RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16116
(612 letters)
>gnl|CDD|241185 cd12741, RRM2_Fusilli, RNA recognition motif 2 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM2 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 100
Score = 187 bits (477), Expect = 2e-57
Identities = 76/100 (76%), Positives = 86/100 (86%)
Query: 422 AGGNNNEAQAFLTRGAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKK 481
AGG NNEAQAFL+RG QVI+RMRGLPY+CTAKQV++FF G C+V+DG EGVLFVKK
Sbjct: 1 AGGANNEAQAFLSRGGQVIVRMRGLPYDCTAKQVLEFFTTGDTPPCHVLDGNEGVLFVKK 60
Query: 482 PDGKATGDAFVLFEKEEEADKALSKHKESIGIRYIELFRS 521
PDG+ATGDAFVLF EE+A KAL KH+ESIG RYIELFRS
Sbjct: 61 PDGRATGDAFVLFATEEDAPKALGKHRESIGSRYIELFRS 100
Score = 35.6 bits (82), Expect = 0.011
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
GR G+A V F +E AL +H+ I RYIE+ ++
Sbjct: 63 GRATGDAFVLFATEEDAPKALGKHRESIGSRYIELFRS 100
Score = 30.6 bits (69), Expect = 0.55
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 79 QGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQ 130
+GV V G+ +G+AF+ +E A A +H R I RYIE+F+
Sbjct: 53 EGVLFVKKPDGRATGDAFVLFATEEDAPKALG-KH-RESI---GSRYIELFR 99
>gnl|CDD|241187 cd12743, RRM3_Fusilli, RNA recognition motif 3 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM3 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 85
Score = 144 bits (364), Expect = 2e-41
Identities = 59/71 (83%), Positives = 63/71 (88%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
VEHILEFLG+FA IV+QGVHMVYN+QGQPSGEAFIQMDSE SA AQ RHNR M+FGK
Sbjct: 15 VEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYMVFGK 74
Query: 122 KQRYIEVFQCS 132
KQRYIEVFQCS
Sbjct: 75 KQRYIEVFQCS 85
Score = 41.0 bits (96), Expect = 1e-04
Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 10/87 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
IR+RGLPYE + +++F + + ++ +GV V G+ +G+AF+ + E+ A
Sbjct: 4 IRLRGLPYEAQVEHILEFLG---DFAKMIV--FQGVHMVYNAQGQPSGEAFIQMDSEQSA 58
Query: 501 DKALSK---HKESIG--IRYIELFRST 522
+ G RYIE+F+ +
Sbjct: 59 SACAQQRHNRYMVFGKKQRYIEVFQCS 85
Score = 34.9 bits (80), Expect = 0.015
Identities = 13/13 (100%), Positives = 13/13 (100%)
Query: 578 KDCIRLRGLPYEA 590
KDCIRLRGLPYEA
Sbjct: 1 KDCIRLRGLPYEA 13
Score = 28.7 bits (64), Expect = 1.9
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 367 GVALCLSAFGRRNGEAIVRFI-DQEHRDMALKRHKHHI----DKRYIEVTKAN 414
GV + +A G+ +GEA ++ +Q A +RH ++ +RYIEV + +
Sbjct: 33 GVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYMVFGKKQRYIEVFQCS 85
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 139 bits (352), Expect = 1e-39
Identities = 52/84 (61%), Positives = 62/84 (73%), Gaps = 4/84 (4%)
Query: 438 QVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKE 497
QVIIRMRGLPY TA ++ FF C V+ G +G+LFV PDG+ TGDAFVLFE E
Sbjct: 1 QVIIRMRGLPYSATAADILAFFGGL----CPVVGGPDGILFVTGPDGRPTGDAFVLFETE 56
Query: 498 EEADKALSKHKESIGIRYIELFRS 521
E+A +AL KHKE++G RYIELFRS
Sbjct: 57 EDAQRALGKHKENLGSRYIELFRS 80
Score = 54.6 bits (132), Expect = 1e-09
Identities = 18/52 (34%), Positives = 27/52 (51%)
Query: 362 VLGLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
V G G+ GR G+A V F +E AL +HK ++ RYIE+ ++
Sbjct: 29 VGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHKENLGSRYIELFRS 80
Score = 49.2 bits (118), Expect = 1e-07
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 63 EHILEFLGEF-ASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
IL F G G+ V G+P+G+AF+ ++E A A +H N+
Sbjct: 16 ADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALG-KHKENL---- 70
Query: 122 KQRYIEVF 129
RYIE+F
Sbjct: 71 GSRYIELF 78
>gnl|CDD|241184 cd12740, RRM2_ESRP2, RNA recognition motif 2 in epithelial splicing
regulatory protein 2 (ESRP2) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP2, also termed
RNA-binding motif protein 35B (RBM35B), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. ESRP2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 107
Score = 133 bits (336), Expect = 4e-37
Identities = 67/110 (60%), Positives = 76/110 (69%), Gaps = 4/110 (3%)
Query: 423 GGNNNEAQAFLTRGAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKP 482
GG +NE FL++ QVIIRMRGLP+ T V+ F G E C V G EG+LFVK P
Sbjct: 1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPTDVLGFL--GPE--CPVTGGTEGLLFVKYP 56
Query: 483 DGKATGDAFVLFEKEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNK 532
DG+ TGDAFVLF EE A AL KHK +G RYIELFRST AEVQQVLN+
Sbjct: 57 DGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRSTAAEVQQVLNR 106
Score = 36.9 bits (85), Expect = 0.004
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINV 421
GR G+A V F +E+ ALK+HK + KRYIE+ ++ + V
Sbjct: 58 GRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRSTAAEVQQV 103
Score = 36.1 bits (83), Expect = 0.009
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 63 EHILEFLG-EFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
+L FLG E +G+ V G+P+G+AF+ E Y L+ ++ ++ GK
Sbjct: 31 TDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEE--YAQNALKKHKGIL-GK 87
Query: 122 KQRYIEVFQCSGEDMNLVLN 141
RYIE+F+ + ++ VLN
Sbjct: 88 --RYIELFRSTAAEVQQVLN 105
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. Additional research indicated that ESRP1
functions as a tumor suppressor in colon cancer cells.
It may be involved in posttranscriptional regulation of
various genes by exerting a differential effect on
protein translation via 5' untranslated regions (UTRs)
of mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 132 bits (334), Expect = 7e-37
Identities = 64/110 (58%), Positives = 78/110 (70%), Gaps = 4/110 (3%)
Query: 423 GGNNNEAQAFLTRGAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKP 482
GG +NE FL++ QVI+RMRGLP+ TA++V+ FF C V G+EG+LFV P
Sbjct: 1 GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVLAFFG----QHCPVTGGKEGILFVTYP 56
Query: 483 DGKATGDAFVLFEKEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNK 532
D + TGDAFVLF EE A AL KHK+ +G RYIELFRST AEVQQVLN+
Sbjct: 57 DSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRSTAAEVQQVLNR 106
Score = 35.8 bits (82), Expect = 0.013
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINV 421
G G+ R G+A V F +E+ ALK+HK + KRYIE+ ++ + V
Sbjct: 46 GKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRSTAAEVQQV 103
Score = 33.9 bits (77), Expect = 0.047
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 60 VLVEHILEFLGEFASNIV-YQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMI 118
E +L F G+ +G+ V +P+G+AF+ E Y L+ +++++
Sbjct: 28 ATAEEVLAFFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEE--YAQNALKKHKDLL 85
Query: 119 FGKKQRYIEVFQCSGEDMNLVLN 141
GK RYIE+F+ + ++ VLN
Sbjct: 86 -GK--RYIELFRSTAAEVQQVLN 105
>gnl|CDD|240953 cd12509, RRM3_ESRPs_Fusilli, RNA recognition motif 3 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM3 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli. Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. Fusilli shows high
sequence homology to ESRPs and contains three RRMs as
well. It also has an N-terminal domain with unknown
function and a C-terminal domain particularly rich in
alanine, glutamine, and serine. .
Length = 81
Score = 111 bits (280), Expect = 1e-29
Identities = 42/71 (59%), Positives = 48/71 (67%), Gaps = 4/71 (5%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
VE IL FLGE A +I QGVHMV N+QG+PSG+AFIQM S A AA H +M
Sbjct: 15 VEDILNFLGELARSIAPQGVHMVLNAQGRPSGDAFIQMLSAEFATRAANELHKHHM---- 70
Query: 122 KQRYIEVFQCS 132
+RYIEVFQCS
Sbjct: 71 GERYIEVFQCS 81
Score = 58.6 bits (142), Expect = 5e-11
Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
IR+RGLPYE T + +++F E + ++ GV V G+ +GDAF+ E A
Sbjct: 4 IRLRGLPYEATVEDILNFLG---ELARSIAPQ--GVHMVLNAQGRPSGDAFIQMLSAEFA 58
Query: 501 DK-ALSKHKESIGIRYIELF 519
+ A HK +G RYIE+F
Sbjct: 59 TRAANELHKHHMGERYIEVF 78
Score = 44.0 bits (104), Expect = 7e-06
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 365 LGGVALCLSAFGRRNGEAIVRFIDQEHRDM-ALKRHKHHIDKRYIEV 410
GV + L+A GR +G+A ++ + E A + HKHH+ +RYIEV
Sbjct: 31 PQGVHMVLNAQGRPSGDAFIQMLSAEFATRAANELHKHHMGERYIEV 77
Score = 34.7 bits (80), Expect = 0.015
Identities = 12/13 (92%), Positives = 13/13 (100%)
Query: 578 KDCIRLRGLPYEA 590
K+CIRLRGLPYEA
Sbjct: 1 KNCIRLRGLPYEA 13
>gnl|CDD|241182 cd12738, RRM1_Fusilli, RNA recognition motif 1 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM1 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 80
Score = 105 bits (264), Expect = 1e-27
Identities = 41/56 (73%), Positives = 46/56 (82%)
Query: 363 LGLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDF 418
+ GGVALCL+ GRRNGEA+VRF EHRD+ALKRHKHHI +RYIEV KA GEDF
Sbjct: 25 IAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATGEDF 80
Score = 64.5 bits (157), Expect = 5e-13
Identities = 30/86 (34%), Positives = 46/86 (53%), Gaps = 7/86 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R RGLP++ + + + FF N+ G GV P G+ G+A V F E
Sbjct: 1 VVRARGLPWQSSDQDIAKFFRG-----LNIAKG--GVALCLNPQGRRNGEALVRFTCTEH 53
Query: 500 ADKALSKHKESIGIRYIELFRSTTAE 525
D AL +HK IG RYIE++++T +
Sbjct: 54 RDLALKRHKHHIGQRYIEVYKATGED 79
Score = 42.6 bits (100), Expect = 3e-05
Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 75 NIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQCSGE 134
NI GV + N QG+ +GEA ++ LA + RH ++ QRYIEV++ +GE
Sbjct: 24 NIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALK-RHKHHI----GQRYIEVYKATGE 78
Query: 135 D 135
D
Sbjct: 79 D 79
>gnl|CDD|241186 cd12742, RRM3_ESRP1_ESRP2, RNA recognition motif in epithelial
splicing regulatory protein ESRP1, ESRP2 and similar
proteins. This subgroup corresponds to the RRM3 of
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B). These are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of the fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 101 bits (252), Expect = 7e-26
Identities = 44/71 (61%), Positives = 52/71 (73%), Gaps = 4/71 (5%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
+E ILEFLGEFA++I GVHMV N QG+PSG+AFIQM S A+LAAQ H + M
Sbjct: 15 IEDILEFLGEFAADIRPHGVHMVLNQQGRPSGDAFIQMKSAERAFLAAQKCHKKMM---- 70
Query: 122 KQRYIEVFQCS 132
K RY+EVFQCS
Sbjct: 71 KDRYVEVFQCS 81
Score = 52.5 bits (126), Expect = 8e-09
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
IR+RGLPY T + +++F E + ++ GV V G+ +GDAF+ + E A
Sbjct: 4 IRLRGLPYTATIEDILEFL---GEFAADIRP--HGVHMVLNQQGRPSGDAFIQMKSAERA 58
Query: 501 DKALSK-HKESIGIRYIELF 519
A K HK+ + RY+E+F
Sbjct: 59 FLAAQKCHKKMMKDRYVEVF 78
Score = 33.6 bits (77), Expect = 0.041
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKR-HKHHIDKRYIEV 410
GV + L+ GR +G+A ++ E +A ++ HK + RY+EV
Sbjct: 33 GVHMVLNQQGRPSGDAFIQMKSAERAFLAAQKCHKKMMKDRYVEV 77
Score = 32.5 bits (74), Expect = 0.082
Identities = 11/13 (84%), Positives = 12/13 (92%)
Query: 578 KDCIRLRGLPYEA 590
+DCIRLRGLPY A
Sbjct: 1 RDCIRLRGLPYTA 13
>gnl|CDD|240951 cd12507, RRM1_ESRPs_Fusilli, RNA recognition motif 1 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM1 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B). These are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of the fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli. Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous fibroblast growth factor
receptor 2 (FGFR2) splicing and functions as a splicing
factor. It shows high sequence homology to ESRPs and
contains three RRMs as well. It also has an N-terminal
domain with unknown function and a C-terminal domain
particularly rich in alanine, glutamine, and serine. .
