NCBI Conserved Domain Search

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: 205.16 E-value: 3.43e-66

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  72 MDWVLKRSGPADYDNCSGCMLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKH 151
Cdd:cd12732     1 MDWVLKHNGPTDTENSSDGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 80

                          90
                  ....*....|....*.
gi 1951406064 152 KERIGHRYIEIFKSSR 167
Cdd:cd12732    81 KERIGHRYIEIFKSSR 96

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: 173.66 E-value: 5.04e-54

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  85 DNCSGCMLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFK 164
Cdd:cd12731     4 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK 83


                  ....*..
gi 1951406064 165 SSRNEIK 171
Cdd:cd12731    84 SSRAEVR 90

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: 163.68 E-value: 1.94e-50

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  90 CMLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12504     1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77

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: 162.10 E-value: 8.66e-50

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNS 351
Cdd:cd12735     1 HFVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 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: 144.05 E-value: 6.34e-43

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNS 351
Cdd:cd12506     1 HTVHMRGLPYRATENDIFEFFSPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75

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: 136.05 E-value: 7.38e-40

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNS 351
Cdd:cd12733     1 HFVHMRGLPFQANGQDIINFFAPLKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75

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: 128.62 E-value: 6.47e-37

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNST 352
Cdd:cd12734     1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST 76

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: 116.42 E-value: 3.00e-32

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064   7 GYVVRIRGLPWSCTQEEVASFFS------------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12729     1 GFVVKVRGLPWSCSADEVQNFFSdckiangasgihfiytreGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79

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: 108.42 E-value: 2.28e-29

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIF 163
Cdd:cd12254     2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

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: 103.24 E-value: 2.79e-27

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS------------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12503     1 VVRARGLPWSATAEDVLNFFTdcrikggengihftytreGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77

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: 102.82 E-value: 4.10e-27

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIV---PNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKS 165
Cdd:cd12508     4 VRMRGLPFSATAADILAFFGGECPVtggKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

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: 100.68 E-value: 2.03e-26

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVpnGITLPVDYQG-RSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKS 165
Cdd:cd12505     3 VVRLRGLPYSCTEADIAHFFSGLDIV--DITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 95.32 E-value: 1.65e-24

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLN--PLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDipPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

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: 93.61 E-value: 8.27e-24

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIV--PNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKS 165
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCRIKggENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 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: 91.82 E-value: 7.03e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVP------NGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFK 164
Cdd:cd12741    19 IIRMRGLPYDCTPKQVVEFFCTGDKIPhvldgaEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFR 98


                  .
gi 1951406064 165 S 165
Cdd:cd12741    99 S 99

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: 87.94 E-value: 1.06e-21

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  93 RLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKS 165
Cdd:cd12507     3 RARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75

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: 87.62 E-value: 1.30e-21

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSgldippdgihivydddGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

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: 82.52 E-value: 1.13e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  89 GCMLRLRGLPFGCSKEEIVQFFSGLRIV--PNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKS 165
Cdd:cd12729     1 GFVVKVRGLPWSCSADEVQNFFSDCKIAngASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79

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: 82.02 E-value: 1.62e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFSG----------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12504     2 VVRLRGLPYGCTKEEIAQFFSGleivpngitlpmdrrgRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRS 76

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: 80.34 E-value: 8.13e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12738     1 VVRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKAT 76

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: 79.84 E-value: 1.06e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS------------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFK 66
Cdd:cd12730     2 FIVRARGLPWSCTAEDVLSFFSdcrirngedgihfllnrdGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78

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: 77.40 E-value: 8.25e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPL--NPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12504     1 GVVRLRGLPYGCTKEEIAQFFSGLeiVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIF 74

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: 77.36 E-value: 9.68e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  10 VRIRGLPWSCTQEEVASFFSG----------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKSNRSEM 72
Cdd:cd12731    11 VRLRGLPFGCSKEEIVQFFSGleivpngitlpvdfqgRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEV 89

