVEKAYAIQAGRELRRIVEDKKLDHFQEKLLK-LKISKKT 196
Query: 629 ERSKNESVIIVKNLF 643
E +K E +K
Sbjct: 197 EEAKAEYPGKIKVTV 211
>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 = 27.7 bits (62), Expect = 5.3
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
Q DL E +CG V V + D +G + F E A E +G R+I
Sbjct: 13 QDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLGREI 69
Score = 27.7 bits (62), Expect = 5.3
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
Q DL E +CG V V + D +G + F E A E +G R+I
Sbjct: 13 QDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLGREI 69
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 27.6 bits (61), Expect = 5.5
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCG 240
+++V NLP D+T+E+F ++ +K G
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYG 26
Score = 27.6 bits (61), Expect = 5.5
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCG 525
+++V NLP D+T+E+F ++ +K G
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYG 26
>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 = 27.7 bits (62), Expect = 5.5
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD--FKGDALCTYI 273
+++ V NLP + +++ ++ + G + DV Q+K YTKD F+ Y
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTI-TDV---QLK-------YTKDGKFRKFGFVGYK 49
Query: 274 KKESVDLALSILDGYEIRGKKIKVERA 300
+E AL + I KI VE
Sbjct: 50 TEEEAQKALKHFNNSFIDTSKITVEIC 76
Score = 27.7 bits (62), Expect = 5.5
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD--FKGDALCTYI 558
+++ V NLP + +++ ++ + G + DV Q+K YTKD F+ Y
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTI-TDV---QLK-------YTKDGKFRKFGFVGYK 49
Query: 559 KKESVDLALSILDGYEIRGKKIKVERA 585
+E AL + I KI VE
Sbjct: 50 TEEEAQKALKHFNNSFIDTSKITVEIC 76
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 27.2 bits (61), Expect = 6.0
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 13/83 (15%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+V VS LP + ++ + ++ G V Y D +D +G+ + + +E
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAGDV------------TYADVD-RDQEGEGVVEFTSQE 48
Query: 277 SVDLALSILDGYEIRGKKIKVER 299
++ AL LDG E RG++++VE
Sbjct: 49 DMERALRKLDGTEFRGRRVRVEE 71
Score = 27.2 bits (61), Expect = 6.0
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 13/83 (15%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+V VS LP + ++ + ++ G V Y D +D +G+ + + +E
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAGDV------------TYADVD-RDQEGEGVVEFTSQE 48
Query: 562 SVDLALSILDGYEIRGKKIKVER 584
++ AL LDG E RG++++VE
Sbjct: 49 DMERALRKLDGTEFRGRRVRVEE 71
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 27.7 bits (61), Expect = 7.0
Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G E +++ +LP + ++ +++ G N + K++ D T K +
Sbjct: 4 GPEGANLFIYHLPQEFGDQDLLQMFMPFG--------NVVSAKVFIDKQTNLSKCFGFVS 55
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVE 298
Y S A+ ++G++I K++KV+
Sbjct: 56 YDNPVSAQAAIQAMNGFQIGMKRLKVQ 82
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 29.4 bits (67), Expect = 7.4
Identities = 11/45 (24%), Positives = 22/45 (48%)
Query: 461 KKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYV 505
K++K E + + K +KK++K K KA+ +++V
Sbjct: 50 KEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSKPRLFV 94
>gnl|CDD|236272 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
Length = 167
Score = 28.4 bits (64), Expect = 8.9
Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 20/101 (19%)
Query: 440 KIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQE 499
K++E+ E++E LKK E K K E T K EAY K +K+ K D+E L K+ E
Sbjct: 68 KLKESKEKKEDALKKLEE---AKEKAELIVETAKKEAYILTQKIEKQTKDDIENLIKSFE 124
Query: 500 NTKVY---------VSNL--------PLDLTQEEFVEVMQK 523
+ V + + L Q+E+V ++ K
Sbjct: 125 ELMEFEVRKMEREVVEEVLNELFESKKVSLNQQEYVNILLK 165
>gnl|CDD|185033 PRK15074, PRK15074, inosine/guanosine kinase; Provisional.
Length = 434
Score = 29.2 bits (66), Expect = 8.9
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 139 KVDDDFLARYQMSYG 153
KVDD+FL RY +S G
Sbjct: 49 KVDDEFLERYGLSKG 63
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 27.0 bits (60), Expect = 9.7
Identities = 25/75 (33%), Positives = 32/75 (42%), Gaps = 17/75 (22%)
Query: 352 IIVKNLFDPALFDKDVT--LILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFK 406
+IV NL KDVT I EY S+ G +K+V+L G+A I FK
Sbjct: 2 VIVSNL------PKDVTEAQIREYFV------SQIGPIKRVLLSYNEGGKSTGIANITFK 49
Query: 407 EPEAADACRELLNGR 421
A + NGR
Sbjct: 50 RAGDATKAYDKFNGR 64
Score = 27.0 bits (60), Expect = 9.7
Identities = 25/75 (33%), Positives = 32/75 (42%), Gaps = 17/75 (22%)
Query: 637 IIVKNLFDPALFDKDVT--LILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFK 691
+IV NL KDVT I EY S+ G +K+V+L G+A I FK
Sbjct: 2 VIVSNL------PKDVTEAQIREYFV------SQIGPIKRVLLSYNEGGKSTGIANITFK 49
Query: 692 EPEAADACRELLNGR 706
A + NGR
Sbjct: 50 RAGDATKAYDKFNGR 64
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
0.313 0.132 0.385
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,669,237
Number of extensions: 3963550
Number of successful extensions: 5897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5611
Number of HSP's successfully gapped: 459
Length of query: 773
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 669
Effective length of database: 6,324,786
Effective search space: 4231281834
Effective search space used: 4231281834
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 63 (28.1 bits)