Length = 75
Score = 97.2 bits (242), Expect = 1e-24
Identities = 38/48 (79%), Positives = 44/48 (91%)
Query: 366 GGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
GGVALCLSA GRRNGEA++RF+DQEHRD+AL+RHKHH+ RYIEV KA
Sbjct: 28 GGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75
Score = 64.8 bits (158), Expect = 3e-13
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R RGLP++ + + + FF N+ G GV G+ G+A + F +E
Sbjct: 1 VVRARGLPWQSSDQDIAQFFRG-----LNIAKG--GVALCLSAQGRRNGEALIRFVDQEH 53
Query: 500 ADKALSKHKESIGIRYIELFRS 521
D AL +HK +G RYIE++++
Sbjct: 54 RDLALQRHKHHMGTRYIEVYKA 75
Score = 44.0 bits (104), Expect = 7e-06
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 75 NIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQ 130
NI GV + ++QG+ +GEA I+ + LA Q RH +M G RYIEV++
Sbjct: 24 NIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQ-RHKHHM--GT--RYIEVYK 74
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein
family includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3
(also termed hnRNP 2H9), which represent a group of
nuclear RNA binding proteins that are involved in
pre-mRNA processing. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. hnRNP H and
hnRNP H2 are almost identical; both have been found to
bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and play an
important role in efficiently silencing the exon.
Members in this family can regulate the alternative
splicing of fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced silencing
activity within hnRNP H3. Members in this family have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains three
potential RRMs responsible for the RNA binding, and two
auxiliary domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 77
Score = 97.1 bits (242), Expect = 1e-24
Identities = 36/82 (43%), Positives = 54/82 (65%), Gaps = 5/82 (6%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R+RGLP+ TA+ V++FF C + GE G+ F +G+ +G+AF+ E EE+
Sbjct: 1 VVRIRGLPWSATAEDVLNFFS-----DCRIKGGENGIHFTYSREGRPSGEAFIELESEED 55
Query: 500 ADKALSKHKESIGIRYIELFRS 521
+KAL KH E +G RYIE+FRS
Sbjct: 56 VEKALEKHNEHMGHRYIEVFRS 77
Score = 58.5 bits (142), Expect = 6e-11
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 9/71 (12%)
Query: 62 VEHILEFLGEFASNIV--YQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIF 119
E +L F + I G+H Y+ +G+PSGEAFI+++SE A + +HN +M
Sbjct: 13 AEDVLNFFSD--CRIKGGENGIHFTYSREGRPSGEAFIELESEEDVEKALE-KHNEHM-- 67
Query: 120 GKKQRYIEVFQ 130
RYIEVF+
Sbjct: 68 --GHRYIEVFR 76
Score = 51.2 bits (123), Expect = 2e-08
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTK 412
G G+ S GR +GEA + +E + AL++H H+ RYIEV +
Sbjct: 28 GENGIHFTYSREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFR 76
>gnl|CDD|241180 cd12736, RRM1_ESRP1, RNA recognition motif 1 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM1 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (p120-Catenin) and
ENAH (hMena) splicing. It enhances epithelial-specific
exons of CD44 and ENAH, silences mesenchymal exons of
CTNND1, or both within FGFR2. Additional research
indicated that ESRP1 functions as a tumor suppressor in
colon cancer cells. It may be involved in
posttranscriptional regulation of various genes by
exerting a differential effect on protein translation
via 5' untranslated regions (UTRs) of mRNAs. ESRP1
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 96.6 bits (240), Expect = 2e-24
Identities = 39/53 (73%), Positives = 46/53 (86%)
Query: 366 GGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDF 418
GG ALCL+A GRRNGEA+VRF+ +EHRD+AL+RHKHH+ RYIEV KA GEDF
Sbjct: 33 GGAALCLNAQGRRNGEALVRFVSEEHRDLALQRHKHHMGNRYIEVYKATGEDF 85
Score = 59.3 bits (143), Expect = 4e-11
Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+IR RGLP++ + + + FF+ N+ G G G+ G+A V F EE
Sbjct: 6 VIRARGLPWQSSDQDIARFFKG-----LNIAKG--GAALCLNAQGRRNGEALVRFVSEEH 58
Query: 500 ADKALSKHKESIGIRYIELFRST 522
D AL +HK +G RYIE++++T
Sbjct: 59 RDLALQRHKHHMGNRYIEVYKAT 81
Score = 45.4 bits (107), Expect = 2e-06
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 75 NIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQCSGE 134
NI G + N+QG+ +GEA ++ SE LA Q RH +M RYIEV++ +GE
Sbjct: 29 NIAKGGAALCLNAQGRRNGEALVRFVSEEHRDLALQ-RHKHHM----GNRYIEVYKATGE 83
Query: 135 D 135
D
Sbjct: 84 D 84
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which includes hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'),
hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 95.5 bits (238), Expect = 4e-24
Identities = 35/83 (42%), Positives = 54/83 (65%), Gaps = 7/83 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R+RGLP+ C+ +++ FF +G E N G+ G++TG+A+V F +E
Sbjct: 2 VVRLRGLPFGCSKEEIAQFF-SGLEIVPN------GITLPMDYRGRSTGEAYVQFASQES 54
Query: 500 ADKALSKHKESIGIRYIELFRST 522
A++AL KHKE IG RYIE+FRS+
Sbjct: 55 AERALGKHKEKIGHRYIEIFRSS 77
Score = 43.9 bits (104), Expect = 7e-06
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
G+ L + GR GEA V+F QE + AL +HK I RYIE+ ++
Sbjct: 30 GITLPMDYRGRSTGEAYVQFASQESAERALGKHKEKIGHRYIEIFRS 76
Score = 42.0 bits (99), Expect = 4e-05
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E I +F IV G+ + + +G+ +GEA++Q S+ SA A +H +
Sbjct: 15 EEIAQFFSGL--EIVPNGITLPMDYRGRSTGEAYVQFASQESAERALG-KHKEKI----G 67
Query: 123 QRYIEVFQCS 132
RYIE+F+ S
Sbjct: 68 HRYIEIFRSS 77
>gnl|CDD|241181 cd12737, RRM1_ESRP2, RNA recognition motif 1 in epithelial splicing
regulatory protein 2 (ESRP2) and similar proteins. This
subgroup corresponds to the RRM1 of ESRP2, also termed
RNA-binding motif protein 35B (RBM35B), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. ESRP2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 80
Score = 94.3 bits (234), Expect = 2e-23
Identities = 38/53 (71%), Positives = 46/53 (86%)
Query: 366 GGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDF 418
GGVALCL+A GRRNGEA+VRF++ E RD+AL+RHKHH+ RYIEV KA GE+F
Sbjct: 28 GGVALCLNAQGRRNGEALVRFVNSEQRDLALQRHKHHMGSRYIEVYKATGEEF 80
Score = 61.9 bits (150), Expect = 4e-12
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 7/86 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+IR RGLP++ + + + FF+ N+ G GV G+ G+A V F E+
Sbjct: 1 VIRARGLPWQSSDQDIARFFKG-----LNIAKG--GVALCLNAQGRRNGEALVRFVNSEQ 53
Query: 500 ADKALSKHKESIGIRYIELFRSTTAE 525
D AL +HK +G RYIE++++T E
Sbjct: 54 RDLALQRHKHHMGSRYIEVYKATGEE 79
Score = 41.9 bits (98), Expect = 5e-05
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 75 NIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQCSGE 134
NI GV + N+QG+ +GEA ++ + LA Q RH +M RYIEV++ +GE
Sbjct: 24 NIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALQ-RHKHHM----GSRYIEVYKATGE 78
Query: 135 D 135
+
Sbjct: 79 E 79
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 91.8 bits (229), Expect = 7e-23
Identities = 30/80 (37%), Positives = 47/80 (58%), Gaps = 7/80 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R+RGLP+ T + + DFF ++ +G+ V DG+ TG+A+V F E+
Sbjct: 1 VVRLRGLPFSATEEDIRDFFS-----GLDI--PPDGIHIVYDDDGRPTGEAYVEFASPED 53
Query: 500 ADKALSKHKESIGIRYIELF 519
A +AL KH +G RYIE+F
Sbjct: 54 ARRALRKHNNKMGGRYIEVF 73
Score = 63.3 bits (155), Expect = 8e-13
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 59 KVLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMI 118
E I +F +I G+H+VY+ G+P+GEA+++ S A A + +HN M
Sbjct: 10 SATEEDIRDFFSGL--DIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALR-KHNNKM- 65
Query: 119 FGKKQRYIEVF 129
RYIEVF
Sbjct: 66 ---GGRYIEVF 73
Score = 57.2 bits (139), Expect = 1e-10
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 366 GGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
G+ + GR GEA V F E AL++H + + RYIEV
Sbjct: 28 DGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNKMGGRYIEV 72
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 86.4 bits (214), Expect = 9e-21
Identities = 34/80 (42%), Positives = 51/80 (63%), Gaps = 5/80 (6%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I+R +GLP+ CTA+ V++FF + C + +GE GV F+ DGK GDA + E EE+
Sbjct: 3 IVRAKGLPWSCTAEDVMNFF-----DDCRIRNGENGVHFLLNRDGKPRGDALIELESEED 57
Query: 500 ADKALSKHKESIGIRYIELF 519
KAL +H+ +G RY+E+
Sbjct: 58 VQKALEQHRHYMGQRYVEVR 77
Score = 46.3 bits (110), Expect = 1e-06
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 80 GVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQ 130
GVH + N G+P G+A I+++SE A + +H M QRY+EV +
Sbjct: 33 GVHFLLNRDGKPRGDALIELESEEDVQKALE-QHRHYM----GQRYVEVRE 78
Score = 40.6 bits (95), Expect = 1e-04
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
G GV L+ G+ G+A++ +E AL++H+H++ +RY+EV
Sbjct: 30 GENGVHFLLNRDGKPRGDALIELESEEDVQKALEQHRHYMGQRYVEV 76
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 85.9 bits (213), Expect = 1e-20
Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 7/80 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++R+RGLPY CT +IDFF G + ++GV+ V G+ TG+A+V F E
Sbjct: 3 VVRLRGLPYSCTEDDIIDFF-RGLDI------VDDGVVIVLNRRGRKTGEAYVQFATPEM 55
Query: 500 ADKALSKHKESIGIRYIELF 519
A+KAL KH+E IG RYIE+F
Sbjct: 56 ANKALLKHREEIGNRYIEVF 75
Score = 59.0 bits (143), Expect = 3e-11
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
GV + L+ GR+ GEA V+F E + AL +H+ I RYIEV
Sbjct: 31 GVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEIGNRYIEV 74
Score = 45.1 bits (107), Expect = 3e-06
