NCBI Conserved Domain Search

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 409932 [Multi-domain] Cd Length: 74 Bit Score: 131.63 E-value: 1.13e-36

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530  29 SLVIKLHGLSTEASSLDIRHFFSGLNIPKGYIYITGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSS 102
Cdd:cd12510    1 SVVIRLQGLPWEAGSLDIRRFFSGLTIPDGGVHIIGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 410142 [Multi-domain] Cd Length: 76 Bit Score: 114.42 E-value: 1.44e-30

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 147898530 381 KCIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHCKKFQGTEILISCI 456
Cdd:cd12748    1 LCIYVRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRFLGTEVLLRLI 76

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410140 [Multi-domain] Cd Length: 86 Bit Score: 104.44 E-value: 6.57e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 141 DTSYIYVHGMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLSDETE 220
Cdd:cd12746    1 DDVYLFLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQ 80


                 ....*.
gi 147898530 221 WTKAGG 226
Cdd:cd12746   81 WIEAGG 86

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 410139 [Multi-domain] Cd Length: 79 Bit Score: 99.90 E-value: 1.97e-25

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530  29 SLVIKLHGLSTEASSLDIRHFFSGLNIPKGYIYITGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSSEAEMQ 107
Cdd:cd12744    1 AVVIRLQGLPVVAGSTDIRHFFTGLTIPDGGVHIIGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEMQ 79

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 241189 [Multi-domain] Cd Length: 92 Bit Score: 93.94 E-value: 4.66e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530  28 MSLVIKLHGLSTEASSLDIRHFFSGLNIPKGYIYITGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSSEAEMQ 107
Cdd:cd12745    1 MAVVIRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIVGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTEMQ 80


                 ....*....
gi 147898530 108 QALdEISRR 116
Cdd:cd12745   81 NMI-ELSRR 88

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409935 [Multi-domain] Cd Length: 81 Bit Score: 86.31 E-value: 1.40e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 266 RFVHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLPISERD 345
Cdd:cd12513    1 FCVHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKA 80


                 .
gi 147898530 346 M 346
Cdd:cd12513   81 M 81

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 409936 [Multi-domain] Cd Length: 73 Bit Score: 80.15 E-value: 1.41e-18

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHCKKFQGTEILIS 454
Cdd:cd12514    1 FIRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREAVVE 73

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409933 [Multi-domain] Cd Length: 73 Bit Score: 73.74 E-value: 2.98e-16

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLM 214
Cdd:cd12511    1 YLSLHGMPYSAMENDVRDFFHGLRVDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410141 [Multi-domain] Cd Length: 75 Bit Score: 73.29 E-value: 4.46e-16

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMG 207
Cdd:cd12747    3 YVHLHGMPFSATEADVRDFFHGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMG 66

RNA recognition motif (RRM) 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).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 70.28 E-value: 4.21e-15

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHCKKFQGTEILI 453
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 410143 [Multi-domain] Cd Length: 88 Bit Score: 70.23 E-value: 7.02e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHCKKFQGTEILISCITEQQM 461
Cdd:cd12749    1 CAHISNIPYNITKKDVLQFLEGIGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGRDAFLHLVTLEEM 80


                 .
gi 147898530 462 K 462
Cdd:cd12749   81 K 81

RNA recognition motif (RRM) 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).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 67.97 E-value: 2.79e-14

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYIYI----TGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQL 98
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIvyddDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72

RNA recognition motif (RRM) 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).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 67.20 E-value: 4.97e-14

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLSV--EDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSL 213
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIppDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 409937 [Multi-domain] Cd Length: 75 Bit Score: 63.40 E-value: 1.36e-12

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 599 LVLVRNLPRTFTVSEALDFFHGYKV--SSVNLAQIDNGI----ARVRFQTNIEAVEAVKELNNKPVGHTKVSMT 666
Cdd:cd12515    2 VVKMRNLPFKATIEDILDFFYGYRVipDSVSIRYNDDGQptgdARVAFPSPREARRAVRELNNRPLGGRKVKLF 75