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: 76.19 E-value: 2.56e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSRNE 169
Cdd:cd12737     1 VIRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEE 79

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: 75.34 E-value: 6.08e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   4 NEEGYVVRIRGLPWSCTQEEVASFFSG----------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12732    15 NSSDGTVRLRGLPFGCSKEEIVQFFSGleivpngitltmdyqgRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFKS 94


                  ..
gi 1951406064  68 NR 69
Cdd:cd12732    95 SR 96

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: 74.67 E-value: 1.06e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12736    11 VIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKAT 86

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: 74.66 E-value: 1.12e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLN--PLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNSTA 353
Cdd:cd12731    10 FVRLRGLPFGCSKEEIVQFFSGLEivPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRA 87

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: 73.61 E-value: 1.70e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064 277 HFVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12502     1 FTVKLRGAPFNVKEKQIREFFSPLKPVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72

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: 73.56 E-value: 1.86e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRivPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12506     3 VHMRGLPYRATENDIFEFFSPLN--PVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75

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: 2.60e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRVHID-----VAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12508     4 VRMRGLPFSATAADILAFFGGECPVTGGKDgilfvTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELF 78

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: 72.51 E-value: 4.42e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  86 NCsgcmLRLRGLPFGCSKEEIVQFFSGL--RIVPNGITLPVDYQGRSTGEAFVQFASKEIAEK-ALGKHKERIGHRYIEI 162
Cdd:cd12509     2 DC----IRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFARLaAQKRHKHHMGERYIEV 77


                  ....
gi 1951406064 163 FKSS 166
Cdd:cd12509    78 FQCS 81

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: 73.54 E-value: 4.49e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNG------ITLPvdyQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFK 164
Cdd:cd12739    18 IVRMRGLPFTATAEEVLAFFGQHCPVTGGkegilfVTYP---DSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFR 94


                  ....*..
gi 1951406064 165 SSRNEIK 171
Cdd:cd12739    95 STAAEVQ 101

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: 72.00 E-value: 6.60e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS-------------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12508     3 IVRMRGLPFSATAADILAFFGgecpvtggkdgilfvtypdGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

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: 73.10 E-value: 6.79e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGIT--LPVDY-QGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSR 167
Cdd:cd12740    18 IIRMRGLPFTATPEDVLGFLGPECPVTGGTEglLFVKYpDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRSTA 97


                  ....
gi 1951406064 168 NEIK 171
Cdd:cd12740    98 AEVQ 101

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: 69.09 E-value: 6.72e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFSG---------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12505     3 VVRLRGLPYSCTEADIAHFFSGldivditfvmdlrggRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 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: 68.57 E-value: 9.46e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLR----VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCRIKGgengIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVF 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: 68.62 E-value: 1.33e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVpnGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSRNE 169
Cdd:cd12746     5 LFLRGMPYSATEDDVRNFFSGLKVD--GVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQ 80

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: 68.17 E-value: 1.34e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS--------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12506     1 HTVHMRGLPYRATENDIFEFFSplnpvnvrirynkdGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELF 72

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: 66.37 E-value: 7.31e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFSG----------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12507     1 VVRARGLPWQSSDQDIAQFFRGlniakggvalclsaqgRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75

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: 65.56 E-value: 1.10e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  94 LRGLPFGCSKEEIVQFFSGLriVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12733     5 MRGLPFQANGQDIINFFAPL--KPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75

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: 65.03 E-value: 2.15e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLriVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12735     3 VHMRGLPFRATESDIANFFSPL--NPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75

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: 64.43 E-value: 3.36e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIV--PNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFK 164
Cdd:cd12730     3 IVRARGLPWSCTAEDVLSFFSDCRIRngEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78

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: 65.46 E-value: 3.47e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   5 EEGYVVRIRGLPWSCTQEEVASFF-------------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12739    14 ENQVIVRMRGLPFTATAEEVLAFFgqhcpvtggkegilfvtypDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELF 93