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 65 ILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDS-EHSAYLAAQLRHNRNMIFGKKQ 123
I++F +IV GV +V N +G+ +GEA++Q + E + A L+H +
Sbjct: 18 IIDFFRGL--DIVDDGVVIVLNRRGRKTGEAYVQFATPEMAN--KALLKHREEI----GN 69
Query: 124 RYIEVF 129
RYIEVF
Sbjct: 70 RYIEVF 75
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 83
Score = 82.8 bits (204), Expect = 2e-19
Identities = 39/87 (44%), Positives = 58/87 (66%), Gaps = 7/87 (8%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+R+RGLP+ C+ ++++ FF +G E N G+ G++TG+AFV F +E A
Sbjct: 4 VRLRGLPFGCSKEEIVQFF-SGLEIVPN------GITLPVDFQGRSTGEAFVQFASQEIA 56
Query: 501 DKALSKHKESIGIRYIELFRSTTAEVQ 527
+KAL KHKE IG RYIE+F+S+ AEV+
Sbjct: 57 EKALKKHKERIGHRYIEIFKSSRAEVR 83
Score = 46.2 bits (109), Expect = 1e-06
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGED 417
G+ L + GR GEA V+F QE + ALK+HK I RYIE+ K++ +
Sbjct: 31 GITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE 81
Score = 36.5 bits (84), Expect = 0.003
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E I++F IV G+ + + QG+ +GEAF+Q S+ A A L+ ++ I
Sbjct: 16 EEIVQFFSGL--EIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKA--LKKHKERI---G 68
Query: 123 QRYIEVFQCSGEDM 136
RYIE+F+ S ++
Sbjct: 69 HRYIEIFKSSRAEV 82
>gnl|CDD|241173 cd12729, RRM1_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM1 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical. Both of them
have been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 79
Score = 79.9 bits (197), Expect = 2e-18
Identities = 30/82 (36%), Positives = 53/82 (64%), Gaps = 5/82 (6%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
++++RGLP+ C+ +V FF + C + +G G+ F+ +G+ +G+AFV E EE+
Sbjct: 3 VVKVRGLPWSCSVDEVQRFF-----SDCKIANGASGIHFIYTREGRPSGEAFVELESEED 57
Query: 500 ADKALSKHKESIGIRYIELFRS 521
AL K +E++G RY+E+F+S
Sbjct: 58 VKLALKKDRETMGHRYVEVFKS 79
Score = 49.9 bits (119), Expect = 6e-08
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
V+ + F + G+H +Y +G+PSGEAF++++SE LA L+ +R +
Sbjct: 15 VDEVQRFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLA--LKKDRETM--- 69
Query: 122 KQRYIEVFQ 130
RY+EVF+
Sbjct: 70 GHRYVEVFK 78
Score = 39.1 bits (91), Expect = 4e-04
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
G G+ + GR +GEA V +E +ALK+ + + RY+EV K+
Sbjct: 30 GASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
>gnl|CDD|241176 cd12732, RRM2_hnRNPH3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H') and hnRNP F. This family
is involved in mRNA processing and exhibit extensive
sequence homology. Currently, little is known about the
functions of hnRNP H3 except for its role in the
splicing arrest induced by heat shock. In addition, the
typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 96
Score = 75.4 bits (185), Expect = 9e-17
Identities = 35/83 (42%), Positives = 52/83 (62%), Gaps = 7/83 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+R+RGLP+ C+ ++++ FF G E N G+ G++TG+AFV F +E
Sbjct: 20 TVRLRGLPFGCSKEEIVQFFS-GLEIVPN------GITLTMDYQGRSTGEAFVQFASKEI 72
Query: 500 ADKALSKHKESIGIRYIELFRST 522
A+ AL KHKE IG RYIE+F+S+
Sbjct: 73 AENALGKHKERIGHRYIEIFKSS 95
Score = 44.2 bits (104), Expect = 9e-06
Identities = 20/48 (41%), Positives = 29/48 (60%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKAN 414
G+ L + GR GEA V+F +E + AL +HK I RYIE+ K++
Sbjct: 48 GITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFKSS 95
Score = 36.1 bits (83), Expect = 0.007
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E I++F IV G+ + + QG+ +GEAF+Q S+ A A +H +
Sbjct: 33 EEIVQFFSGL--EIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALG-KHKERI----G 85
Query: 123 QRYIEVFQCS 132
RYIE+F+ S
Sbjct: 86 HRYIEIFKSS 95
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence GGGA.
They can either stimulate or repress splicing upon
binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
the splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. For instance, members in this family can regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. The family also
includes a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. It may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 also contains
three potential RRMs responsible for the RNA binding,
and two auxiliary domains (an acidic alpha-helical
domain and an N-terminal alanine-rich region) that may
play a role in protein-protein interactions and provide
binding specificity. .
Length = 75
Score = 68.5 bits (168), Expect = 1e-14
Identities = 33/80 (41%), Positives = 42/80 (52%), Gaps = 9/80 (11%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+ MRGLPY T + +FF N NV DG+ATG+A V F E+
Sbjct: 2 TVHMRGLPYRATENDIFEFFSP--LNPVNVR-------IEYNADGRATGEADVEFATHED 52
Query: 500 ADKALSKHKESIGIRYIELF 519
A A+SK +E +G RYIELF
Sbjct: 53 AVAAMSKDREHMGHRYIELF 72
Score = 39.2 bits (92), Expect = 3e-04
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 71 EFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVF 129
EF S + V + YN+ G+ +GEA ++ + H +AA + +M RYIE+F
Sbjct: 19 EFFSPLNPVNVRIEYNADGRATGEADVEFAT-HEDAVAAMSKDREHM----GHRYIELF 72
Score = 36.5 bits (85), Expect = 0.002
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIE 409
GR GEA V F E A+ + + H+ RYIE
Sbjct: 37 GRATGEADVEFATHEDAVAAMSKDREHMGHRYIE 70
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 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 and is also 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 = 72
Score = 67.0 bits (164), Expect = 5e-14
Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
++MRG P+ K + +FF + VK G+ TG AFV + EE+
Sbjct: 3 VKMRGAPFNVKEKHIREFFSPLKPVAIR---------IVKNDHGRKTGFAFVDLKSEEDL 53
Query: 501 DKALSKHKESIGIRYIELF 519
KAL ++K+ +G RYIELF
Sbjct: 54 KKALKRNKDYMGGRYIELF 72
Score = 42.4 bits (100), Expect = 2e-05
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
+HI EF S + + +V N G+ +G AF+ + SE L L+ N++ + G
Sbjct: 15 KHIREFF----SPLKPVAIRIVKNDHGRKTGFAFVDLKSE--EDLKKALKRNKDYMGG-- 66
Query: 123 QRYIEVF 129
RYIE+F
Sbjct: 67 -RYIELF 72
Score = 37.0 bits (86), Expect = 0.002
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
GR+ G A V +E ALKR+K ++ RYIE+
Sbjct: 37 GRKTGFAFVDLKSEEDLKKALKRNKDYMGGRYIEL 71
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 78
Score = 63.3 bits (154), Expect = 1e-12
Identities = 30/83 (36%), Positives = 47/83 (56%), Gaps = 9/83 (10%)
Query: 443 MRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
+RGLP+ T V DFF +G +DG V+F+K G G++ V F +E+A +
Sbjct: 4 LRGLPFSVTEDNVRDFF-SGL-----KVDG---VIFLKNRRGLNNGNSMVKFATKEDAIE 54
Query: 503 ALSKHKESIGIRYIELFRSTTAE 525
L + ++ +G RYIE+ R+T E
Sbjct: 55 GLKRDRQYMGSRYIEISRTTEEE 77
Score = 41.7 bits (98), Expect = 4e-05
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDF 418
G NG ++V+F +E LKR + ++ RYIE+++ E++
Sbjct: 36 GLNNGNSMVKFATKEDAIEGLKRDRQYMGSRYIEISRTTEEEW 78
Score = 32.1 bits (73), Expect = 0.11
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 72 FASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQC 131
F S + GV + N +G +G + ++ ++ A + R + M RYIE+ +
Sbjct: 19 FFSGLKVDGVIFLKNRRGLNNGNSMVKFATKEDA-IEGLKRDRQYM----GSRYIEISRT 73
Query: 132 SGED 135
+ E+
Sbjct: 74 TEEE 77
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding protein
12 (RBM12) and similar proteins. This subfamily
corresponds to the RRM3 of RBM12. RBM12, also termed
SH3/WW domain anchor protein in the nucleus (SWAN), is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 101
Score = 60.7 bits (147), Expect = 2e-11
Identities = 29/78 (37%), Positives = 47/78 (60%), Gaps = 7/78 (8%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ ++GLPYE K VIDFF+ +++ E+ + P+GKATG+ FV F E +
Sbjct: 12 VYLKGLPYEAENKHVIDFFK-----KLDIV--EDSIYIAYGPNGKATGEGFVEFRNEADY 64
Query: 501 DKALSKHKESIGIRYIEL 518
AL +HK+ +G R+I++
Sbjct: 65 KAALCRHKQYMGNRFIQV 82
Score = 35.7 bits (82), Expect = 0.011
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
+H+++F + +IV +++ Y G+ +GE F++ +E Y AA RH + M
Sbjct: 24 KHVIDFFKKL--DIVEDSIYIAYGPNGKATGEGFVEFRNEAD-YKAALCRHKQYM----G 76
Query: 123 QRYIEVFQCSGEDM 136
R+I+V + + M
Sbjct: 77 NRFIQVHPITKKAM 90
Score = 31.8 bits (72), Expect = 0.23
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
G+ GE V F ++ AL RHK ++ R+I+V
Sbjct: 48 GKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQV 82
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 53.2 bits (128), Expect = 3e-09
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ + GLPY V +FF G + E V+F+K+ +G+ G+A V F ++A
Sbjct: 2 VFLHGLPYTADEHDVKEFF-HGLD--------VEDVIFLKRHNGRNNGNAIVKFATFQDA 52
Query: 501 DKALSKHKESIGIRYIELFRS 521
+AL +H+E +G RYIEL S
Sbjct: 53 KEALKRHRELMGSRYIELMLS 73
Score = 45.2 bits (107), Expect = 3e-06
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKA 413
V GR NG AIV+F + ALKRH+ + RYIE+ +
Sbjct: 27 DVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHRELMGSRYIELMLS 73
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 75
Score = 53.1 bits (127), Expect = 5e-09
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ MRGLP+ T + +FF T ++ G DG+ATG+A V F E+A
Sbjct: 3 VHMRGLPFRATESDIANFFSPLTPIRVHIDIG---------ADGRATGEADVEFVTHEDA 53
Query: 501 DKALSKHKESIGIRYIELF 519
A+SK K + RYIELF
Sbjct: 54 VAAMSKDKNHMQHRYIELF 72
Score = 32.3 bits (73), Expect = 0.091
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 368 VALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