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 410144 [Multi-domain] Cd Length: 77 Bit Score: 60.98 E-value: 1.07e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 600 VLVRNLPRTFTVSEALDFFHGYKV--SSVNLAQIDNGI----ARVRFQTNIEAVEAVKELNNKPVGHTKVSMTII 668
Cdd:cd12750    3 VKLFNLPFKATVNEILDFFYGYRVipDSVSIQYNEQGLptgdAIIAMETYEEAMAAVQDLNDRPIGPRKVKLSLL 77

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409935 [Multi-domain] Cd Length: 81 Bit Score: 60.89 E-value: 1.19e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHCKKFQGTEILISCITEQQM 461
Cdd:cd12513    2 CVHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKAM 81

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 410145 [Multi-domain] Cd Length: 76 Bit Score: 59.52 E-value: 2.87e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 599 LVLVRNLPRTFTVSEALDFFHGYKV--SSVNLAQIDNGI----ARVRFQTNIEAVEAVKELNNKPVGHTKVSMT 666
Cdd:cd12751    3 VIKVQNMPFTVSVDEILDFFYGYQVipGSVCLKYNEKGMptgeAMVAFESRDEAMAAVVDLNDRPIGSRKVKLV 76

RNA recognition motif (RRM) 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).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 57.96 E-value: 8.70e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVL 339
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409934 [Multi-domain] Cd Length: 101 Bit Score: 55.62 E-value: 1.27e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 258 RARSPYEERF-VHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLV 336
Cdd:cd12512    1 RSRSPHEKGFcVYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFI 80

                         90       100
                 ....*....|....*....|
gi 147898530 337 DVLPISERDMLDLIARSEKK 356
Cdd:cd12512   81 QVHPITKKAMLEKIDMIRKR 100

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 409937 [Multi-domain] Cd Length: 75 Bit Score: 51.84 E-value: 1.38e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAES 437
Cdd:cd12515    2 VVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARR 57

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 409936 [Multi-domain] Cd Length: 73 Bit Score: 51.26 E-value: 2.23e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530 145 IYVHGMPLNTTKVEIKPFFA--GLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPV 211
Cdd:cd12514    2 IRITNLPYDATPVDIQRFFEdhGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREA 70

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).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 50.74 E-value: 3.25e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGFSlKEEDIFLLYDDNGIGLGEALVLFSTEKEAEST-KKLHCKKFQGTEILIS 454
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG-EVVSVRIVRDRDGKSKGFAFVEFESPEDAEKAlEALNGTELGGRPLKVS 72

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409930 [Multi-domain] Cd Length: 80 Bit Score: 49.66 E-value: 9.90e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 149 GMPLNTTKVEIKPFFAGLSV-----EDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLS 216
Cdd:cd12508    8 GLPFSATAADILAFFGGECPvtggkDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

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).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 49.20 E-value: 1.17e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGL-SVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALK 200
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFgEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALE 57

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 410142 [Multi-domain] Cd Length: 76 Bit Score: 48.17 E-value: 3.00e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLSV--EDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLML 215
Cdd:cd12748    2 CIYVRNLPFDVTKVEVQDFFEGFALaeDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRFLGTEVLLRL 75

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 409936 [Multi-domain] Cd Length: 73 Bit Score: 47.02 E-value: 6.46e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLV 336
Cdd:cd12514    1 FIRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREA 70

RNA recognition motif 2 (RRM2) found 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. 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.

Pssm-ID: 409927 [Multi-domain] Cd Length: 77 Bit Score: 45.81 E-value: 2.39e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 147898530 382 CIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLH 442
Cdd:cd12504    2 VVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKH 62

RNA recognition motif 2 (RRM2) found 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. 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.

Pssm-ID: 409927 [Multi-domain] Cd Length: 77 Bit Score: 45.04 E-value: 4.38e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTS 316
Cdd:cd12504    2 VVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFAS 51

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 240951 [Multi-domain] Cd Length: 75 Bit Score: 44.41 E-value: 7.65e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 147 VHGMPLNTTKVEIKPFFAGLSVED--VIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGS 208
Cdd:cd12507    4 ARGLPWQSSDQDIAQFFRGLNIAKggVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGT 67

