NCBI Conserved Domain Search

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: 172.24 E-value: 1.52e-50

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  153 ENPYLFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGSEQQ 232
Cdd:cd12746     1 DDVYLFLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQ 80


                  ....*.
gi 118722349  233 WIEFGG 238
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: 161.92 E-value: 6.03e-47

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    2 AVVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHIIGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAEMQ 80
Cdd:cd12744     1 AVVIRLQGLPVVAGSTDIRHFFTGLTIPDGGVHIIGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEMQ 79

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: 154.58 E-value: 2.40e-44

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  925 TPIKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKLTLL 1001
Cdd:cd12750     1 VAVKLFNLPFKATVNEILDFFYGYRVIPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAVQDLNDRPIGPRKVKLSLL 77

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: 151.78 E-value: 2.28e-43

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  400 LCIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLRLI 475
Cdd:cd12748     1 LCIYVRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRFLGTEVLLRLI 76

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: 139.33 E-value: 4.34e-39

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349    2 AVVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHIIGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12510     1 SVVIRLQGLPWEAGSLDIRRFFSGLTIPDGGVHIIGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74

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: 136.91 E-value: 2.92e-38

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  156 YLFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQG 228
Cdd:cd12511     1 YLSLHGMPYSAMENDVRDFFHGLRVDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVSPA 73

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: 136.77 E-value: 4.19e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  284 FYVHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKD-ENRTRYAFVMFKTLKDYNTALSLHKTVLQYRPVHIDPISRKQ 362
Cdd:cd12513     1 FCVHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKyGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKA 80


                  .
gi 118722349  363 M 363
Cdd:cd12513    81 M 81

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: 136.70 E-value: 5.99e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    1 MAVVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHIIGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAEMQ 80
Cdd:cd12745     1 MAVVIRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIVGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTEMQ 80


                  ....*..
gi 118722349   81 KTIEMKR 87
Cdd:cd12745    81 NMIELSR 87

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: 123.10 E-value: 2.23e-33

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  925 TPIKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKLT 999
Cdd:cd12515     1 CVVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGGRKVKLF 75

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: 118.07 E-value: 1.37e-31

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  925 TPIKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKLT 999
Cdd:cd12751     2 TVIKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAAVVDLNDRPIGSRKVKLV 76

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: 108.65 E-value: 2.53e-28

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLR 473
Cdd:cd12514     1 FIRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREAVVE 73

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: 83.76 E-value: 1.34e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLR 473
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

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: 82.56 E-value: 5.96e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLRLISEAQI 480
Cdd:cd12749     1 CAHISNIPYNITKKDVLQFLEGIGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGRDAFLHLVTLEEM 80


                  ....*.
gi 118722349  481 QEFGVN 486
Cdd:cd12749    81 KEIEKN 86

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: 80.68 E-value: 1.31e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELF 72
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVydddGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

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: 79.53 E-value: 3.48e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  156 YLFLRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIppDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72

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: 78.68 E-value: 8.02e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  154 NPYLFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12747     1 DLYVHLHGMPFSATEADVRDFFHGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEV 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: 73.16 E-value: 7.85e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCV-----DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12508     6 MRGLPFSATAADILAFFGGECPvtggkDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIEL 77

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: 71.05 E-value: 3.92e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  285 YVHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKDENR-TRYAFVMFKTLKDYNTALSLHKTVLQYRPVHI 355
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: 69.51 E-value: 1.34e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRpVGPRKVKLT 999
Cdd:cd12254     2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGK-MGGRYIEVF 73

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: 64.68 E-value: 6.47e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12504     5 LRGLPYGCTKEEIAQFFSGLEIvpNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77

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: 61.39 E-value: 2.23e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVD--------GVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQ 227
Cdd:cd12741    22 MRGLPYDCTPKQVVEFFCTGDKIphvldgaeGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFR 98

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: 57.75 E-value: 2.08e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    2 AVVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII-------GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLS 74
Cdd:cd12508     1 QVIVRMRGLPFSATAADILAFFGGECPVTGGKDGIlfvtypdGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

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: 57.40 E-value: 2.44e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCV----DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12503     4 ARGLPWSATAEDVLNFFTDCRIkggeNGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEV 74

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: 57.53 E-value: 2.78e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVDGVIF-LKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12505     6 LRGLPYSCTEADIAHFFSGLDIVDITFvMDLRGGRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEI 73

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: 56.74 E-value: 4.21e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  160 RGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12507     5 RGLPWQSSDQDIAQFFRGLNIakGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEV 72

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: 56.65 E-value: 4.85e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  400 LCIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGTEVLLRLISEAQ 479
Cdd:cd12513     1 FCVHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKA 80


                  .
gi 118722349  480 I 480
Cdd:cd12513    81 M 81

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: 57.55 E-value: 5.33e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  277 RSRSP--LGFYVHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKDENR-TRYAFVMFKTLKDYNTALSLHKTVLQYRPV 353
Cdd:cd12512     1 RSRSPheKGFCVYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRaTGEGFVEFRNEIDYKAALCRHKQYMGNRFI 80

                          90       100
                  ....*....|....*....|
gi 118722349  354 HIDPISRKQMLKFIARYEKK 373
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: 55.31 E-value: 1.20e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLGT 468
Cdd:cd12515     2 VVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGG 69

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: 55.79 E-value: 1.41e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  149 PLKAENPYLFLRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVM 226
Cdd:cd12731     3 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIvpNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 82


                  ....*.
gi 118722349  227 QGSEQQ 232
Cdd:cd12731    83 KSSRAE 88

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: 56.15 E-value: 1.89e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  150 LKAENPYLF-LRGLPYLVNEDDVRVFFSGLC-----VDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFI 223
Cdd:cd12740    11 LSKENQVIIrMRGLPFTATPEDVLGFLGPECpvtggTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYI 90


                  ....*.
gi 118722349  224 EVMQGS 229
Cdd:cd12740    91 ELFRST 96

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: 54.60 E-value: 1.95e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDdIYLLYDDKGVGLGEALVKFKSEEQAMKA-ERLNRRRFLG 467
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVS-VRIVRDRDGKSKGFAFVEFESPEDAEKAlEALNGTELGG 66

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: 54.28 E-value: 9.39e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  150 LKAENPYLF-LRGLPYLVNEDDVRVFFSGLC-----VDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFI 223
Cdd:cd12739    11 LSKENQVIVrMRGLPFTATAEEVLAFFGQHCpvtggKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYI 90


                  ....*.
gi 118722349  224 EVMQGS 229
Cdd:cd12739    91 ELFRST 96

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: 53.84 E-value: 9.68e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    3 VVIRLLGLPFIAGPVDIRHFFTGLTIPDGGV-------HIIGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12740    17 VIIRMRGLPFTATPEDVLGFLGPECPVTGGTegllfvkYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRST 96


                  ....*...
gi 118722349   76 KAEMQKTI 83
Cdd:cd12740    97 AAEVQQVL 104

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: 53.08 E-value: 1.03e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  160 RGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGSEQQW 233
Cdd:cd12737     5 RGLPWQSSDQDIARFFKGLNIakGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEEF 80

RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.