V + + A GR GEA V F+ E A+ + K+H+ RYIE+
Sbjct: 29 VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIEL 71
>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM3 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F, which represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; bothe have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 76
Score = 52.0 bits (124), Expect = 9e-09
Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ MRGLPY T + +FF ++ G PDG+ TG+A V F E+A
Sbjct: 3 VHMRGLPYRATENDIYNFFSPLNPVRVHIEIG---------PDGRVTGEADVEFATHEDA 53
Query: 501 DKALSKHKESIGIRYIELFRSTT 523
A+SK K ++ RY+ELF ++T
Sbjct: 54 VAAMSKDKANMQHRYVELFLNST 76
>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM3 of G-rich sequence factor 1
(GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. GRSF-1 contains three potential RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which are
responsible for the RNA binding. In addition, GRSF-1 has
two auxiliary domains, an acidic alpha-helical domain
and an N-terminal alanine-rich region, that may play a
role in protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 51.4 bits (123), Expect = 2e-08
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 9/79 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ MRGLP++ + + +++FF +L DG+ATG+A V FE ++A
Sbjct: 3 VHMRGLPFQASGQDIVNFFAPLKPTR---------ILIEYSSDGRATGEADVHFESHDDA 53
Query: 501 DKALSKHKESIGIRYIELF 519
A++K + + RYIELF
Sbjct: 54 VAAMAKDRAHMQHRYIELF 72
Score = 31.0 bits (70), Expect = 0.27
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 373 SAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
S+ GR GEA V F + A+ + + H+ RYIE+
Sbjct: 34 SSDGRATGEADVHFESHDDAVAAMAKDRAHMQHRYIEL 71
Score = 29.0 bits (65), Expect = 1.2
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 71 EFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVF 129
F + + + + Y+S G+ +GEA + +S H +AA + +M + RYIE+F
Sbjct: 19 NFFAPLKPTRILIEYSSDGRATGEADVHFES-HDDAVAAMAKDRAHM----QHRYIELF 72
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 48.1 bits (115), Expect = 2e-07
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I+++ +P++ T +V+ FF + E+G+ + GK G+A+V F EE+
Sbjct: 1 CIKIKNIPFDVTKGEVLAFFA-------GIAIAEQGIHILYDKTGKTLGEAYVEFVSEED 53
Query: 500 ADKALSKHKESIGIRYIEL 518
A +A H++ + R I L
Sbjct: 54 AMRAERLHRKKLKGREILL 72
Score = 41.5 bits (98), Expect = 4e-05
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 65 ILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNR 115
+L F A I QG+H++Y+ G+ GEA+++ SE A A +L +
Sbjct: 16 VLAFFAGIA--IAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLHRKK 64
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 47.6 bits (114), Expect = 3e-07
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+ + LP + T +++ + F G S ++ K GK+ G AFV FE EE+
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLV--------RDKETGKSKGFAFVEFESEED 53
Query: 500 ADKALSK-HKESIGIRYIEL 518
A+KAL + + + R +++
Sbjct: 54 AEKALEALNGKELDGRPLKV 73
Score = 32.2 bits (74), Expect = 0.10
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 5/66 (7%)
Query: 58 KKVLVEHILEFLGEFASNIVYQGVHMVYNSQ-GQPSGEAFIQMDSEHSAYLAAQLRHNRN 116
E + E +F + V +V + + G+ G AF++ +SE A A N
Sbjct: 9 PDTTEEELRELFSKFG-KVES--VRLVRDKETGKSKGFAFVEFESEEDA-EKALEALNGK 64
Query: 117 MIFGKK 122
+ G+
Sbjct: 65 ELDGRP 70
Score = 27.9 bits (63), Expect = 2.7
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKR-HKHHIDKRYIEV 410
G+ G A V F +E + AL+ + +D R ++V
Sbjct: 38 GKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 46.8 bits (112), Expect = 6e-07
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 441 IRMRGLPYECTAKQVIDFFE-AGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+ + LP + T + + D F G S ++ + G++ G AFV FE EE+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV---------RDETGRSKGFAFVEFEDEED 51
Query: 500 ADKALSK 506
A+KAL
Sbjct: 52 AEKALEA 58
Score = 29.5 bits (67), Expect = 0.69
Identities = 12/62 (19%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E + + +F + + +V + G+ G AF++ + E A A + + + + G++
Sbjct: 13 EDLKDLFSKFGP---IESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGK-ELGGRE 68
Query: 123 QR 124
R
Sbjct: 69 LR 70
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 74
Score = 46.9 bits (112), Expect = 7e-07
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 439 VIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
V+IR++ LP+E + + FF + DG GV + G G+AF+ F +E
Sbjct: 2 VVIRLQNLPWEAGSLDIRRFFSG-----LTIPDG--GVHII----GGEMGEAFIAFATDE 50
Query: 499 EADKALSKHKESIGIRYIELFRST 522
+A A+S+ ++I ++LF S+
Sbjct: 51 DARLAMSRDGQTIKGSKVKLFLSS 74
>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 = 46.5 bits (111), Expect = 7e-07
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 11/80 (13%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+ + LP + T + + + F G S ++ + DGK+ G AFV FE E+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIV---------RDKDGKSKGFAFVEFESPED 51
Query: 500 ADKALSK-HKESIGIRYIEL 518
A+KAL + + + R +++
Sbjct: 52 AEKALEALNGKELDGRKLKV 71
Score = 28.0 bits (63), Expect = 2.9
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKR-HKHHIDKRYIEV 410
G+ G A V F E + AL+ + +D R ++V
Sbjct: 36 GKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKV 71
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 46.4 bits (111), Expect = 8e-07
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ +R LP T + + +FF V EGV V+ D + G AFV F E+A
Sbjct: 1 LYVRNLPPSVTEEDLREFFS----PYGKV----EGVRLVRNKD-RPRGFAFVEFASPEDA 51
Query: 501 DKALSKHKE-SIGIRYIE 517
+ AL K + R +
Sbjct: 52 EAALKKLNGLVLDGRTLR 69
Score = 40.2 bits (95), Expect = 1e-04
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 58 KKVLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNM 117
V E + EF + + +GV +V N +P G AF++ S A AA + N +
Sbjct: 8 PSVTEEDLREFFSPY-GKV--EGVRLVRNKD-RPRGFAFVEFASPEDA-EAALKKLNGLV 62
Query: 118 IFGKKQRYIE 127
+ G R +
Sbjct: 63 LDG---RTLR 69
Score = 35.6 bits (83), Expect = 0.005
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHK-HHIDKRYIE 409
R G A V F E + ALK+ +D R +
Sbjct: 36 RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
>gnl|CDD|241188 cd12744, RRM1_RBM12B, RNA recognition motif 1 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM1 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 79
Score = 45.6 bits (108), Expect = 2e-06
Identities = 29/89 (32%), Positives = 48/89 (53%), Gaps = 11/89 (12%)
Query: 439 VIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
V+IR++GLP ++ + FF + DG GV + G G+AF++F +E
Sbjct: 2 VVIRLQGLPVVAGSEDIRHFF-----TGLRIPDG--GVHII----GGELGEAFIIFATDE 50
Query: 499 EADKALSKHKESIGIRYIELFRSTTAEVQ 527
+A +A+S+ I +ELF S+ AE+Q
Sbjct: 51 DARRAMSRSGGFIKDSTVELFLSSKAEMQ 79
>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 = 43.4 bits (103), Expect = 1e-05
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 10/70 (14%)
Query: 446 LPYECTAKQVIDFFEAGTENSC-NVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
L Y ++ F C + D V VK GK+ G A+V FE EE +AL
Sbjct: 7 LDYSVPEDELRKLFS-----KCGEITD----VRLVKNYKGKSKGYAYVEFENEESVQEAL 57
Query: 505 SKHKESIGIR 514
+E I R
Sbjct: 58 KLDRELIKGR 67
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I + GLPY T + +F G + EE V+ + GK+ G FV F+ +E
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFG--------EIEEAVVITDRQTGKSRGYGFVTFKDKES 54
Query: 500 ADKAL 504
A++A
Sbjct: 55 AERAC 59
>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 = 41.5 bits (98), Expect = 5e-05
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 441 IRMRGLPYECTAKQVIDFF-EAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+ + L + + +FF E G V+D V + DG++ G V F EE
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGE-----VVD----VRIAQDDDGRSKGFGHVEFATEEG 52
Query: 500 ADKALSKHKESIGIRYI 516
A KAL K E + R I
Sbjct: 53 AQKALEKSGEELLGREI 69
>gnl|CDD|241191 cd12747, RRM2_RBM12, RNA recognition motif 2 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM2 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 75
Score = 39.4 bits (92), Expect = 3e-04
Identities = 22/65 (33%), Positives = 34/65 (52%)
Query: 349 LSLLLNTIPGYEQVLGLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYI 408
S+L + I + L + + L GR NG A+V+F ALKR++ + +RYI
Sbjct: 11 FSVLEHDIRDFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRMLMGQRYI 70
Query: 409 EVTKA 413
EV+ A
Sbjct: 71 EVSPA 75
Score = 34.0 bits (78), Expect = 0.023
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ + GLP+ + DFF + + +K G+ G+A V F +
Sbjct: 4 VSLHGLPFSVLEHDIRDFFHG---------LRIDAIHLLKDHVGRNNGNALVKFYSPHDT 54
Query: 501 DKALSKHKESIGIRYIEL 518
+AL +++ +G RYIE+
Sbjct: 55 FEALKRNRMLMGQRYIEV 72
Score = 32.1 bits (73), Expect = 0.10
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 71 EFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEV 128
+F + +H++ + G+ +G A ++ S H + A L+ NR ++ QRYIEV
Sbjct: 20 DFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEA--LKRNRMLMG---QRYIEV 72
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 43.2 bits (102), Expect = 4e-04
Identities = 33/185 (17%), Positives = 40/185 (21%), Gaps = 28/185 (15%)
Query: 162 GMLPHSSQPLYPQHNTQINPGLSHLDPLVNVHLTQALAQAQYAKSQQD-------NLMLM 214
G P +Q P L + L Q Q A M
Sbjct: 127 GTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPP 186