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409928 [Multi-domain] Cd Length: 77 Bit Score: 44.05 E-value: 9.32e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPK---GYIYITGGQYGEAFIIFANYEDARQAI 84
Cdd:cd12505    3 VVRLRGLPYSCTEADIAHFFSGLDIVDitfVMDLRGGRKTGEAFVQFASPEMAAQAL 59

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 240951 [Multi-domain] Cd Length: 75 Bit Score: 44.02 E-value: 9.40e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYIYIT----GGQYGEAFIIFANYE 78
Cdd:cd12507    1 VVRARGLPWQSSDQDIAQFFRGLNIAKGGVALClsaqGRRNGEALIRFVDQE 52

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 241189 [Multi-domain] Cd Length: 92 Bit Score: 43.48 E-value: 1.93e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLSVEDVIFlkYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLSDETE 220
Cdd:cd12745    5 IRLQGLPIVAGTMDIRHFFSGLTIPDGGV--HIVGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTE 78

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409930 [Multi-domain] Cd Length: 80 Bit Score: 43.11 E-value: 2.01e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSG----LNIPKGYIYIT---GGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFS 101
Cdd:cd12508    3 IVRMRGLPFSATAADILAFFGGecpvTGGKDGILFVTypdGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410140 [Multi-domain] Cd Length: 86 Bit Score: 43.20 E-value: 2.12e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGfsLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHcKKFQGTE-ILISCITEQQM 461
Cdd:cd12746    5 LFLRGMPYSATEDDVRNFFSG--LKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRH-RQYMGSRfIEVTRTTEEQW 81


                 ....
gi 147898530 462 KAFG 465
Cdd:cd12746   82 IEAG 85

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 410139 [Multi-domain] Cd Length: 79 Bit Score: 42.89 E-value: 2.16e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLSVED----VIflkypsGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLSDETE 220
Cdd:cd12744    4 IRLQGLPVVAGSTDIRHFFTGLTIPDggvhII------GGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAE 77

RNA recognition motif 2 (RRM2) found 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. 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.

Pssm-ID: 409927 [Multi-domain] Cd Length: 77 Bit Score: 43.11 E-value: 2.16e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNI-PKGYIYIT---GGQYGEAFIIFANYEDARQAI 84
Cdd:cd12504    2 VVRLRGLPYGCTKEEIAQFFSGLEIvPNGITLPMdrrGRSTGEAFVQFASQEIAEQAL 59

RNA recognition motif 2 (RRM2) found 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).

Pssm-ID: 410136 [Multi-domain] Cd Length: 111 Bit Score: 43.88 E-value: 2.27e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 136 YFKKRDTSYIYVHGMPLNTTKVEIKPFFAGL-----SVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTP 210
Cdd:cd12739   10 FLSKENQVIVRMRGLPFTATAEEVLAFFGQHcpvtgGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRY 89

                         90
                 ....*....|
gi 147898530 211 VSLMLSDETE 220
Cdd:cd12739   90 IELFRSTAAE 99

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 241182 [Multi-domain] Cd Length: 80 Bit Score: 42.98 E-value: 2.38e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLSVED--VIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMG 207
Cdd:cd12738    2 VRARGLPWQSSDQDIAKFFRGLNIAKggVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIG 66

RNA recognition motif 1 (RRM1) found 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).

Pssm-ID: 410135 [Multi-domain] Cd Length: 80 Bit Score: 43.07 E-value: 2.40e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLSVED--VIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGS 208
Cdd:cd12737    2 IRARGLPWQSSDQDIARFFKGLNIAKggVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGS 67

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409928 [Multi-domain] Cd Length: 77 Bit Score: 42.90 E-value: 2.63e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 147898530 149 GMPLNTTKVEIKPFFAGLSVEDVIF-LKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGS 208
Cdd:cd12505    8 GLPYSCTEADIAHFFSGLDIVDITFvMDLRGGRKTGEAFVQFASPEMAAQALLKHKEEIGN 68

RNA recognition motif 2 (RRM2) found 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. 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.