Pssm-ID: 410129 [Multi-domain] Cd Length: 79 Bit Score: 51.72 E-value: 2.67e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  160 RGLPYLVNEDDVRVFFSGLCV----DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQ 227
Cdd:cd12730     7 RGLPWSCTAEDVLSFFSDCRIrngeDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78

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: 51.94 E-value: 2.90e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTI-PDG---GVHIIGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAEMQ 80
Cdd:cd12731    11 VRLRGLPFGCSKEEIVQFFSGLEIvPNGitlPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 90

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 and similar proteins; This subgroup corresponds to the RRM3 of ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410138 [Multi-domain] Cd Length: 81 Bit Score: 51.73 E-value: 3.06e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVD----GVIFLKHHDGRNNGDAIVKFASCVDA-SGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12742     6 LRGLPYAATIEDILEFLGEFAADirphGVHMVLNHQGRPSGDAFIQMKSADRAfLAAQKCHKKTMKDRYVEVFQCS 81

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: 51.26 E-value: 3.55e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12502     5 LRGAPFNVKEKQIREFFSPLKPVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEV 71

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: 51.20 E-value: 3.69e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12504     2 VVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPmdrrGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77

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: 51.22 E-value: 4.05e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIE 224
Cdd:cd12506     5 MRGLPYRATENDIFEFFSPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIE 70

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: 50.99 E-value: 4.31e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII---GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLS 74
Cdd:cd12505     3 VVRLRGLPYSCTEADIAHFFSGLDIVDITFVMDlrgGRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 50.67 E-value: 6.54e-08

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349    401 CIYIRNFPFDVTKVEVQKFFADFllAE-DDIYLLYD-DKGVGLGEALVKFKSEEQAMKA-ERLNRRRFLGTEV 470
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKF--GKvESVRLVRDkETGKSKGFAFVEFESEEDAEKAlEALNGKELDGRPL 71

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: 51.08 E-value: 7.55e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12732    23 LRGLPFGCSKEEIVQFFSGLEIvpNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFKSS 95

tegument protein VP11/12; Provisional

Pssm-ID: 223041 [Multi-domain] Cd Length: 694 Bit Score: 55.35 E-value: 1.53e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  689 GEWRRPPEDDFRRPPEEDFRHSPEEDFRQsPQEHFRRPPQEHFRRPPPEHFRRPPPEHfrrPPPEHFRRPPP----EHFR 764
Cdd:PHA03321  431 PGAPAPRRDNDPPPPPRARPGSTPACARR-ARAQRARDAGPEYVDPLGALRRLPAGAA---PPPEPAAAPSPatyyTRMG 506

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  765 RPPPehfrRPPPEHFRRPPQEHFRRPPQEHFRRSREEDFRHPPDEDF---RGPPDEDFRHPPdedfRSPQEEDFrcPSDE 841
Cdd:PHA03321  507 GGPP----RLPPRNRATETLRPDWGPPAAAPPEQMEDPYLEPDDDRFdrrDGAAAAATSHPR----EAPAPDDD--PIYE 576

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  842 DFRQLPEEDLREAPEED---PRLPDNFRPPGEdfrsPPDDFRSHRPFVNFGRPeggKFDFGKHNMGSFPEGRFMPDP 915
Cdd:PHA03321  577 GVSDSEEPVYEEIPTPRvyqNPLPRPMEGAGE----PPDLDAPTSPWVEEENP---IYGWGDSPLFSPPPAARFPPP 646

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: 49.32 E-value: 1.75e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKdLNDRPVGPRKVKLTLL 1001
Cdd:cd12748     3 IYVRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAER-LNGQRFLGTEVLLRLI 76

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: 49.31 E-value: 2.04e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDG--GVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLS 74
Cdd:cd12503     1 VVRARGLPWSATAEDVLNFFTDCRIKGGenGIHFTytreGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77

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: 49.63 E-value: 2.42e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  153 ENPYLFLRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGSE 230
Cdd:cd12736     8 DNTVIRARGLPWQSSDQDIARFFKGLNIakGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKATG 87


                  ....*
gi 118722349  231 QQWIE 235
Cdd:cd12736    88 EDFLK 92

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

Pssm-ID: 409931 [Multi-domain] Cd Length: 81 Bit Score: 49.01 E-value: 2.49e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVD----GVIFLKHHDGRNNGDAIVKFASCVDAS-GGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12509     6 LRGLPYSATVEDILNFLGEFAKHiapqGVHMVINAQGRPSGDAFIQMLSAEFARlAAQKRHKHHMGERYIEVFQCS 81

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: 48.76 E-value: 3.51e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  160 RGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGSEQQW 233
Cdd:cd12738     5 RGLPWQSSDQDIAKFFRGLNIakGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATGEDF 80

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

Pssm-ID: 409931 [Multi-domain] Cd Length: 81 Bit Score: 48.24 E-value: 5.09e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  927 IKIMNLPFKANVNEILDFF--HGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKL 998
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLgeFAKHIAPQGVHMVINAQGRPSGDAFIQMLSAEFARLAAQKRHKHHMGERYIEV 77

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: 47.96 E-value: 5.20e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA 457
Cdd:cd12751     4 IKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAA 59

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: 48.68 E-value: 6.07e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    3 VVIRLLGLPFIAGPVDIRHFF-TGLTIP-----DGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELF 72
Cdd:cd12741    18 VIIRMRGLPYDCTPKQVVEFFcTGDKIPhvldgAEGVLFVkkpdGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELF 97