                          90
                  ....*....|...
gi 1951406064  66 KSNRSEMDWVLKR 78
Cdd:cd12739    94 RSTAAEVQQVLNR 106

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: 64.62 E-value: 6.64e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   5 EEGYVVRIRGLPWSCTQEEVASFF-------------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12740    14 ENQVIIRMRGLPFTATPEDVLGFLgpecpvtggtegllfvkypDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELF 93

                          90
                  ....*....|...
gi 1951406064  66 KSNRSEMDWVLKR 78
Cdd:cd12740    94 RSTAAEVQQVLNR 106

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: 63.31 E-value: 7.78e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRVHID-VAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12505     4 VRLRGLPYSCTEADIAHFFSGLDIVDITFVmDLRGGRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIF 74

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: 63.28 E-value: 8.48e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLR--VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12507     2 VRARGLPWQSSDQDIAQFFRGLNIAKggVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVY 73

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: 63.26 E-value: 1.05e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  10 VRIRGLPWSCTQEEVASFF------------------SGRPSGEAFIELKTAED-FKNALAKDRKYMGHRYIEVFK 66
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLgefakhiapqgvhmvinaQGRPSGDAFIQMLSAEFaRLAAQKRHKHHMGERYIEVFQ 79

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: 63.70 E-value: 1.06e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS----------------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFK 66
Cdd:cd12741    19 IIRMRGLPYDCTPKQVVEFFCtgdkiphvldgaegvlfvkkpdGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFR 98


                  .
gi 1951406064  67 S 67
Cdd:cd12741    99 S 99

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: 62.82 E-value: 1.12e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  93 RLRGLPFGCSKEEIVQFFSGLRivPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIF 163
Cdd:cd12502     4 KLRGAPFNVKEKQIREFFSPLK--PVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72

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: 62.51 E-value: 1.48e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFS--GLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGK-HKERIGHRYIEIFKSS 166
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLGefAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQCS 81

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: 61.80 E-value: 2.92e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIvpNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIF 163
Cdd:cd12511     2 LSLHGMPYSAMENDVRDFFHGLRV--DGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71

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: 61.18 E-value: 3.91e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS--------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12735     1 HFVHMRGLPFRATESDIANFFSplnpirvhidigadGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELF 72

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: 60.92 E-value: 7.86e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIEL 347
Cdd:cd12746     4 YLFLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEV 73

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: 60.31 E-value: 9.43e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064 279 VHMRGLPFRATEGDIAKFFS--PLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMsKDKNH--MQHRYIELF 348
Cdd:cd12515     3 VKMRNLPFKATIEDILDFFYgyRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAV-RELNNrpLGGRKVKLF 75

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

Pssm-ID: 409936 [Multi-domain] Cd Length: 73 Bit Score: 59.35 E-value: 1.69e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSP--LNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKD 336
Cdd:cd12514     1 FIRITNLPYDATPVDIQRFFEDhgVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLN 61

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: 60.25 E-value: 1.77e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  81 PADYDNCsgcmLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYI 160
Cdd:cd12512     5 PHEKGFC----VYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFI 80

                          90       100
                  ....*....|....*....|.
gi 1951406064 161 EIFKSSRNEIKAYYELPRRGM 181
Cdd:cd12512    81 QVHPITKKAMLEKIDMIRKRL 101

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: 59.41 E-value: 2.19e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064 276 GHFVHMRGLPFRATEGDIAKFFSPLNPLR----VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12729     1 GFVVKVRGLPWSCSADEVQNFFSDCKIANgasgIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVF 77

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: 58.58 E-value: 2.92e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS--------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12502     1 FTVKLRGAPFNVKEKQIREFFSplkpvairivknahGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72

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: 59.16 E-value: 2.97e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLR--VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12738     2 VRARGLPWQSSDQDIAKFFRGLNIAKggVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVY 73