Pssm-ID: 409927 [Multi-domain] Cd Length: 77 Bit Score: 42.34 E-value: 3.33e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 149 GMPLNTTKVEIKPFFAGLSV--EDVIFLKYPSGLRNGNAIVRFATSGDAHEALKR 201
Cdd:cd12504    7 GLPYGCTKEEIAQFFSGLEIvpNGITLPMDRRGRSTGEAFVQFASQEIAEQALGK 61

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409930 [Multi-domain] Cd Length: 80 Bit Score: 42.34 E-value: 3.41e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGF---SLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLH 442
Cdd:cd12508    4 VRMRGLPFSATAADILAFFGGEcpvTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKH 66

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410130 [Multi-domain] Cd Length: 90 Bit Score: 42.31 E-value: 5.32e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLS-VEDVIFLKY-PSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLSDETE 220
Cdd:cd12731   10 FVRLRGLPFGCSKEEIVQFFSGLEiVPNGITLPVdFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE 88

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).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 41.50 E-value: 6.45e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530 600 VLVRNLPRTFTVSEALDFFHGY-KVSSVNL----AQIDNGIARVRFQTNIEAVEAVKELNNKPVGHTKV 663
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFgEVVSVRIvrdrDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPL 69

RNA recognition motif 2 (RRM2) found 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).

Pssm-ID: 241184 [Multi-domain] Cd Length: 107 Bit Score: 42.28 E-value: 8.55e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 136 YFKKRDTSYIYVHGMPLNTTKVEIKPFFAGL-----SVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTP 210
Cdd:cd12740   10 FLSKENQVIIRMRGLPFTATPEDVLGFLGPEcpvtgGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRY 89

                         90
                 ....*....|
gi 147898530 211 VSLMLSDETE 220
Cdd:cd12740   90 IELFRSTAAE 99

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 409937 [Multi-domain] Cd Length: 75 Bit Score: 41.05 E-value: 8.82e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYI---YITGGQ-YGEAFIIFANYEDARQAIN-YSGRPLKNSCVQLS 99
Cdd:cd12515    2 VVKMRNLPFKATIEDILDFFYGYRVIPDSVsirYNDDGQpTGDARVAFPSPREARRAVReLNNRPLGGRKVKLF 75

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410137 [Multi-domain] Cd Length: 99 Bit Score: 41.75 E-value: 9.92e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGL--------SVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLMLS 216
Cdd:cd12741   20 IRMRGLPYDCTPKQVVEFFCTGdkiphvldGAEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFRS 99

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).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 40.73 E-value: 1.05e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 268 VHLINLPYDVNKRDIKAHF---GNLamkdSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQ-HGRVFCSRLVDV 338
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFskfGEV----VSVRIVRDRDGKSKGFAFVEFESPEDAEKALEAlNGTELGGRPLKV 71

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409929 [Multi-domain] Cd Length: 75 Bit Score: 40.82 E-value: 1.14e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSLML 215
Cdd:cd12506    3 VHMRGLPYRATENDIFEFFSPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFL 73

RNA recognition motif 4 (RRM4) found 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.

Pssm-ID: 410142 [Multi-domain] Cd Length: 76 Bit Score: 40.85 E-value: 1.21e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 600 VLVRNLPRTFTVSEALDFFHGYKVSS--VNLAQIDNGI----ARVRFQTNIEAVEAVKeLNNKPVGHTKVSMTII 668
Cdd:cd12748    3 IYVRNLPFDVTKVEVQDFFEGFALAEddIILLYDDKGVglgeALVKFKSEEEAMKAER-LNGQRFLGTEVLLRLI 76

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409935 [Multi-domain] Cd Length: 81 Bit Score: 40.86 E-value: 1.39e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530  32 IKLHGLSTEASSLDIRHFFSGLNIPKGYIYITGGQYG----EAFIIFANYEDARQAINYSGRPLKNSCVQLSFSSEAEM 106
Cdd:cd12513    3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGkrtrEAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKAM 81

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 characteriztic 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.