                  ..
gi 118722349   73 LS 74
Cdd:cd12741    98 RS 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: 47.66 E-value: 6.59e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIpDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKL 998
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: 47.75 E-value: 7.47e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  932 LPFKANVNEILDFFHGYRiiPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKdlNDRP-VGPRKVKLTL 1000
Cdd:cd12506     8 LPYRATENDIFEFFSPLN--PVNVRIRYNKDGRATGEADVEFATHEDAVAAMS--KDREnMGHRYIELFL 73

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: 47.23 E-value: 8.69e-07

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349   402 IYIRNFPFDVTKVEVQKFFADFLLAEdDIYLLYDDKGVGLGEALVKFKSEEQAMKA-ERLNRRRFLGTEVL 471
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIK-SIRLVRDETGRSKGFAFVEFEDEEDAEKAiEALNGKELGGRELK 70

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM1 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical. Both of them have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

Pssm-ID: 410128 [Multi-domain] Cd Length: 79 Bit Score: 47.08 E-value: 1.22e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  159 LRGLPYLVNEDDVRVFFSGlC-----VDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQ 227
Cdd:cd12729     6 VRGLPWSCSADEVQNFFSD-CkiangASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFK 78

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: 47.23 E-value: 1.73e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSK 76
Cdd:cd12732    20 TVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTmdyqGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFKSSR 96

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: 45.48 E-value: 4.27e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  157 LFLRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSR 221
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDHGVrpEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.

Pssm-ID: 409834 [Multi-domain] Cd Length: 74 Bit Score: 45.29 E-value: 4.40e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  290 NLSLSIDERDLRNFFRGTDLTDeQIRFLY-KDENRTR-YAFVMFKTLKDYNTALSLHKTVLQYRPVHI 355
Cdd:cd12400     7 NLPYDTTAEDLKEHFKKAGEPP-SVRLLTdKKTGKSKgCAFVEFDNQKALQKALKLHHTSLGGRKINV 73

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: 45.77 E-value: 5.44e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRpVGPRKVKL 998
Cdd:cd12731    11 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER-IGHRYIEI 81

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: 6.34e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRR 464
Cdd:cd12504     2 VVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEK 65

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: 45.00 E-value: 7.24e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTIPDggVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12735     3 VHMRGLPFRATESDIANFFSPLNPIR--VHIDigadGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75

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: 44.74 E-value: 1.04e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADflLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMkaERLNR-RRFLGTE-VLLRLISEAQ 479
Cdd:cd12746     5 LFLRGMPYSATEDDVRNFFSG--LKVDGVIFLKHPNGRNNGNGLVKFATKEDAS--EGLKRhRQYMGSRfIEVTRTTEEQ 80


                  ....*
gi 118722349  480 IQEFG 484
Cdd:cd12746    81 WIEAG 85

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: 44.62 E-value: 1.22e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRR 464
Cdd:cd12731    11 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER 73

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 49.03 E-value: 1.37e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   273 PRRTRSRSPLGFY--VHLKNLSLSIDERDLRNFF-RGTDLTDEQIRflyKDE-NRTR-YAFVMFKTLKDYNTAL-SLHKT 346
Cdd:TIGR01628  166 KKHEREAAPLKKFtnLYVKNLDPSVNEDKLRELFaKFGEITSAAVM---KDGsGRSRgFAFVNFEKHEDAAKAVeEMNGK 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   347 vlqyrpvHIDPISRKQMLkFIARYEKK--RSGSLERDRpghvsQKYSQEG-NSGQKLCIYIRNFPFDVTKVEVQKFFADF 423
Cdd:TIGR01628  243 -------KIGLAKEGKKL-YVGRAQKRaeREAELRRKF-----EELQQERkMKAQGVNLYVKNLDDTVTDEKLRELFSEC 309

                          170       180       190
                   ....*....|....*....|....*....|....
gi 118722349   424 LLAEDdIYLLYDDKGVGLGEALVKFKSEEQAMKA 457
Cdd:TIGR01628  310 GEITS-AKVMLDEKGVSRGFGFVCFSNPEEANRA 342

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: 45.04 E-value: 1.45e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    3 VVIRLLGLPFIAGPVDIRHFF------TG-------LTIPDGGvhiiggEIGEAFIIFATDEDARRAISRSGGFIKDSSV 69
Cdd:cd12739    17 VIVRMRGLPFTATAEEVLAFFgqhcpvTGgkegilfVTYPDSR------PTGDAFVLFACEEYAQNALKKHKDLLGKRYI 90

                          90
                  ....*....|....
gi 118722349   70 ELFLSSKAEMQKTI 83
Cdd:cd12739    91 ELFRSTAAEVQQVL 104

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: 43.55 E-value: 1.65e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKdLNDRPVGPRKV 996
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLK-LNGKKLGKREA 70

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: 44.45 E-value: 1.75e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  157 LFLRGLPYLVNEDDVRVFFSGL-CVDGVIFLKH-HDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12512    12 VYLKGLPYEAENKHVIEFFKKLdIVEDSIYIAYgPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 43.74 E-value: 1.76e-05

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349    286 VHLKNLSLSIDERDLRNFFRGT-DLTDEQIRFLYKDENRTRYAFVMFKTLKDYNTALS-LHKTVLQYRPVHI 355
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73

Extensin-like region;

Pssm-ID: 252669 [Multi-domain] Cd Length: 57 Bit Score: 43.22 E-value: 1.76e-05

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349   734 PPPEHFRRPPPEHFRRPPPEHfrrPPPEHFRRPPPEHFRRPPpehfrrPPQEHFRRPP 791
Cdd:pfam04554    7 PPPVKQYSPPPPYYYKSPPPP---VKSPVYKSPPPPVYKSPP------PPKYVYKSPP 55

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: 43.67 E-value: 1.78e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  286 VHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKDENRTRYAFVMFKTLKDYNTALSLHKTVLQYRPVHIDP 357
Cdd:cd12505     4 VRLRGLPYSCTEADIAHFFSGLDIVDITFVMDLRGGRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFP 75

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: 43.64 E-value: 1.84e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHI----IGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELF 72
Cdd:cd12507     1 VVRARGLPWQSSDQDIAQFFRGLNIAKGGVALclsaQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVY 73

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: 43.46 E-value: 1.91e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  156 YLFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12735     2 FVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75

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: 43.56 E-value: 1.98e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAEM 79
Cdd:cd12513     3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLhdkyGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISRKAM 81