Query: 215 NQIAAQQMAALNKPHNMALNGHTPTLIPAPSPNALMPPPLNSKSTTIPTNLPALPAVPTS 274
Q A Q +P P +P P + + P LP
Sbjct: 187 RQAAFPQQGPPEQPPGYP--QPPQGHPEQVQPQQFLPAPSQAPAQ------PPLPPQL-- 236
Query: 275 GGYFPQFQLPINMNTAHLLQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTPTVYTIPTP 334
PQ P L QP MP P P + P Q P
Sbjct: 237 ----PQQPPP-------LQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPH 285
Query: 335 GNPVA 339
Sbjct: 286 PGLPQ 290
Score = 35.9 bits (83), Expect = 0.074
Identities = 30/200 (15%), Positives = 42/200 (21%), Gaps = 20/200 (10%)
Query: 145 PPTSPAISPVGKTLLSPGMLPH--SSQPLYPQHNTQINPGLSHLDPLVNVHLTQALAQAQ 202
P + P + +LS + + PQ L P Q Q
Sbjct: 140 PESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQ 199
Query: 203 YAKSQQDNLMLMNQIAAQQMAALNKPHNMALNGHTPTLIPAP------------SPNALM 250
+ Q L P P +P S
Sbjct: 200 P--PGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPP 257
Query: 251 PPPLNSKSTTIPTNLPALPAVPTSGGYFPQFQLPINMNTAHLLQPMNTPFFFN---MPRM 307
PPP + P A P P N QP P R
Sbjct: 258 PPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRG 317
Query: 308 PVTPQVLPK-FPVHQLNQTP 326
P + L + + +
Sbjct: 318 PQFREQLVQLSQQQREALSQ 337
Score = 32.8 bits (75), Expect = 0.70
Identities = 23/149 (15%), Positives = 35/149 (23%), Gaps = 9/149 (6%)
Query: 140 LNGVLPPTSPAISPVGKTLLSPGMLPHSSQPLYPQHNTQINPGLSHLDPLVNVHLTQALA 199
P P P G G + +Q L L
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQP--PPLQ 244
Query: 200 QAQYAKSQQDNLMLMNQIAAQQMAALNKPHNMALNGHTPTLIPAP--SPNALMPPPLNSK 257
Q Q + QQ +P + PT P NA +PPP +
Sbjct: 245 QPQ-FPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQ 303
Query: 258 STTIPTNLPALPAVPTSGGYFPQFQLPIN 286
+ P F + + ++
Sbjct: 304 LLPLVQQPQGQQRGPQ----FREQLVQLS 328
Score = 29.7 bits (67), Expect = 5.0
Identities = 26/138 (18%), Positives = 33/138 (23%), Gaps = 4/138 (2%)
Query: 204 AKSQQDNLMLMNQIAAQQMAALNKPHNMALNGHTPTLIPAPSPNALMPPPLNSKSTTIPT 263
A + + Q K ++L L L PP +P
Sbjct: 129 APKPEPQPPQAPESQPQPQTPAQKM--LSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPP 186
Query: 264 NLPALPAVPTSGGYFPQFQLPINMNTAHLLQPMNTPFFFNMPRMPVTPQVLPKFPVH-QL 322
A P Q P Q P P P P LP+ P Q
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFL-PAPSQAPAQPPLPPQLPQQPPPLQQ 245
Query: 323 NQTPTVYTIPTPGNPVAL 340
Q P + P P
Sbjct: 246 PQFPGLSQQMPPPPPQPP 263
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 38.7 bits (91), Expect = 5e-04
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 443 MRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
++G P + T + +FFE V + + D K G FV F+ EE+A K
Sbjct: 4 VKGFPKDATLDDIQEFFEKF----GKV----NNIRMRRDLDKKFKGSVFVEFKTEEDAKK 55
Query: 503 ALSKHK 508
L K K
Sbjct: 56 FLEKEK 61
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 38.7 bits (91), Expect = 5e-04
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 439 VIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
+I++ LP T ++ + FE+ E V D V ++ DGK+ FV F+ EE
Sbjct: 3 IIVK--NLPKYVTEDRLREHFESKGE----VTD----VKVMRTRDGKSRRFGFVGFKSEE 52
Query: 499 EADKALS 505
+A +A+
Sbjct: 53 DAQQAVK 59
>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 = 38.5 bits (90), Expect = 5e-04
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 11/74 (14%)
Query: 445 GLPYECTAKQVIDFFE-AGTENSCNVMDGEEGVLFVKKPD-GKATGDAFVLFEKEEEADK 502
G+PY T ++ +F G ++M F PD G+ G AF+ F+ EE A +
Sbjct: 5 GIPYYSTEDEIRSYFSYCGEIEELDLMT------F---PDTGRFRGIAFITFKTEEAAKR 55
Query: 503 ALSKHKESIGIRYI 516
AL+ E +G R++
Sbjct: 56 ALALDGEDMGGRFL 69
>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM3 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 81
Score = 38.1 bits (89), Expect = 8e-04
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
I + LP+ + + FF ++ + + F+ GK T AFV+F+ +
Sbjct: 3 IHLENLPFSVEKRDIRAFFG-------DLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDY 55
Query: 501 DKALSKHKESIGIRYIELF 519
AL+ HK + R + +F
Sbjct: 56 CAALAHHKRVLYNREVYVF 74
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 37.2 bits (87), Expect = 0.002
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 13/66 (19%)
Query: 444 RGLPYECTAKQVIDFF-EAGTENSCNVMDGEEGVLFV--KKPDGKATGDAFVLFEKEEEA 500
R LPY+ T +Q+ +FF E G C FV K K G +V F EE+A
Sbjct: 5 RNLPYDTTDEQLEEFFSEVGPIKRC----------FVVKDKGSKKCRGFGYVTFALEEDA 54
Query: 501 DKALSK 506
+AL +
Sbjct: 55 KRALEE 60
>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 = 36.9 bits (86), Expect = 0.002
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 446 LPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKALS 505
LPY+ TA+ ++ F +V L K GK+ G AFV F+ E KAL
Sbjct: 8 LPYDTTAEDLLAHF-KNAGAPPSVR------LLTDKKTGKSKGCAFVEFDTAEAMTKALK 60
Query: 506 KHKESIGIRYI 516
H + R I
Sbjct: 61 LHHTLLKGRKI 71
Score = 31.6 bits (72), Expect = 0.14
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
G+ G A V F E ALK H + R I V
Sbjct: 39 GKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKINV 73
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 36.8 bits (86), Expect = 0.002
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 439 VIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
+I+R LP++CT EA + + V +KPDGK G AFV F +
Sbjct: 2 LIVR--NLPFKCT--------EADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKA 51
Query: 499 EADKAL 504
+A+KA+
Sbjct: 52 DAEKAI 57
>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 = 36.4 bits (85), Expect = 0.003
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 15/65 (23%)
Query: 446 LPYECTAKQVIDFFEAGTENSC-NVMDGEEGVLFVKKPD---GKATGDAFVLFEKEEEAD 501
LP++ +++ FE C +V E V V+ GK G +VLF+ ++
Sbjct: 7 LPFDIEEEELRKHFE-----DCGDV----EAVRIVRDRKTGIGK--GFGYVLFKTKDSVA 55
Query: 502 KALSK 506
AL
Sbjct: 56 LALKL 60
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 39.5 bits (91), Expect = 0.003
Identities = 29/120 (24%), Positives = 48/120 (40%), Gaps = 14/120 (11%)
Query: 440 IIRMRGLPYECTAKQVIDFF-EAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
+ + LPY+ T + + + F + G ++ + GK+ G AFV FE EE
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLV--------RDRETGKSRGFAFVEFESEE 168
Query: 499 EADKALSKHKESIGIRYIELFRSTTAEVQQVLNKTMELPKNNSLTSSNNGLSAQQPMLSH 558
A+KA+ +E G R + Q ++ NN S LS + +L
Sbjct: 169 SAEKAI---EELNGKELEG--RPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLE 223
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 77
Score = 35.3 bits (81), Expect = 0.008
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 59 KVLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLA 108
K + IL+F ++ V M YN QG P+G A + M++ + A A
Sbjct: 11 KATINEILDFF--HGYRVIPDSVSMQYNEQGLPTGTAIVAMENYYEAMAA 58
Score = 29.9 bits (67), Expect = 0.81
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
IR+ LP++ T +++DFF + V+ + V G TG A V E EA
Sbjct: 3 IRLENLPFKATINEILDFF-----HGYRVI--PDSVSMQYNEQGLPTGTAIVAMENYYEA 55
Query: 501 DKALSKHKES-IGIRYIEL 518
A+++ + IG R ++L
Sbjct: 56 MAAINELNDRPIGPRKVKL 74
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 35.2 bits (82), Expect = 0.010
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 453 KQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKALSKH 507
K + D F A G SC V E +G + G FV FE EE A +A+ K
Sbjct: 17 KALYDTFSAFGNILSCKVATDE---------NGGSKGYGFVHFETEEAAVRAIEKV 63
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 34.8 bits (81), Expect = 0.010
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 11/60 (18%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPD-GKATGDAFVLFEKEEEADKA 503
LP T + V FE G ++ + D G++ G AFV F EEA KA
Sbjct: 7 LPKTATEEDVRALFEEYGNIEEVTII---------RDKDTGQSKGCAFVKFSSREEAQKA 57
>gnl|CDD|241189 cd12745, RRM1_RBM12, RNA recognition motif 1 in RNA-binding protein
12 (RBM12) and similar proteins. This subgrup
corresponds to the RRM1 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 92
Score = 35.0 bits (80), Expect = 0.016
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 11/92 (11%)
Query: 439 VIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEE 498
V+IR++GLP + FF T + DG GV V G G+AF++F +E
Sbjct: 3 VVIRLQGLPIVAGTMDIRHFFSGLT-----IPDG--GVHIV----GGELGEAFIVFATDE 51
Query: 499 EADKALSKHKESIGIRYIELFRSTTAEVQQVL 530
+A + + +I + L S+ E+Q ++
Sbjct: 52 DARLGMMRTGGTIKGSKVSLLLSSKTEMQNMI 83
>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 = 34.5 bits (80), Expect = 0.016
Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 6/78 (7%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I +R L ++ + F G S + ++ +K G AFV F+
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQD-----EKQGRLNNGFAFVTFKDASS 57
Query: 500 ADKALSKHKESIGIRYIE 517
A+ AL + +G R I
Sbjct: 58 AENALQLNGTELGGRKIS 75
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 34.4 bits (79), Expect = 0.016
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 443 MRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
++ LPY T ++ + FE + + DG + G A++ F+ E EA+K
Sbjct: 8 VKNLPYNITVDELKEVFEDAVD-----------IRLPSGKDGSSKGIAYIEFKTEAEAEK 56
Query: 503 ALS 505
AL
Sbjct: 57 ALE 59
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 34.2 bits (79), Expect = 0.018
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
LP ++ FEA GT + + K DGK FV ++ EEEA KAL
Sbjct: 8 LPKGIKEDKLRKLFEAFGTITDVQLK-------YTK--DGKFRKFGFVGYKTEEEAQKAL 58
Query: 505 SK 506
Sbjct: 59 KH 60
>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 = 34.5 bits (80), Expect = 0.020
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 444 RGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPD-GKATGDAFVLFEKEEEAD 501