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: 58.77 E-value: 3.09e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  90 CMLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGK-HKERIGHRYIEIF 163
Cdd:cd12515     1 CVVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

Pssm-ID: 409936 [Multi-domain] Cd Length: 73 Bit Score: 58.19 E-value: 5.06e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHR 158
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68

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: 57.63 E-value: 6.02e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVpNGITLPVDYQGRSTGEAFVQFASKEIAEKAL-GKHKERIGHRYIE 161
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRDETGRSKGFAFVEFEDEEDAEKAIeALNGKELGGRELK 70

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: 57.89 E-value: 6.60e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  10 VRIRGLPWSCTQEEVASFF------------------SGRPSGEAFIELKTAED-FKNALAKDRKYMGHRYIEVFK 66
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLgefaadirphgvhmvlnhQGRPSGDAFIQMKSADRaFLAAQKCHKKTMKDRYVEVFQ 79

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: 57.88 E-value: 7.28e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIvpNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIF 163
Cdd:cd12747     4 VHLHGMPFSATEADVRDFFHGLRI--DAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73

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: 57.84 E-value: 9.55e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  10 VRIRGLPWSCTQEEVASFFSG--------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKSNrsEMDWV 75
Cdd:cd12746     5 LFLRGMPYSATEDDVRNFFSGlkvdgviflkhpngRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTT--EEQWI 82

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: 57.08 E-value: 1.37e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFF--------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12733     1 HFVHMRGLPFQANGQDIINFFaplkpvritmeygpDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72

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: 57.54 E-value: 1.43e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRVHIDVA--------PNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12741    20 IRMRGLPYDCTPKQVVEFFCTGDKIPHVLDGAegvlfvkkPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELF 97

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: 1.63e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 269 SCSSFHSGHFVHMRGLPFRATEGDIAKFFSPLNPLR--VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIE 346
Cdd:cd12512     2 SRSPHEKGFCVYLKGLPYEAENKHVIEFFKKLDIVEdsIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQ 81


                  .
gi 1951406064 347 L 347
Cdd:cd12512    82 V 82

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: 56.71 E-value: 1.83e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLN----PLRVHIDVAPNGKSTGEADVEFRSHEDAV-AAMSKDKNHMQHRYIELF 348
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLGEFAkhiaPQGVHMVINAQGRPSGDAFIQMLSAEFARlAAQKRHKHHMGERYIEVF 78

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: 55.78 E-value: 3.74e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064   9 VVRIRGLPWSCTQEEVASFF----------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKSNRSE 71
Cdd:cd12737     1 VIRARGLPWQSSDQDIARFFkglniakggvalclnaQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEE 79

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: 6.25e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 265 GQSDSCSSFHSGH---FVHMRGLPFRATEGDIAKFFSPLNPLRVHID-----VAPNGKSTGEADVEFRSHEDAVAAMSKD 336
Cdd:cd12740     2 GTSNEVAQFLSKEnqvIIRMRGLPFTATPEDVLGFLGPECPVTGGTEgllfvKYPDGRPTGDAFVLFACEEYAQNALKKH 81

                          90
                  ....*....|....*..
gi 1951406064 337 KNHMQHRYIELFLNSTA 353
Cdd:cd12740    82 KGILGKRYIELFRSTAA 98

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: 55.05 E-value: 6.83e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRivPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12734     3 VHMRGLPYRATENDIYNFFSPLN--PVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNS 75

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: 55.41 E-value: 8.87e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   1 MSLNEEGYVVRIRGLPWSCTQEEVASFF----------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEV 64
Cdd:cd12736     3 MEIIDDNTVIRARGLPWQSSDQDIARFFkglniakggaalclnaQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEV 82


                  ...
gi 1951406064  65 FKS 67
Cdd:cd12736    83 YKA 85

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: 53.83 E-value: 1.46e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGL-RIVpnGITLPVDYQGRSTGEAFVQFASKEIAEKAL-GKHKERIGHRYIEI 162
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFgEVV--SVRIVRDRDGKSKGFAFVEFESPEDAEKALeALNGTELGGRPLKV 71