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: 43.60 E-value: 2.01e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  156 YLFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12733     2 FVHMRGLPFQANGQDIINFFAPLKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75

RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM3 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

Pssm-ID: 241187 [Multi-domain] Cd Length: 85 Bit Score: 43.73 E-value: 2.44e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  927 IKIMNLPFKANVNEILDFF--HGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDR 989
Cdd:cd12743     4 IRLRGLPYEAQVEHILEFLgdFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNR 68

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409825 [Multi-domain] Cd Length: 72 Bit Score: 42.98 E-value: 2.73e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  286 VHLKNLSLSIDERDLRNFFRGTDlTDEQIRFLYKDENRTR-YAFVMFKTLKDYNTALSLHKTVLQYRPVHID 356
Cdd:cd12391     2 VFVSNLDYSVPEDKIREIFSGCG-EITDVRLVKNYKGKSKgYCYVEFKDEESAQKALKLDRQPVEGRPMFVS 72

Extensin-like region;

Pssm-ID: 252669 [Multi-domain] Cd Length: 57 Bit Score: 42.45 E-value: 3.36e-05

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 118722349   726 PPQEHFRRPPPEHFRRPPP----EHFRRPPPEHFRRPPpehfrrPPPEHFRRPPP 776
Cdd:pfam04554    8 PPVKQYSPPPPYYYKSPPPpvksPVYKSPPPPVYKSPP------PPKYVYKSPPP 56

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: 43.30 E-value: 4.38e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  398 QKLCIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQaMKAERLNRRRFLG 467
Cdd:cd12512     8 KGFCVYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEID-YKAALCRHKQYMG 76

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: 42.60 E-value: 7.30e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRpVGPRKVKL 998
Cdd:cd12732    21 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKER-IGHRYIEI 91

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: 42.21 E-value: 7.49e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  284 FYVHLKNLSLSIDERDLRNFFRgtDLTDEQIRfLYKDENRTR---YAFVMFKTLKDYNTALSLHKTVLQYRPVHID 356
Cdd:cd12402     3 YTAYLGNLPYDVTEDDIEDFFR--GLNISSVR-LPRENGPGRlrgFGYVEFEDRESLIQALSLNEESLKNRRIRVD 75

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 41.81 E-value: 7.80e-05

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349    927 IKIMNLPFKANVNEILDFFHGY------RIIPDSVSiqyneqGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKL 998
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFgkvesvRLVRDKET------GKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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: 41.67 E-value: 7.99e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  927 IKIMNLPFKANVNEILDFFhgYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAI 983
Cdd:cd12733     3 VHMRGLPFQANGQDIINFF--APLKPVRITMEYGPDGKATGEADVHFASHEDAVAAM 57

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: 41.86 E-value: 8.29e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  286 VHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKDENRTR----YAFVMFKTLKDYNTALSLHKTVLQYRPVHI 355
Cdd:cd12298     3 IRVRNLDFELDEEALRGIFEKFGEIESINIPKKQKNRKGRhnngFAFVTFEDADSAESALQLNGTLLDNRKISV 76

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: 8.87e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 118722349  157 LFLRGLPYLVNEDDVRVFFSGLC-VDGVIFLKHHDGRNNGDAIVKFASCVDA 207
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGeVVSVRIVRDRDGKSKGFAFVEFESPEDA 52

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: 41.62 E-value: 9.89e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  156 YLFLRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLKC-HRSFMGSrfiEVM 226
Cdd:cd12748     2 CIYVRNLPFDVTKVEVQDFFEGFALaeDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLnGQRFLGT---EVL 72

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 46.07 E-value: 1.00e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   249 RSEEHSPPRGINDRHFRK-RSHSKSPRRTRSRSPLGF--------YVHLKNLSLSIDERDLRNFF-RGTDLTDEQIrflY 318
Cdd:TIGR01622   71 RPREKRRRRGDSYRRRRDdRRSRREKPRARDGTPEPLtederdrrTVFVQQLAARARERDLYEFFsKVGKVRDVQI---I 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   319 KDENRTR---YAFVMFKTLKDYNTALSLHKTVLQYRPVHIDPisrkqmlkfiARYEKKRSGSLERDRPGHVSqkysqegN 395
Cdd:TIGR01622  148 KDRNSRRskgVGYVEFYDVDSVQAALALTGQKLLGIPVIVQL----------SEAEKNRAARAATETSGHHP-------N 210

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349   396 SGQKLCIYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA-ERLN 461
Cdd:TIGR01622  211 SIPFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEAlEKMN 277

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: 1.01e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  286 VHLKNLSLSIDERDLRNFFR--GtdlTDEQIRFLYKDENRTR-YAFVMFKTLKDYNTALS-LHKTVLQYRPVHID 356
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSkfG---EVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEaLNGTELGGRPLKVS 72

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM1 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical. Both of them have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

Pssm-ID: 410128 [Multi-domain] Cd Length: 79 Bit Score: 41.30 E-value: 1.24e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDG--GVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLS 74
Cdd:cd12729     3 VVKVRGLPWSCSADEVQNFFSDCKIANGasGIHFIytreGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79

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: 41.66 E-value: 1.27e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  285 YVHLKNLSLSIDERDLRNFFRGTDLtDEQIRFLYKDENRTRYAFVMFKTLKDYNTALSLHKTVLQYRPVHIDPISRKQML 364
Cdd:cd12746     4 YLFLRGMPYSATEDDVRNFFSGLKV-DGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQWI 82


                  ..
gi 118722349  365 KF 366
Cdd:cd12746    83 EA 84

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: 41.57 E-value: 1.28e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADF---LLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNR 462
Cdd:cd12508     4 VRMRGLPFSATAADILAFFGGEcpvTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHK 67

Spumavirus gag protein;

Pssm-ID: 460872 [Multi-domain] Cd Length: 614 Bit Score: 45.89 E-value: 1.36e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   620 RRPLEEDWRRPLEEDFRR--SPTEDFRQLPEEDFRQPpEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRPPED 697
Cdd:pfam03276   59 QDEDHEIIPRARHEHIMFalNGHLAELLLAFLAEDLL-AFPDLDGPEANGHFGEGANGHRSEGDPTMAETAPMTMAELAD 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   698 DFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRR-----PPPEHFRRPPPEHFRRPPPE------HFRRPPPEHFRRP 766
Cdd:pfam03276  138 MLNDELEDEINMINEIEIQEIELLALREQEAEALRIglaeiSPGAQGGIPPGASFSGLPSLpaiggiHLPAIPGIHARAP 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   767 PPEHFRR-----PPPEHFRRPPQEHFRRPPQEHFRRSREEDFRHPPDEDFRGPPDEDFRHPPDEDFRS--------PQEE 833
Cdd:pfam03276  218 PGNIARSlgddiMPSLGDAGMPQPRFAFHPGNPFAEAEGHPFAEAEGERPRDIPRAPRIDAPSAPAIPaiqpiappMIPP 297