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 40.29 E-value: 1.60e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530  600 VLVRNLPRTFTVSEALDFFHGY-KVSSVNLAQID----NGIARVRFQTNIEAVEAVKELNNKPVGHTKV 663
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFgPIKSIRLVRDEtgrsKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

Pssm-ID: 240822 [Multi-domain] Cd Length: 79 Bit Score: 40.30 E-value: 1.88e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530 602 VRNLPRTFTVSEALDFFHGY------KVSSVNLAQIDNGIARVRFQTNIEAVEAVKELNN-KPVGHTK 662
Cdd:cd12376    5 VSGLPKTMTQKELEQLFSQYgriitsRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGqKPEGASE 72

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410130 [Multi-domain] Cd Length: 90 Bit Score: 40.76 E-value: 2.19e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530  32 IKLHGLSTEASSLDIRHFFSGLNI-PKGY---IYITGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSSEAEMQ 107
Cdd:cd12731   11 VRLRGLPFGCSKEEIVQFFSGLEIvPNGItlpVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 90

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 39.88 E-value: 2.24e-04

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530   600 VLVRNLPRTFTVSEALDFFHGY-KVSSVNLA-----QIDNGIARVRFQTNIEAVEAVKELNNKPVGHTKV 663
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFgKVESVRLVrdketGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL 71

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409933 [Multi-domain] Cd Length: 73 Bit Score: 39.84 E-value: 2.32e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKdsQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLP 340
Cdd:cd12511    1 YLSLHGMPYSAMENDVRDFFHGLRVD--GVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVSP 72

RNA recognition motif 2 (RRM2) found 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).

Pssm-ID: 409925 [Multi-domain] Cd Length: 72 Bit Score: 40.09 E-value: 2.32e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530 149 GMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMG 207
Cdd:cd12502    7 GAPFNVKEKQIREFFSPLKPVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMG 65

RNA recognition motif 1 (RRM1) found 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).

Pssm-ID: 410134 [Multi-domain] Cd Length: 93 Bit Score: 40.00 E-value: 4.17e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 141 DTSYIYVHGMPLNTTKVEIKPFFAGLSVED--VIFLKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGS 208
Cdd:cd12736    8 DNTVIRARGLPWQSSDQDIARFFKGLNIAKggAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGN 77

RNA recognition motif 1 (RRM1) found 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).

Pssm-ID: 410135 [Multi-domain] Cd Length: 80 Bit Score: 39.22 E-value: 4.77e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYIYI----TGGQYGEAFIIFANYEDARQAIN 85
Cdd:cd12737    1 VIRARGLPWQSSDQDIARFFKGLNIAKGGVALclnaQGRRNGEALVRFVNSEQRDLALE 59

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410130 [Multi-domain] Cd Length: 90 Bit Score: 39.61 E-value: 5.14e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLPISERDM 346
Cdd:cd12731   10 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEV 89

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409934 [Multi-domain] Cd Length: 101 Bit Score: 39.45 E-value: 6.61e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530  32 IKLHGLSTEASSLDIRHFFSGLNIPKGYIYITGG----QYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSSEAEMQ 107
Cdd:cd12512   12 VYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGpngrATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQVHPITKKAML 91


                 ....*....
gi 147898530 108 QALDEISRR 116
Cdd:cd12512   92 EKIDMIRKR 100

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 409928 [Multi-domain] Cd Length: 77 Bit Score: 38.66 E-value: 6.96e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 268 VHLINLPYDVNKRDIKAHFGNLAMKDsqITFLRDWSGKR-TREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLP 340
Cdd:cd12505    4 VRLRGLPYSCTEADIAHFFSGLDIVD--ITFVMDLRGGRkTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFP 75

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409934 [Multi-domain] Cd Length: 101 Bit Score: 39.45 E-value: 7.43e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 380 GKCIYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLHcKKFQGTE-ILISCITE 458
Cdd:cd12512    9 GFCVYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRH-KQYMGNRfIQVHPITK 87


                 ...
gi 147898530 459 QQM 461
Cdd:cd12512   88 KAM 90

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410141 [Multi-domain] Cd Length: 75 Bit Score: 37.85 E-value: 1.41e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147898530 267 FVHLINLPYDVNKRDIKAHFGNLAMKdsQITFLRDWSGKRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLP 340
Cdd:cd12747    3 YVHLHGMPFSATEADVRDFFHGLRID--AIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVSP 74

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 409934 [Multi-domain] Cd Length: 101 Bit Score: 38.68 E-value: 1.41e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGLS-VEDVIFLKY-PSGLRNGNAIVRFATSGDAHEALKRSGHLMGS 208
Cdd:cd12512   12 VYLKGLPYEAENKHVIEFFKKLDiVEDSIYIAYgPNGRATGEGFVEFRNEIDYKAALCRHKQYMGN 77