R LP++ T +++ + F G + VK G + G AFV F+ +E A
Sbjct: 6 RNLPFDATEEELKELFSQFGEVKYARI---------VKDKLTGHSKGTAFVKFKTKESAQ 56
Query: 502 KALS 505
K L
Sbjct: 57 KCLE 60
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 33.7 bits (78), Expect = 0.029
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
LPY T + + D F G S V+ + G++ G FV E EEA+ A+
Sbjct: 7 LPYNVTEEDLKDLFGQFGEVTSARVI--------TDRETGRSRGFGFVEMETAEEANAAI 58
Query: 505 SK 506
K
Sbjct: 59 EK 60
>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 = 33.8 bits (77), Expect = 0.030
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 13/65 (20%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLF--VKKPDGKATGDAFVLFEKEE 498
I +R LP++ T K + D F N C VL+ +K +GK+ G V FE E
Sbjct: 2 IFVRNLPFDFTWKMLKDKF-----NECGH------VLYADIKMENGKSKGCGVVRFESPE 50
Query: 499 EADKA 503
A++A
Sbjct: 51 VAERA 55
>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 = 33.7 bits (78), Expect = 0.030
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKA 503
L + +++ + F G S VM K +GK+ G FV FE E A KA
Sbjct: 9 LGEDMDDEKLKELFGKYGKITSAKVM---------KDDEGKSKGFGFVNFENHEAAQKA 58
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 37.1 bits (86), Expect = 0.030
Identities = 36/169 (21%), Positives = 50/169 (29%), Gaps = 22/169 (13%)
Query: 172 YPQHNTQINPGLSHLDPLVNVHLTQALAQAQYAKSQQDNLMLMNQIAAQQM-AALNKPHN 230
YPQ +Q++ G + H A A + Q + +Q+ A HN
Sbjct: 9 YPQAQSQVHTGAASSKKSARPHRAYANFSAGQMGMPPYTTPPLQQQSRRQIDQAATAMHN 68
Query: 231 MALNGHTPTLI-PAPSPNALMPPPLNSKSTTIPTNLPALPAVPTSGGYFPQFQLPINMNT 289
N P+++ PA P P P VP F PI+
Sbjct: 69 TGANNPAPSVMSPAFQSQQKFSSPYGGSMADGTAPKPTNPLVPVD--LFEDQPPPIS--- 123
Query: 290 AHLLQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTP-----TVYTIPT 333
F P V P Q N +P T+Y IP
Sbjct: 124 ----------DLFLPPPPIVPPLTTNFVGSEQSNCSPKYVRSTMYAIPE 162
>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 = 33.0 bits (76), Expect = 0.044
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 444 RGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
R LP+ T +++ + FEA G + ++ + K ++ G AFV F E A K
Sbjct: 5 RNLPFTTTEEELRELFEAFGEISEVHLP--------LDKETKRSKGFAFVSFMFPEHAVK 56
Query: 503 ALSKHKESI 511
A S+ SI
Sbjct: 57 AYSELDGSI 65
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 76
Score = 33.0 bits (75), Expect = 0.049
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+I+++ +P+ T +++DFF V+ G + F K G TG+A V FE +E
Sbjct: 3 VIKVQNMPFTVTVDEILDFFYG-----YQVIPGSVCLKFSDK--GMPTGEAMVAFESRDE 55
Query: 500 ADKA-LSKHKESIGIRYIEL 518
A A + + IG R ++L
Sbjct: 56 AMAAVVDLNDRPIGSRKVKL 75
Score = 29.5 bits (66), Expect = 0.79
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 60 VLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLA 108
V V+ IL+F + ++ V + ++ +G P+GEA + +S A A
Sbjct: 13 VTVDEILDFF--YGYQVIPGSVCLKFSDKGMPTGEAMVAFESRDEAMAA 59
>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 = 35.6 bits (82), Expect = 0.082
Identities = 23/67 (34%), Positives = 29/67 (43%), Gaps = 10/67 (14%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I ++ L K + D F G SC V E +GK+ G FV FEKEE
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE---------NGKSRGYGFVHFEKEES 141
Query: 500 ADKALSK 506
A A+ K
Sbjct: 142 AKAAIQK 148
>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 = 32.3 bits (74), Expect = 0.11
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 9/84 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
I + L TA Q+++FF E M G+ + + T AFV F ++
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD---------ETQPTRYAFVEFAEQTSV 57
Query: 501 DKALSKHKESIGIRYIELFRSTTA 524
AL + G R +++ S A
Sbjct: 58 INALKLNGAMFGGRPLKVNHSNNA 81
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 32.2 bits (74), Expect = 0.11
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I + G+P + T +++ DFF G+ V D V + G + G FV FE +E+
Sbjct: 5 IFVGGIPPDTTEEELRDFFSRFGS-----VKD----VKIITDRAGVSKGYGFVTFETQED 55
Query: 500 ADKAL 504
A+K L
Sbjct: 56 AEKIL 60
>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 = 31.9 bits (73), Expect = 0.11
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 441 IRMRGLPYECTAKQVIDFF-EAGTENSCNVMDGEEGVLFVK-KPDGKATGDAFVLFEKEE 498
I +R LP+ T + + D F E G NV+ + VK DG++ G VLFE E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECG-----NVLRAD-----VKTDNDGRSKGFGTVLFESPE 50
Query: 499 EADKALSKHKESI 511
+A +A+
Sbjct: 51 DAQRAIEMFNGYD 63
>gnl|CDD|241192 cd12748, RRM4_RBM12B, RNA recognition motif 4 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM4 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 76
Score = 32.1 bits (73), Expect = 0.12
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 75 NIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNM 117
NI ++++Y+ +G GEA ++ SE A A +L R +
Sbjct: 25 NIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNGQRFL 67
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 32.0 bits (73), Expect = 0.12
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVM-DGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
GLP T + +F GT VM D E+ K+P G F+ FE E+ D+
Sbjct: 9 GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEK-----KRP----RGFGFITFESEDSVDQ 59
Query: 503 ALSKHKESIGIRYIELFRS 521
+++H I + +E+ R+
Sbjct: 60 VVNEHFHDINGKKVEVKRA 78
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 31.4 bits (72), Expect = 0.19
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 444 RGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
R +P+E T K++ + F G S + KK DG G AFV F ++EA
Sbjct: 6 RNVPFEATKKELRELFSPFGQVKSVRL---------PKKFDGSHRGFAFVEFVTKQEAQN 56
Query: 503 ALSK 506
A+
Sbjct: 57 AMEA 60
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 31.6 bits (71), Expect = 0.20
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 11/79 (13%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGK-ATGDAFVLFEKEEEADK 502
GL +E T + + +++E G C VM + P K + G FV F E D
Sbjct: 9 GLSFETTEESLRNYYEQWGKLTDCVVM---------RDPASKRSRGFGFVTFSCMNEVDA 59
Query: 503 ALSKHKESIGIRYIELFRS 521
A++ +I R +E R+
Sbjct: 60 AMAARPHTIDGRVVEPKRA 78
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 31.0 bits (71), Expect = 0.21
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 11/63 (17%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKP-DGKATGDAFVLFEKEEEADK 502
GL ++ T + + ++F G C +M K P G++ G FV F DK
Sbjct: 5 GLSWDTTEESLREYFSKYGEVVDCVIM---------KDPITGRSRGFGFVTFADPSSVDK 55
Query: 503 ALS 505
L+
Sbjct: 56 VLA 58
>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 = 31.2 bits (71), Expect = 0.23
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 446 LPYECTAKQVIDFFEAGTENSCNVMDGEEG-VLFVKKPDGKATGDAFVLFEKEEEADKAL 504
+PY+ + + D F GE V K +GK+ G V F+ +E KAL
Sbjct: 7 IPYDLKWQDLKDLFREKV--------GEVTYVELFKDEEGKSRGCGVVEFKDKESVQKAL 58
Query: 505 SK-HKESIGIRYI 516
++ + R +
Sbjct: 59 ETMNRYELKGRKL 71
Score = 30.9 bits (70), Expect = 0.32
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 360 EQVLGLGGVALCLSAFGRRNGEAIVRFIDQEHRDMAL-KRHKHHIDKRYIEV 410
E+V + V L G+ G +V F D+E AL +++ + R + V
Sbjct: 22 EKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 75
Score = 31.3 bits (71), Expect = 0.24
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 59 KVLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNM 117
+E IL+F + ++ V ++YN G P+GEA + D+ A A + + R +
Sbjct: 11 TATIEEILDFF--YGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVRELNGRPI 67
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 31.2 bits (71), Expect = 0.26
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 59 KVLVEHILEFLGE------FASNI-VYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQL 111
KV+V ++ + + E F S I + V + YN G+ +G A I A A
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYD- 59
Query: 112 RHNRNMIFGKKQRYIEVF 129
+ N + G ++ +EV
Sbjct: 60 KFNGRIDDGNRKMKVEVV 77
Score = 28.5 bits (64), Expect = 1.7
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ + LP + T Q+ ++F + + + VL GK+TG A + F++ +A
Sbjct: 2 VIVSNLPKDVTEAQIREYFVSQ-------IGPIKRVLLSYNEGGKSTGIANITFKRAGDA 54
Query: 501 DKALSKHKESI--GIRYIEL 518
KA K I G R +++
Sbjct: 55 TKAYDKFNGRIDDGNRKMKV 74
>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 = 30.7 bits (70), Expect = 0.39
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 477 LFVK--KPDGKATGDAFVLFEKEEEADKALSK-HKESIGIR 514
LF K G+ G FV FE +EEA+KAL + ++ +
Sbjct: 32 LFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGK 72
>gnl|CDD|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM4 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 88
Score = 30.6 bits (69), Expect = 0.44
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 446 LPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKALS 505
+PY T K ++ F E + E V + +G+ G A V F+ E++A K+
Sbjct: 7 IPYSITKKDILQFLEG-------IGVDENSVQVLVDNNGQGLGQALVQFKSEDDARKSER 59
Query: 506 KHKESIGIRYIELFRSTTAEVQQV 529
H++ + R + L T E++ +
Sbjct: 60 LHRKKLNGRDVFLHLVTAEEMRDI 83
>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 = 30.6 bits (69), Expect = 0.49
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGV-LFVKKPDGKATGDAFVLFEKEEE 499
I ++GL T +++ DFF+ N G+ V ++ K GK GDA V +E
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 500 ADKAL 504
A A+
Sbjct: 63 AKAAV 67
>gnl|CDD|144451 pfam00859, CTF_NFI, CTF/NF-I family transcription modulation
region.