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 118722349   834 DFRCPSDEDFRQLPEEDLREAPEEDPRLPDNFrpPGEDFRSPP 876
Cdd:pfam03276  298 IGAPIPIPHGASIPGEHIRNPREEPIRLGREA--PAIDGRFAP 338

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; bothe have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

Pssm-ID: 410133 [Multi-domain] Cd Length: 76 Bit Score: 41.18 E-value: 1.50e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEVMQGS 229
Cdd:cd12734     5 MRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNS 75

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: 1.79e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDggVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12506     2 TVHMRGLPYRATENDIFEFFSPLNPVN--VRIRynkdGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 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: 40.95 E-value: 1.93e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA-ERLNRR 463
Cdd:cd12750     3 VKLFNLPFKATVNEILDFFYGYRVIPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAvQDLNDR 65

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 and similar proteins; This subgroup corresponds to the RRM3 of ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410138 [Multi-domain] Cd Length: 81 Bit Score: 40.94 E-value: 2.03e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  927 IKIMNLPFKANVNEILDFF--HGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKL 998
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLgeFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKCHKKTMKDRYVEV 77

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: 40.68 E-value: 3.15e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA-----ERLNRR 463
Cdd:cd12732    21 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENAlgkhkERIGHR 87

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.93 E-value: 3.37e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  678 PPEEDFRRPLQ-GEWRRPPEDDFRRPPEEDFRHSPEEDfrqspqehfRRPPQEHFRRPPPEhfrrPPPEHFRRPPPEHFR 756
Cdd:PHA03247 2841 PPPGPPPPSLPlGGSVAPGGDVRRRPPSRSPAAKPAAP---------ARPPVRRLARPAVS----RSTESFALPPDQPER 2907

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 118722349  757 RPPPEHFRRPPPEHFRRPPPEHFRRPPQEHFRRPP 791
Cdd:PHA03247 2908 PPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPP 2942

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: 40.06 E-value: 3.62e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADFLLAEDD--IYLLYDDKGVGLGEALVKFKSEEQAMKAERLNR 462
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCRIKGGEngIHFTYTREGRPSGEAFIELESEEDVEKALEKHN 64

Spumavirus gag protein;

Pssm-ID: 460872 [Multi-domain] Cd Length: 614 Bit Score: 44.35 E-value: 3.67e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   620 RRPLEEDWRRPLEEdfrRSPTEDFRQLPEEDFRQPPEedLRWLPEEDFRRPPEEDWRRPPEEdfrRPLQGEWRRPPEDDF 699
Cdd:pfam03276  164 REQEAEALRIGLAE---ISPGAQGGIPPGASFSGLPS--LPAIGGIHLPAIPGIHARAPPGN---IARSLGDDIMPSLGD 235

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   700 RRPPEEDFRHSPEEDFRQSPQEHFRRPpQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPehfrrppPEHF 779
Cdd:pfam03276  236 AGMPQPRFAFHPGNPFAEAEGHPFAEA-EGERPRDIPRAPRIDAPSAPAIPAIQPIAPPMIPPIGAPIP-------IPHG 307

                          170       180       190
                   ....*....|....*....|....*....|....
gi 118722349   780 RRPPQEHFRRPPQEHFRRSREE---DFRHPPDED 810
Cdd:pfam03276  308 ASIPGEHIRNPREEPIRLGREApaiDGRFAPAID 341

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

Pssm-ID: 409931 [Multi-domain] Cd Length: 81 Bit Score: 40.15 E-value: 3.92e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLT--IPDGGVHII----GGEIGEAFIIFATDEDARR-AISRSGGFIKDSSVELFLSS 75
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLGEFAkhIAPQGVHMVinaqGRPSGDAFIQMLSAEFARLaAQKRHKHHMGERYIEVFQCS 81

Uncharacterized conserved protein, DUF2345 family [Function unknown];

Pssm-ID: 443395 [Multi-domain] Cd Length: 900 Bit Score: 44.65 E-value: 3.93e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  498 RSQSRERGDHSHLFDSKDPPIYSVGAFENFRHQLEDLRQLDNFKHPQRDFRQPDRHPPEDFRHSSEDFRFPPEDFRHSPE 577
Cdd:COG4253   144 LQAFSRRALDELLALLLLRLRRRRALLRLRLADAALVRSTVEELLSRRHGDEVAFADDRLTERRASAEAASRADAAALRD 223

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  578 DFRRPREEDFRRPSEEDFRRPWEEDFRRPPEDDFR-------HPREEDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEED 650
Cdd:COG4253   224 LRLALRLARRAATAADDAQTTDDARLTADDSAADAgslsgsgGDGGAAGGSLAEATSSLRVPAASVSLARYQRARRAAAA 303

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  651 FRQP-------------PEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRPPEDDF------RRPPEEDFRHSP 711
Cdd:COG4253   304 AAAAdaraggadaaggvGTGGGRRLAAGLAGAAAEEEEAVGAEARARRRRLLRAARAAIRLLaaaalaLLALGRGALAGR 383

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  712 EEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHfrrPPPEHFRRPPPEHFRRPPQEHFRRPP 791
Cdd:COG4253   384 SPAAAAGPGIVGGTDRRARRRATAFVDRAAGPPPRTQRARRPLLPRPRGAG---GPPPRVVSTRAGDTPSADDDDGGRRV 460

                         330
                  ....*....|..
gi 118722349  792 QEHFRRSREEDF 803
Cdd:COG4253   461 VRDDRRVAWVGG 472

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.54 E-value: 4.17e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  692 RRPPEddfrRPPEEDFRHSPEEDFRQSPQEHFRRPPqEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHF 771
Cdd:PHA03247 2864 RRPPS----RSPAAKPAAPARPPVRRLARPAVSRST-ESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR 2938