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410130 [Multi-domain] Cd Length: 90 Bit Score: 38.07 E-value: 1.60e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAESTKKLH 442
Cdd:cd12731   11 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKH 70

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 241179 [Multi-domain] Cd Length: 75 Bit Score: 37.68 E-value: 1.87e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530  32 IKLHGLSTEASSLDIRHFFSGLNIPKGYIYI--TGGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFSS 102
Cdd:cd12735    3 VHMRGLPFRATESDIANFFSPLNPIRVHIDIgaDGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75

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 characteriztic 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.

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 37.21 E-value: 1.90e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530  145 IYVHGMPLNTTKVEIKPFFAGL-SVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKR 201
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFgPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEA 58

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 409926 [Multi-domain] Cd Length: 77 Bit Score: 37.37 E-value: 2.12e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNI--PKGYIYIT----GGQYGEAFIIFANYEDARQAI 84
Cdd:cd12503    1 VVRARGLPWSATAEDVLNFFTDCRIkgGENGIHFTytreGRPSGEAFIELESEEDVEKAL 60

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 37.19 E-value: 2.18e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530   268 VHLINLPYDVNKRDIKAHFGNLAmKDSQITFLRDW-SGKRTREGFVKLTSLSQYRDACAQ-HGRVFCSRLVDV 338
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKeTGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 409714 [Multi-domain] Cd Length: 72 Bit Score: 36.92 E-value: 2.30e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGL-SVEDVIFLKYP-SGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVSL 213
Cdd:cd12271    1 VYVGGIPYYSTEAEIRSYFSSCgEVRSVDLMRFPdSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

Pssm-ID: 410168 [Multi-domain] Cd Length: 84 Bit Score: 37.39 E-value: 2.79e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530 602 VRNLPRTFTVSEALDFFHGY------KVSSVNLAQIDNGIARVRFQTNIEAVEAVKELN-NKPVGHTK 662
Cdd:cd12775   10 VSGLPKTMTQKELEQLFSQYgriitsRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNgQKPPGATE 77

RNA recognition motif 1 (RRM1) found 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.

Pssm-ID: 241182 [Multi-domain] Cd Length: 80 Bit Score: 36.82 E-value: 3.43e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYIYI----TGGQYGEAFIIFANYE 78
Cdd:cd12738    1 VVRARGLPWQSSDQDIAKFFRGLNIAKGGVALclnpQGRRNGEALVRFTCTE 52

RNA recognition motif (RRM) 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).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 36.38 E-value: 3.62e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 600 VLVRNLPRTFTVSEALDFFHGYKVSSVNLAQIDN------GIARVRFQTNIEAVEAVKELNNK 656
Cdd:cd12254    2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDddgrptGEAYVEFASEEDAQRALRRHKGK 64

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

Pssm-ID: 409737 [Multi-domain] Cd Length: 71 Bit Score: 36.48 E-value: 4.13e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530 386 RNFASDVSKTDIQSFFSGF-SLKEEDIFLLYDDNgiglgEALVLFSTEKEAESTKKLHCKKFQGTEILIS 454
Cdd:cd12296    6 KNLPKSITENKIRQFFKDCgEIREVKILESGNGL-----VAVIEFETEDEALAALTKDHKRIGGNEISVS 70

RNA recognition motif 1 (RRM1) found 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).

Pssm-ID: 410134 [Multi-domain] Cd Length: 93 Bit Score: 36.92 E-value: 4.43e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKG----YIYITGGQYGEAFIIFANYE 78
Cdd:cd12736   11 VIRARGLPWQSSDQDIARFFKGLNIAKGgaalCLNAQGRRNGEALVRFVNEE 62

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 characteriztic 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.

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 36.06 E-value: 4.65e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 147898530  272 NLPYDVNKRDIKAHFGNLA-MKDSQItfLRDWSGKRTREGFVKLTSLSQYRDACAQ-HGRVFCSRLV 336
Cdd:pfam00076   5 NLPPDTTEEDLKDLFSKFGpIKSIRL--VRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGREL 69

RNA recognition motif 2 (RRM2) found 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).