Length = 295
Score = 32.7 bits (74), Expect = 0.50
Identities = 34/146 (23%), Positives = 47/146 (32%), Gaps = 22/146 (15%)
Query: 145 PPTSPAISPVGKTLLSPGMLPHSSQPLYPQHNTQINPGLSHLDPLVNVHLTQALAQAQYA 204
SP +P + +LP +P + P L DPL
Sbjct: 146 ISASPHPTPSPLHFPTSPILPQQPSSYFPHTAIRYPPHLHPQDPL--------------- 190
Query: 205 KSQQDNLMLMNQIAAQQMAALNKPHNMALNGH---TPTLIPAPSPNALMPPPLNSKSTTI 261
++ + L+ ++QQ N + H TP L P P P P PL T
Sbjct: 191 ---KEFVQLVCDPSSQQAGQPNGSGQGKVPNHFLPTPMLAPPPPPPMARPVPLPMPDTKP 247
Query: 262 P-TNLPALPAVPTSGGYFPQFQLPIN 286
P T+ PTS Y P N
Sbjct: 248 PTTSTEGGATSPTSPTYSTPSTSPAN 273
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 30.3 bits (68), Expect = 0.50
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 445 GLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
GL ++ T K + D+F E V+D L + G++ G FVLF++ E DK +
Sbjct: 5 GLSWDTTKKDLKDYFSKFGE----VVDC---TLKLDPITGRSRGFGFVLFKESESVDKVM 57
Query: 505 SKHKESIGIRYIE 517
+ + + + I+
Sbjct: 58 DQKEHKLNGKVID 70
>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 = 29.8 bits (68), Expect = 0.60
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 484 GKATGDAFVLFEKEEEADKALSK 506
G++ G AFV F E+A++A+ K
Sbjct: 38 GQSRGFAFVTFHTREDAERAIEK 60
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 30.0 bits (67), Expect = 0.62
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGK-ATGDAFVLFEKEEEADK 502
GL +E T + + FE GT C VM + P+ K + G FV + EE D
Sbjct: 9 GLSFETTDESLRSHFEQWGTLTDCVVM---------RDPNTKRSRGFGFVTYSSVEEVDA 59
Query: 503 ALSKHKESIGIRYIELFRSTT 523
A++ + R +E R+ +
Sbjct: 60 AMNARPHKVDGRVVEPKRAVS 80
>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 = 29.6 bits (67), Expect = 0.72
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 490 AFVLFEKEEEADKALSKHKESIGIRYIELFRSTTAEVQ 527
A V F K E+A+KAL K +LF EV
Sbjct: 44 AIVFFRKPEDAEKALEVSKG-------KLFFGAEIEVT 74
>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 = 29.9 bits (68), Expect = 0.79
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPD-GKATGDAFVLFEKEEEADK 502
GL T K++ F G +M K P+ G++ G FV FE E+AD
Sbjct: 8 GLSTRTTEKELEALFSKFGRVEEVLLM---------KDPETGESRGFGFVTFESVEDADA 58
Query: 503 ALSK 506
A+
Sbjct: 59 AIRD 62
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 31.9 bits (73), Expect = 0.92
Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 11/91 (12%)
Query: 362 VLGLGGVALCLSAFGR-RNGEAIVRFIDQEHRDMALKRHKHH-IDKR----YIEVTKANG 415
VLG GGV L + + IV E ++A + H ID + E+ G
Sbjct: 140 VLGAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHVIDYKEEDLEEELRLTGG 199
Query: 416 EDF---INVAGGNN--NEAQAFLTRGAQVII 441
I+ GG +A L G ++++
Sbjct: 200 GGADVVIDAVGGPETLAQALRLLRPGGRIVV 230
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 29.9 bits (67), Expect = 1.0
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 11/68 (16%)
Query: 443 MRGLPYECTAKQVIDFFE--AGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+R LPY+ T + + F + V+D K G+A G FV F+ +
Sbjct: 6 VRNLPYDATEESLAPHFSKFGSVRYALPVID---------KSTGRAKGTGFVCFKDQYTY 56
Query: 501 DKALSKHK 508
+ L
Sbjct: 57 NACLKNAP 64
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 29.1 bits (66), Expect = 1.1
Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 9/63 (14%)
Query: 444 RGLPYECTAKQVIDFFE-AGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
RGLP T + + + G S + + K K G FV F+ E A K
Sbjct: 6 RGLPPNTTDEDLEKLCQPFGKIISTKAI--------LDKKTNKCKGYGFVDFDSPEAALK 57
Query: 503 ALS 505
A+
Sbjct: 58 AIE 60
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.3 bits (66), Expect = 1.1
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKAT--GDAFVLFEKEE 498
I +R +P+E T K++ + F E V KK G + G FV F ++
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKT--------VRLPKKMTGTGSHRGFGFVDFITKQ 54
Query: 499 EADKALSKHKES 510
+A +A S
Sbjct: 55 DAKRAFKALCHS 66
>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 = 28.7 bits (65), Expect = 1.3
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 17/62 (27%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
LP T++++ FE GT C+V VK FV E+EE+A+ A+
Sbjct: 7 LPDATTSEELRALFEKYGTVTECDV---------VKNY-------GFVHMEEEEDAEDAI 50
Query: 505 SK 506
Sbjct: 51 KA 52
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 29.1 bits (66), Expect = 1.3
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKA 503
GL + T + + ++F G S ++ K GK G AFV F+ + DK
Sbjct: 6 GLKEDVTEEDLREYFSQYGNVESVEIV--------TDKETGKKRGFAFVTFDDYDPVDKI 57
Query: 504 LSKHKESIGIRYIE 517
+ + +I +E
Sbjct: 58 VLQKYHTINGHRVE 71
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 28.2 bits (64), Expect = 1.3
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 65 ILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
+ + F N+ + ++ G AF++ +E +A A Q + G+
Sbjct: 1 LYKLFSPFG-NVE--KIKLLKKKPGF----AFVEFSTEEAAEKAVQYLNGVL-FGGRP 50
>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 = 28.9 bits (65), Expect = 1.3
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 445 GLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKA 503
GLP + T ++ ++F G V+D + L G++ G FV F+ E ++
Sbjct: 6 GLPPDVTEEEFKEYFSQFGK-----VVDAQ---LMQDHDTGRSRGFGFVTFDSESAVERV 57
Query: 504 LSKHKESIGIRYIE 517
S +G + +E
Sbjct: 58 FSAGMLELGGKQVE 71
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 29.1 bits (66), Expect = 1.3
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 9/46 (19%)
Query: 458 FFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKA 503
F GT S VM G++ G FV F EEA KA
Sbjct: 22 FSPFGTITSAKVM---------TDEKGRSKGFGFVCFSSPEEATKA 58
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.0 bits (65), Expect = 1.5
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 443 MRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
+R L + T + + DFF +V + V+ G++ G FV F E+A +
Sbjct: 4 VRNLAFSVTQEDLTDFFS-------DVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQE 56
Query: 503 ALSKHKES 510
AL+K K
Sbjct: 57 ALAKLKNK 64
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 29.0 bits (65), Expect = 1.6
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 441 IRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
I ++ LP+E T K V F + G S V KK D A G AFV F +E
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRV---------PKKFDQSARGFAFVEFSTAKE 53
Query: 500 ADKALS--KHKESIGIRYI 516
A A++ K +G R +
Sbjct: 54 ALNAMNALKDTHLLGRRLV 72
>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 = 29.1 bits (65), Expect = 1.6
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 446 LPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
LP + T ++ FEA G CN++ K G G AFV ++K EEA A+
Sbjct: 8 LPRQLTEDELRKIFEAYGNIVQCNLLR--------DKSTGLPRGVAFVRYDKREEAQAAI 59
Query: 505 S 505
S
Sbjct: 60 S 60
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 28.9 bits (65), Expect = 1.6
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 444 RGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADK 502
GLP+ T +++ F+ G + V V GK G A+V +E E A +
Sbjct: 8 SGLPFSVTKEELEKLFKKHGVV---------KSVRLVTNRSGKPKGLAYVEYENESSASQ 58
Query: 503 ALSK 506
A+ K
Sbjct: 59 AVLK 62
>gnl|CDD|236530 PRK09466, metL, bifunctional aspartate kinase II/homoserine
dehydrogenase II; Provisional.