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  772 RRPPPEHFRRP-----PQEHFRRPPQEHFRRSREE--DFRHPPDEDFRGPP------------------------DEDFR 820
Cdd:PHA03247 2939 PQPPLAPTTDPagagePSGAVPQPWLGALVPGRVAvpRFRVPQPAPSREAPasstppltghslsrvsswasslalHEETD 3018

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  821 HPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPDNFRPPG-EDFRSPPDDFRSHRPFVNFGRP 891
Cdd:PHA03247 3019 PPPVSLKQTLWPPDDTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAhEPDPATPEAGARESPSSQFGPP 3090

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 39.50 E-value: 4.84e-04

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349    157 LFLRGLPYLVNEDDVRVFFS--GLCVDGVIFLKHHDGRNNGDAIVKFASCVDASGGLKC-HRSFMGSRFIEV 225
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSkfGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

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: 39.65 E-value: 5.43e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIV 971
Cdd:cd12504     3 VRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFV 47

RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1; This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 409712 [Multi-domain] Cd Length: 69 Bit Score: 39.06 E-value: 6.53e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349  286 VHLKNLSLSIDERDLRNFFRGT-DLTDEQIRflyKDENRTRYAFVMFKTLKDYNTALSL 343
Cdd:cd12269     1 VEVTNVSPLATERDLHEFFSFSgDIEHIEIQ---REGEQSRIAFVTFKDPYALETAVLL 56

Cornifin (SPRR) family; SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteriztic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high.

Pssm-ID: 280537 [Multi-domain] Cd Length: 135 Bit Score: 40.81 E-value: 6.70e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   711 PEEDFRQSPQE--HFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPQEHFR 788
Cdd:pfam02389   13 PQEPCVPTTKEpcHSKVPEPCNPKVPEPCCPKVPEPCCPKVPEPCCPKVPEPCCPKVPEPCYPKVPEPCSPKVPEPCHPK 92


                   ....*.
gi 118722349   789 RPPQEH 794
Cdd:pfam02389   93 APEPCH 98

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 43.77 E-value: 6.74e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  613 HPREEDWRRPLEEdwrrpLEEDFRRSPTedfrqlpeedfrqPPEEDLRWLPEEDFRRPPEEDWRRPPEEdfrrPLQGEWR 692
Cdd:PHA03247 2530 HPRMLTWIRGLEE-----LASDDAGDPP-------------PPLPPAAPPAAPDRSVPPPRPAPRPSEP----AVTSRAR 2587

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  693 RPPEddfrrPPEEDFRHSPeedfrQSPQEHFRRPPQEHfrrPPPEHFRRPPPehfrrPPPEhfrrPPPEHFRRPPPEHFR 772
Cdd:PHA03247 2588 RPDA-----PPQSARPRAP-----VDDRGDPRGPAPPS---PLPPDTHAPDP-----PPPS----PSPAANEPDPHPPPT 2645

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 118722349  773 RPPPEHFRRPPQEHFRRPPQEHFRRSREEDFRHPP 807
Cdd:PHA03247 2646 VPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPP 2680

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: 38.85 E-value: 7.46e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  157 LFLRGLPYLVNEDDVRVFFSGLCVDGVIFLKHHD--GRNNGDAIVKFASCVDASGGLKCHRSFMGSRFIEV 225
Cdd:cd12271     1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRFPdsGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

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: 38.98 E-value: 8.10e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTI--------PDGGVhiiggeIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12733     3 VHMRGLPFQANGQDIINFFAPLKPvritmeygPDGKA------TGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.59 E-value: 8.83e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  449 KSEEQAMKAERLNRRRFLGTEVLLRLISEAQIQEFGVNFSVMSSEKMQARSQSRERGDHSHLFDSKDPPIYSVGAFENFR 528
Cdd:PTZ00121 1540 KKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAK 1619

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  529 HQLEDLRQldnfkhpqrdfrqpdrhpPEDFRHSSEDFRFPPEDFRHSPEDFRRPREEDFRRPSEEdfRRPWEEDFRRPPE 608
Cdd:PTZ00121 1620 IKAEELKK------------------AEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEE--AKKAEEDKKKAEE 1679

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 118722349  609 DDfrhpREEDWRRPLEEDWRRPLEEdfrRSPTEDFRQLPEEDFRQPPE----EDLRWLPEEDFRRPPEEDWRRPPE 680
Cdd:PTZ00121 1680 AK----KAEEDEKKAAEALKKEAEE---AKKAEELKKKEAEEKKKAEElkkaEEENKIKAEEAKKEAEEDKKKAEE 1748

Predicted ATPase [General function prediction only];

Pssm-ID: 443109 [Multi-domain] Cd Length: 933 Bit Score: 43.08 E-value: 9.70e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  617 EDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEEDFRQPPEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRPPE 696
Cdd:COG3903     1 AAAAAAAAAAAAAAALALLALAAAAAAAAAAAALAAALEALRAALALLLLLLAALALALAALALLLAAAALLLRLLLLLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  697 DDFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPP 776
Cdd:COG3903    81 AARLLARLAAAAAAALARAAAAALALLLRLRLAARRLLLARALAAAALAAAAAAAAAAAAAPAPPPPAPPPPAPLAALAR 160

                         170       180
                  ....*....|....*....|...
gi 118722349  777 EHFRRppqehfRRPPQEHFRRSR 799
Cdd:COG3903   161 RAAAL------AAAARALLSAAR 177

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: 38.83 E-value: 1.15e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAE 78
Cdd:cd12737     1 VIRARGLPWQSSDQDIARFFKGLNIAKGGVALClnaqGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEE 79

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409825 [Multi-domain] Cd Length: 72 Bit Score: 38.36 E-value: 1.26e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADflLAE-DDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNRRRFLG 467
Cdd:cd12391     1 TVFVSNLDYSVPEDKIREIFSG--CGEiTDVRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEG 66

Predicted ATPase [General function prediction only];

Pssm-ID: 443109 [Multi-domain] Cd Length: 933 Bit Score: 42.70 E-value: 1.27e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  615 REEDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEEDFRQPPEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRP 694
Cdd:COG3903     6 AAAAAAAAAALALLALAAAAAAAAAAAALAAALEALRAALALLLLLLAALALALAALALLLAAAALLLRLLLLLLAARLL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  695 PEDDFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRP 774
Cdd:COG3903    86 ARLAAAAAAALARAAAAALALLLRLRLAARRLLLARALAAAALAAAAAAAAAAAAAPAPPPPAPPPPAPLAALARRAAAL 165


                  ....*..
gi 118722349  775 PPEHFRR 781
Cdd:COG3903   166 AAAARAL 172

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: 38.36 E-value: 1.40e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349    3 VVIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAI-SRSGGFIKDSSVELF 72
Cdd:cd12515     1 CVVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRynddGQPTGDARVAFPSPREARRAVrELNNRPLGGRKVKLF 75

Proline-rich protein; This family includes several eukaryotic proline-rich proteins.

Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 40.41 E-value: 1.40e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   638 SPTEDFRQLpEEDFRQPPEEDLRWLPEEDFRRPPeedwrrPPEEDFRRPLQGEWRRPPEDD--FRRPPEEDFRHS----P 711
Cdd:pfam15240   18 SSSEDVSQE-DSPSLISEEEGQSQQGGQGPQGPP------PGGFPPQPPASDDPPGPPPPGgpQQPPPQGGKQKPqgppP 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   712 EEDFRQSPQEHFRRPPQE---HFRRPPPEHFRRPPPEHFRRPP-PEHFRRPPPehfrrPPPEHFRRPPpehfRRPPQ-EH 786
Cdd:pfam15240   91 QGGPRPPPGKPQGPPPQGgnqQQGPPPPGKPQGPPPQGGGPPPqGGNQQGPPP-----PPPGNPQGPP----QRPPQpGN 161


                   ....*.
gi 118722349   787 FRRPPQ 792
Cdd:pfam15240  162 PQGPPQ 167

Proline-rich protein; This family includes several eukaryotic proline-rich proteins.

Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 40.41 E-value: 1.57e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   710 SPEEDFRQSPQEHFRRPPQEHF------R-----RPPPEHFRRPPPE----HFRRPPPEHFRRPPPEHFRRPPP----EH 770
Cdd:pfam15240   33 SEEEGQSQQGGQGPQGPPPGGFppqppaSddppgPPPPGGPQQPPPQggkqKPQGPPPQGGPRPPPGKPQGPPPqggnQQ 112

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 118722349   771 FRRPPPEHFRRPPQEHFRRPPQEHFRRSREEdfrhPPDEDFRGPP 815
Cdd:pfam15240  113 QGPPPPGKPQGPPPQGGGPPPQGGNQQGPPP----PPPGNPQGPP 153

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: 37.97 E-value: 1.59e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  159 LRGLPYLVNEDDVRVFFSGLCV--DGVIFLKHHDGRNNGDAIVKFASCVDASGGLK-CHRSFMGSRFIEV 225
Cdd:cd12515     5 MRNLPFKATIEDILDFFYGYRVipDSVSIRYNDDGQPTGDARVAFPSPREARRAVReLNNRPLGGRKVKL 74

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 42.28 E-value: 1.77e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  654 PPEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEWRRPPEDDFRR--PPEEDFRHSPEEDFRQSPQEHFRRPPQEHF 731
Cdd:PRK07764  599 GPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGvaAPEHHPKHVAVPDASDGGDGWPAKAGGAAP 678

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  732 RRPPPehfrRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHfRRPPQEHFRRPPQEHFRRSREEDfrhPPDEDF 811
Cdd:PRK07764  679 AAPPP----APAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQP-PQAAQGASAPSPAADDPVPLPPE---PDDPPD 750

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 118722349  812 RGPPDEDFRHPPDEDFRSPQEEDFRCPSDEDFRQLPEEDLREAPEEDPRLPD 863
Cdd:PRK07764  751 PAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802

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: 37.75 E-value: 2.12e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIIPDSVSIQ--YNEQGLPTGEAIVAM 973
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCRIKGGENGIHftYTREGRPSGEAFIEL 50

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

Pssm-ID: 409893 [Multi-domain] Cd Length: 82 Bit Score: 38.15 E-value: 2.15e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349  286 VHLKNLSLSIDERDLRNFFRGTDLTDEQIRFLYKDENRTRYAFVMFKTLKDYNTALSLHKTVLQYRPVHIDP 357
Cdd:cd12460     7 IYCTNIDKKVTQDDVKAFFESLCGEVHRLRLLGDYVHSTRIAFVEFVMAESAIAALNCSGALLGSLPIRVSP 78

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

Pssm-ID: 409848 [Multi-domain] Cd Length: 76 Bit Score: 37.53 E-value: 2.30e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  929 IMNLPFKANVNEILDFFHGYRIIPDsVSIQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKV 996
Cdd:cd12414     4 VRNLPFKCTEDDLKKLFSKFGKVLE-VTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPV 70

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: 2.30e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTIPdgGVHI----IGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELF 72
Cdd:cd12747     4 VHLHGMPFSATEADVRDFFHGLRID--AIHMlkdhLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73

Cornifin (SPRR) family; SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteriztic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high.

Pssm-ID: 280537 [Multi-domain] Cd Length: 135 Bit Score: 38.88 E-value: 2.98e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   702 PPEEDFRHSPEEDFRQSPQE--HFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHF 779
Cdd:pfam02389   12 PPQEPCVPTTKEPCHSKVPEpcNPKVPEPCCPKVPEPCCPKVPEPCCPKVPEPCCPKVPEPCYPKVPEPCSPKVPEPCHP 91

                           90
                   ....*....|...
gi 118722349   780 RRPPQEHFRRPPQ 792
Cdd:pfam02389   92 KAPEPCHPKVPEP 104

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: 37.59 E-value: 3.14e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHI----IGGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAE 78
Cdd:cd12738     1 VVRARGLPWQSSDQDIAKFFRGLNIAKGGVALclnpQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATGED 79

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

Pssm-ID: 401645 [Multi-domain] Cd Length: 846 Bit Score: 41.56 E-value: 3.14e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   694 PPEDDFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHfRRPPPEHFRRPPPEHF-- 771
Cdd:pfam09770  221 PPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSI-QPQAQQFHQQPPPVPVqp 299

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 118722349   772 -------RRPPPEHFRRPPQEHFRRPPQ-EHFRRSREEDFRHPP 807
Cdd:pfam09770  300 tqilqnpNRLSAARVGYPQNPQPGVQPApAHQAHRQQGSFGRQA 343

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: 37.87 E-value: 3.15e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 118722349   10 LPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRA 56
Cdd:cd12749     7 IPYNITKKDVLQFLEGIGLDENSVQVLvdnnGQGLGQALVQFKSEDDARKA 57