Pssm-ID: 410136 [Multi-domain] Cd Length: 111 Bit Score: 37.34 E-value: 4.65e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530  30 LVIKLHGLSTEASSLDIRHFFsGLNIP-----KGYIYIT---GGQYGEAFIIFANYEDARQAINYSGRPLKNSCVQLSFS 101
Cdd:cd12739   17 VIVRMRGLPFTATAEEVLAFF-GQHCPvtggkEGILFVTypdSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRS 95

                         90
                 ....*....|...
gi 147898530 102 SEAEMQQALDEIS 114
Cdd:cd12739   96 TAAEVQQVLNRYS 108

RNA recognition motif 2 (RRM2) found 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.

Pssm-ID: 410131 [Multi-domain] Cd Length: 96 Bit Score: 36.83 E-value: 4.85e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530  31 VIKLHGLSTEASSLDIRHFFSGLNIPKGYIYIT----GGQYGEAFIIFANYEDARQAI 84
Cdd:cd12732   20 TVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTmdyqGRSTGEAFVQFASKEIAENAL 77

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.

Pssm-ID: 409836 [Multi-domain] Cd Length: 81 Bit Score: 36.43 E-value: 4.87e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 147898530 269 HLINLPYDVNKRDIKAHFGNLAMkdSQITFLRDWSGKRTReGF 311
Cdd:cd12402    6 YLGNLPYDVTEDDIEDFFRGLNI--SSVRLPRENGPGRLR-GF 45

RNA recognition motif (RRM) found 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.

Pssm-ID: 409886 [Multi-domain] Cd Length: 83 Bit Score: 36.34 E-value: 5.06e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530 268 VHLINLPYDVNKRDIKAHFGNLAMKDSQITFLRDWSG-KRTREGFVKLTSLSQYRDACAQHGRVFCSRLVDVLPISER 344
Cdd:cd12452    3 LYMNGLPHDTTQSELESWFTQHGVRPVAFWTLKTPEQiKPSGSGFAVFQSHEEAAESLALNGRALGDRAIEVQPSSSR 80

RNA recognition motif 3 (RRM3) found 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.

Pssm-ID: 410132 [Multi-domain] Cd Length: 75 Bit Score: 36.28 E-value: 5.41e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 147898530 144 YIYVHGMPLNTTKVEIKPFFAGLSVEDVIFLKYPSGLRNGNAIVRFATSGDAHEALKR 201
Cdd:cd12733    2 FVHMRGLPFQANGQDIINFFAPLKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAK 59

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 35.65 E-value: 8.65e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147898530    36 GLSTEASSLDIRHFFSG------LNIPKGYIyiTGGQYGEAFIIFANYEDARQAIN-YSGRPLKNSCVQL 98
Cdd:smart00360   6 NLPPDTTEEELRELFSKfgkvesVRLVRDKE--TGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73

RNA recognition motif 5 (RRM5) found 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.

Pssm-ID: 410145 [Multi-domain] Cd Length: 76 Bit Score: 35.63 E-value: 8.82e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGFSLKEEDIFLLYDDNGIGLGEALVLFSTEKEAES 437
Cdd:cd12751    4 IKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMA 58

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.

Pssm-ID: 409739 [Multi-domain] Cd Length: 78 Bit Score: 35.70 E-value: 9.12e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147898530 145 IYVHGMPLNTTKVEIKPFFAGL-SVEDVIF----LKYPSGLRNGNAIVRFATSGDAHEALKRSGHLMGSTPVS 212
Cdd:cd12298    3 IRVRNLDFELDEEALRGIFEKFgEIESINIpkkqKNRKGRHNNGFAFVTFEDADSAESALQLNGTLLDNRKIS 75

RNA recognition motif (RRM) found 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.

Pssm-ID: 409846 [Multi-domain] Cd Length: 81 Bit Score: 35.67 E-value: 9.35e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 147898530 383 IYLRNFASDVSKTDIQSFFSGF-SLKEEDIFLlyDDNGIGLGEALVLFSTEKEAESTKK 440
Cdd:cd12412    5 IFVGGIDWDTTEEELREFFSKFgKVKDVKIIK--DRAGVSKGYGFVTFETQEDAEKIQK 61