Length = 810
Score = 31.4 bits (72), Expect = 1.7
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 19/93 (20%)
Query: 511 IGIRYIELFRSTTAEVQQVLNKTMELPKNNSLTSS------NNGLSAQQPMLSHLAQVPV 564
IG R++ELF + + L + S +GL A + L+ V
Sbjct: 469 IGSRWLELFAREQSTLSARTGFEFVLV---GVVDSRRSLLNYDGLDASR-ALAFFDDEAV 524
Query: 565 PYLPQHIITSGTRKDCIRLRGLPYEALCILMDI 597
+ + + LR PY+ L +L D+
Sbjct: 525 EWDEESLFL--------WLRAHPYDELVVL-DV 548
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.4 bits (71), Expect = 1.8
Identities = 25/114 (21%), Positives = 38/114 (33%), Gaps = 9/114 (7%)
Query: 228 PHNMALNGHTPTLIPAPSPNALMPPPLNSKSTTIP-TNLPALPAVPTSGGYFPQFQL--- 283
A+ L PA SP +PPP +++ T P P P++P G P +
Sbjct: 2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRR 2865
Query: 284 PINMNTAHLLQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTPTVYTIPTPGNP 337
P + + A P + R V+ F + P P P
Sbjct: 2866 PPSRSPAAKPAAPARPPVRRLARPAVSRSTES-FALPPDQPERP----PQPQAP 2914
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 31.2 bits (70), Expect = 1.9
Identities = 43/190 (22%), Positives = 65/190 (34%), Gaps = 12/190 (6%)
Query: 144 LPPTSPAISPVGKTLLSPGMLPHSSQPLYPQHNTQINPGLSHLDPLVNVHLTQALAQAQY 203
LP P + P + SP SS+ H+ P L + Q
Sbjct: 237 LPSPHPPLQPQTASQQSPQPPAPSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSSNPPQP 296
Query: 204 AKSQQDNLMLMNQIAAQQMAALNKPHNMALNGHTP----TLIPAPSPNALMPPPLNSKST 259
Q + + + Q + P AL P L PAPS + PPP +T
Sbjct: 297 FGLAQSQVPPLPLPSQAQPHSHTPPSQSALQPQQPPREQPLPPAPSMPHIKPPP----TT 352
Query: 260 TIPTNLP-ALPAVPTSGGYFPQFQLPINMNTAHLLQPMNTPFFFNMPRMPVTP-QVLPKF 317
IP + P G P Q+P N+ L+P+++ + P P Q++P+
Sbjct: 353 PIPQLPNQSHKHPPHLQGPSPFPQMPSNLPPPPALKPLSSLPTHHPPSAHPPPLQLMPQ- 411
Query: 318 PVHQLNQTPT 327
L P
Sbjct: 412 -SQPLQSVPA 420
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 31.2 bits (70), Expect = 2.1
Identities = 37/166 (22%), Positives = 53/166 (31%), Gaps = 20/166 (12%)
Query: 174 QHNTQINPGLSHLDPLVNVHLTQALAQAQ---YAKSQQD--NLMLMNQIAAQQMAAL--N 226
QH+ +N D L + AQ Q Y+ Q N ++ M AL +
Sbjct: 681 QHDVPVNA--EDADAAAEAELARQFAQTQQQRYSGEQPAGANPFSLDDFEFSPMKALLDD 738
Query: 227 KPHNMALNGHTPTLIPAPSPNALMPPPLNSKSTTIPT------NLPALPAVPTSGGYFPQ 280
PH TP + P P + P + P P P P PQ
Sbjct: 739 GPHEPLF---TPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQ 795
Query: 281 FQLPINMNTAHLLQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTP 326
+ QP+ + P+ PV PQ P++ Q P
Sbjct: 796 QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQ--PQYQQPQQPVAP 839
Score = 30.1 bits (67), Expect = 4.5
Identities = 37/170 (21%), Positives = 50/170 (29%), Gaps = 23/170 (13%)
Query: 176 NTQINPGLSHLDPLVNVH-LTQALAQAQYAKSQQDNLMLMNQIAAQQMAALNKPHNMALN 234
N P DPL+N +T+ +A A A + A Q AA +P
Sbjct: 297 NRATQPEYDEYDPLLNGAPITEPVAVAAAATT-----------ATQSWAAPVEPV----- 340
Query: 235 GHTPTLIPAPSPNALMPPPLNSKSTT--IPTNLPALPAVPTSGGYFPQFQLPINMNTAHL 292
T T P S + P + T P + P Q+ P L
Sbjct: 341 --TQT-PPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPL 397
Query: 293 LQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTPTVYTIPTPGNPVALCP 342
QP+ + P Q P + Y P P PVA
Sbjct: 398 QQPVQPQQPYYAPAAEQPAQQ-PYYAPAPEQPAQQPYYAPAPEQPVAGNA 446
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 28.2 bits (63), Expect = 2.6
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 451 TAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKALS 505
T V FE GT C ++ G PDG + G AFV F EA A++
Sbjct: 14 TEDDVRRLFEPFGTIEECTILRG---------PDGNSKGCAFVKFSSHAEAQAAIN 60
>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 = 28.5 bits (64), Expect = 2.6
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 476 VLFVKKPDGKATGD----AFVLFEKEEEADKALS 505
V++V P K TGD AF+ FE EEA KA
Sbjct: 26 VVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 28.0 bits (63), Expect = 3.1
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 444 RGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKA 503
R LP E + D + +S VM GK AF F+ E+ A +A
Sbjct: 5 RHLPPELSEDDKEDLLKHFGASSVRVM----------SRRGKLKNTAFATFDNEQAASQA 54
Query: 504 LSK 506
LS+
Sbjct: 55 LSR 57
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 30.1 bits (68), Expect = 3.3
Identities = 26/168 (15%), Positives = 39/168 (23%), Gaps = 17/168 (10%)
Query: 188 PLVNVHLTQALAQAQYAKSQQDNLMLMNQIAAQQMAALNKPHNMALNGHTPTLIPAPSP- 246
P L Q L Q ++ Q QQ N P T P
Sbjct: 56 PPPVAQLPQPLPQPPPTQALQ-----ALPAGDQQQ--HNTPTGSPAANPPATFALPAGPA 108
Query: 247 -NALMPPPLNSKSTTIPTNLPALPAVPTSGGYFPQFQLPINMNTAHLLQPMNTPFFFNMP 305
+ P +P + PA P Q L Q P +P
Sbjct: 109 GPTIQTEPGQLYPVQVPVMVTQNPANS------PLDQPAQQRALQQLQQRYGAPASGQLP 162
Query: 306 RMPVTPQVLPKFPVHQLNQTPTVYTI--PTPGNPVALCPLVQNIWLSL 351
+ Q + + Q T + ++ +L
Sbjct: 163 SQQQSAQKNDESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGTL 210
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 30.2 bits (69), Expect = 3.3
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 88 QGQPSGEAFIQMDSEHSAYLAAQLRHNR 115
GQ A I +D + +A +L
Sbjct: 213 AGQGPDTAVIGVDDAYCRAIADRLEAAG 240
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 27.9 bits (63), Expect = 3.4
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 473 EEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
G+ GK G AFV F EEA +A+
Sbjct: 36 IVGIYMPVDETGKTKGYAFVEFATPEEAKEAV 67
>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 = 28.3 bits (64), Expect = 3.7
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 445 GLPYECTAKQVIDFFEAGTENSCNVM-----DGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
GLP + T ++ ++ F C ++ G+ + + +G GDA + KEE
Sbjct: 8 GLPLDITVEEFVEVFS-----KCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEES 62
Query: 500 ADKAL 504
+ A+
Sbjct: 63 VELAI 67
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 30.4 bits (68), Expect = 4.0
Identities = 38/187 (20%), Positives = 54/187 (28%), Gaps = 10/187 (5%)
Query: 160 SPGMLPHSSQPLYPQHNTQINPGLSHLDPLVNVHLTQALAQAQYAKSQQDNLML--MNQI 217
PG +P Q + + L + Q Q Q MNQ
Sbjct: 317 RPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQ 376
Query: 218 AAQ--QMAALNKPHNMALNGHTPTLIPAPSPNALMPPPLNSKSTTIPTNLPALPAVPTSG 275
Q QM AL + G +M P ++P P
Sbjct: 377 VGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQVQTNQSMPQPPQPSVPS 436
Query: 276 GYFPQFQLPINMNTAHL-----LQPMNTPFFFNMPRMPVTPQVLPKFPVHQLNQTPTVYT 330
P Q P +++ + L P +P P T Q P LN TP +
Sbjct: 437 PGGPGSQPPQSVSGGMIPSPPALMPSPSPQMSQSPASQRTIQQDMVSPGGPLN-TPGQSS 495
Query: 331 IPTPGNP 337
+ +P NP
Sbjct: 496 VNSPANP 502
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 28.0 bits (63), Expect = 4.1
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 480 KKPDGKATGDAFVLFEKEEEADKALSK 506
K D K +A+V+F++EE A+KAL
Sbjct: 52 KFHDKKDNVNAYVVFKEEESAEKALKL 78
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 27.6 bits (61), Expect = 5.0
Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 30/104 (28%)
Query: 440 IIRMRGLPYECTAKQVIDF---FEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEK 496
++ +R LP+ECT +++I+ F CNV G AFV F
Sbjct: 4 VLHLRNLPWECTEEELIELCKPFGKIVNTKCNV--------------GANRNQAFVEFAD 49
Query: 497 EEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNKTMELPKNN 540
+A +S + ++++E QV KT+ L +N
Sbjct: 50 LNQAIAMVS-------------YYASSSEPAQVRGKTVYLQYSN 80
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 27.8 bits (62), Expect = 5.1
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 17/92 (18%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLF--VKKPD------GKATGDAF 491
++ + LP + T ++ +F T+ G V F +K PD K + F
Sbjct: 2 VLYISNLPPDTTQLELESWF---TQY------GVRPVAFWTLKTPDEDAYVSSKDSISGF 52
Query: 492 VLFEKEEEADKALSKHKESIGIRYIELFRSTT 523
+F+ EEA +AL+ + +G R IE+ S++
Sbjct: 53 AVFQSHEEAMEALALNGRCLGERAIEVQPSSS 84
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 30.0 bits (67), Expect = 5.1
Identities = 49/235 (20%), Positives = 78/235 (33%), Gaps = 42/235 (17%)
Query: 145 PPTSPAISPVGKTLLSPGMLPHSSQPLYPQHNTQINPGLSHLDPL--VNVH--LTQALAQ 200
PPT P P G P + +P P + Q+ P + H P V H + L +
Sbjct: 457 PPTQPLEGPTG-----PLSVQAPLEPWQPLPHPQVTPVILHQPPAQGVQAHGSMLDLLEK 511
Query: 201 AQYAKSQQDNLMLMNQIAAQQMAALNKP----HNMALNGHTPT--------LIPAPSPNA 248
Q+ L+ Q A P ++ + P L+PAP
Sbjct: 512 DDEDMEQRVMATLLPPSPPQPRAGRRAPCVYTEDLDIESDEPASTEPVHDQLLPAPGLGP 571
Query: 249 LMPPPLNSKSTT-IPTNLPAL-------------PAVPTSGGYFPQF----QLPINMNTA 290
L PL S +T+ + ++ P+ P PT+ + P+ Q P+ +
Sbjct: 572 LQIQPLTSPTTSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPI 631
Query: 291 HLLQPMNTPFFFNMPRMPV---TPQVLPKFPVHQLNQTPTVYTIPTPGNPVALCP 342
+ P FN+ P PQV Q + P+P + P
Sbjct: 632 PMRPLRMQPITFNVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANTMLP 686
>gnl|CDD|182907 PRK11023, PRK11023, outer membrane lipoprotein; Provisional.
Length = 191
Score = 28.9 bits (65), Expect = 6.3
Identities = 21/71 (29%), Positives = 28/71 (39%), Gaps = 18/71 (25%)
Query: 35 VIIDSYVNKVLITSQYKEPIQGFKKVLVEHILEFLGEFASNIV--YQGVHMVYNS--QGQ 90
+ + +Y KVL+T Q L E A I +GV+ VYN QGQ
Sbjct: 70 INVTAYQGKVLLTGQSPN--------------AELSERAKQIAMGVEGVNEVYNEIRQGQ 115
Query: 91 PSGEAFIQMDS 101
P G D+
Sbjct: 116 PIGLGTASKDT 126
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.402
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,370,272
Number of extensions: 3090099
Number of successful extensions: 3269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3177
Number of HSP's successfully gapped: 205
Length of query: 612
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 509
Effective length of database: 6,369,140
Effective search space: 3241892260
Effective search space used: 3241892260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.8 bits)