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: 37.05 E-value: 3.50e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  402 IYIRNFPFDVTKVEVQKFFADflLAEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNR 462
Cdd:cd12733     3 VHMRGLPFQANGQDIINFFAP--LKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDR 61

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: 37.49 E-value: 3.75e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 118722349  162 LPYLVNEDDVRVFFSGLCVD--GVIFLKHHDGRNNGDAIVKFASCVDASGGLKCHRSFMGSR--FIEVMQGSEQQWIE 235
Cdd:cd12749     7 IPYNITKKDVLQFLEGIGLDenSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGRdaFLHLVTLEEMKEIE 84

Predicted ATPase [General function prediction only];

Pssm-ID: 443109 [Multi-domain] Cd Length: 933 Bit Score: 41.16 E-value: 3.90e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  612 RHPREEDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEEDFRQPPEEDLRWLPEEDFRRPPEEDWRRPPEEDFRRPLQGEW 691
Cdd:COG3903     7 AAAAAAAAALALLALAAAAAAAAAAAALAAALEALRAALALLLLLLAALALALAALALLLAAAALLLRLLLLLLAARLLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  692 RRPPEDDFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPehfRRPPPEHFRRPPPEHF 771
Cdd:COG3903    87 RLAAAAAAALARAAAAALALLLRLRLAARRLLLARALAAAALAAAAAAAAAAAAAPAPPPP---APPPPAPLAALARRAA 163


                  ....*
gi 118722349  772 RRPPP 776
Cdd:COG3903   164 ALAAA 168

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.

Pssm-ID: 410186 [Multi-domain] Cd Length: 79 Bit Score: 36.92 E-value: 5.00e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  931 NLPFKANVNEILDFFhgyriipDSVS------IQYNEQGLPTGEAIVAMINYNEAMAAIKDLNDRPVGPRKVKLT 999
Cdd:cd21607     9 NLPLSTAESDLYDLF-------ETIGkvnnaeLKYDETGDPTGSAVVEYENLDDADVCISKLNNYNYGGCDLKIS 76

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: 37.30 E-value: 5.11e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349    4 VIRLLGLPFIAGPVDIRHFFTGLTIPDGGVHII----GGEIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSSKAEM 79
Cdd:cd12736    11 VIRARGLPWQSSDQDIARFFKGLNIAKGGAALClnaqGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKATGEDF 90


                  ..
gi 118722349   80 QK 81
Cdd:cd12736    91 LK 92

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; bothe have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

Pssm-ID: 410133 [Multi-domain] Cd Length: 76 Bit Score: 36.95 E-value: 5.22e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 118722349    5 IRLLGLPFIAGPVDIRHFFTGLTI--------PDGGVhiiggeIGEAFIIFATDEDARRAISRSGGFIKDSSVELFLSS 75
Cdd:cd12734     3 VHMRGLPYRATENDIYNFFSPLNPvrvhieigPDGRV------TGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNS 75

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

Pssm-ID: 401645 [Multi-domain] Cd Length: 846 Bit Score: 40.79 E-value: 5.32e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349   702 PPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRP------PPEHFRRPPPEHFRRPP 775
Cdd:pfam09770  213 QPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPqspqpdPAQPSIQPQAQQFHQQP 292


                   ....*....
gi 118722349   776 PEHFRRPPQ 784
Cdd:pfam09770  293 PPVPVQPTQ 301

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: 36.44 E-value: 6.02e-03

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 118722349   157 LFLRGLPYLVNEDDVRVFFS--GLCVDGVIFLKHHdGRNNGDAIVKFASCVDA 207
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSkfGPIKSIRLVRDET-GRSKGFAFVEFEDEEDA 52

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM1 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical. Both of them have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

Pssm-ID: 410128 [Multi-domain] Cd Length: 79 Bit Score: 36.29 E-value: 7.17e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118722349  404 IRNFPFDVTKVEVQKFFADFLLAED--DIYLLYDDKGVGLGEALVKFKSEEQAMKAERLNR 462
Cdd:cd12729     6 VRGLPWSCSADEVQNFFSDCKIANGasGIHFIYTREGRPSGEAFVELESEEDVKLALKKDR 66

Predicted ATPase [General function prediction only];

Pssm-ID: 443109 [Multi-domain] Cd Length: 933 Bit Score: 40.39 E-value: 7.19e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  604 RRPPEDDFRHPREEDWRRPLEEDWRRPLEEDFRRSPTEDFRQLPEEDFRQPPEEDLRWLPEEDFRRPPEEDWRRPPEEDF 683
Cdd:COG3903     4 AAAAAAAAAAAALALLALAAAAAAAAAAAALAAALEALRAALALLLLLLAALALALAALALLLAAAALLLRLLLLLLAAR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118722349  684 RRPLQGEWRRPPEDDFRRPPEEDFRHSPEEDFRQSPQEHFRRPPQEHFRRPPPEHFRRPPPEHFRRPPPEHFRRPPPEHF 763
Cdd:COG3903    84 LLARLAAAAAAALARAAAAALALLLRLRLAARRLLLARALAAAALAAAAAAAAAAAAAPAPPPPAPPPPAPLAALARRAA 163


                  ....*
gi 118722349  764 RRPPP 768
Cdd:COG3903   164 ALAAA 168

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

Pssm-ID: 409931 [Multi-domain] Cd Length: 81 Bit Score: 36.30 E-value: 9.21e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 118722349  401 CIYIRNFPFDVTKVEVQKFFADF--LLAEDDIYLLYDDKGVGLGEALVKFKSEEQA-MKAERLNR 462
Cdd:cd12509     3 CIRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFArLAAQKRHK 67

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: 36.75 E-value: 9.25e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 118722349  932 LPFKANVNEILDFFHGYRIIPDSVSIQYNEQGLPTGEAIVAMINYNEAMAAI 983
Cdd:cd12512    17 LPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAAL 68

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: 36.26 E-value: 9.61e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 118722349  927 IKIMNLPFKANVNEILDFFHGYRIipDSVSIQYNEQGLPTGEAIVAMINYNEAMAAIKdlNDRP-VGPRKVKLT 999
Cdd:cd12746     5 LFLRGMPYSATEDDVRNFFSGLKV--DGVIFLKHPNGRNNGNGLVKFATKEDASEGLK--RHRQyMGSRFIEVT 74