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: 53.85 E-value: 1.95e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPN--GKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12737     2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNaqGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVY 73

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: 53.76 E-value: 1.98e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064   9 VVRIRGLPWSCTQEEVASFF----------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVFKS 67
Cdd:cd12738     1 VVRARGLPWQSSDQDIAKFFrglniakggvalclnpQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKA 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: 53.96 E-value: 2.00e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSR 167
Cdd:cd12513     3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISR 78

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: 54.08 E-value: 3.16e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064   2 SLNEEGYVVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12512     4 SPHEKGFCVYLKGLPYEAENKHVIEFFKkldivedsiyiaygpnGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQVH 83


                  ....*..
gi 1951406064  66 KSNRSEM 72
Cdd:cd12512    84 PITKKAM 90

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: 52.97 E-value: 4.18e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKER-IGHRYIEI 162
Cdd:cd12751     3 VIKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAAVVDLNDRpIGSRKVKL 75

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: 52.87 E-value: 4.19e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12747     3 YVHLHGMPFSATEADVRDFFHGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73

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: 53.10 E-value: 4.49e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPN--GKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12736    12 IRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNaqGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVY 83

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 52.60 E-value: 4.55e-09

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  279 VHMRGLPFRATEGDIAKFFSPLNPLrVHIDVAPN---GKSTGEADVEFRSHEDAVAAMSKDKNHM 340
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKV-ESVRLVRDketGKSKGFAFVEFESEEDAEKALEALNGKE 65

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: 52.29 E-value: 6.35e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPL-NPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHM 340
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFgEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTE 63

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: 52.35 E-value: 6.61e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS--------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12734     1 HCVHMRGLPYRATENDIYNFFSplnpvrvhieigpdGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELF 72

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 51.44 E-value: 9.95e-09

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064   92 LRLRGLPFGCSKEEIVQFFSG------LRIVPNGITlpvdyqGRSTGEAFVQFASKEIAEKAL-GKHKERIGHRYIEI 162
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKfgkvesVRLVRDKET------GKSKGFAFVEFESEEDAEKALeALNGKELDGRPLKV 73

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: 52.74 E-value: 1.09e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 265 GQSDSCSSFHSGH---FVHMRGLPFRATEGDIAKFFSPLNPLR-----VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKD 336
Cdd:cd12739     2 GTSNEVAQFLSKEnqvIVRMRGLPFTATAEEVLAFFGQHCPVTggkegILFVTYPDSRPTGDAFVLFACEEYAQNALKKH 81

                          90
                  ....*....|....*..
gi 1951406064 337 KNHMQHRYIELFLNSTA 353
Cdd:cd12739    82 KDLLGKRYIELFRSTAA 98

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: 50.98 E-value: 2.12e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIvPNGitlPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSRNEI 170
Cdd:cd12744     3 VIRLQGLPVVAGSTDIRHFFTGLTI-PDG---GVHIIGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEM 78


                  .
gi 1951406064 171 K 171
Cdd:cd12744    79 Q 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: 50.19 E-value: 3.05e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQF--------ASKEIAEKALGKHKERI 155
Cdd:cd12750     3 VKLFNLPFKATVNEILDFFYGYRVIPDSVSIQYNEQGLPTGDAIIAMetyeeamaAVQDLNDRPIGPRKVKL 74

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: 50.59 E-value: 3.15e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  97 LPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHR 158
Cdd:cd12749     7 IPYNITKKDVLQFLEGIGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGR 68

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: 49.80 E-value: 6.21e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSP----LNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSK-DKNHMQHRYIELF 348
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLGEfaadIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVF 78

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: 49.41 E-value: 7.79e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNpLR-----VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12730     4 VRARGLPWSCTAEDVLSFFSDCR-IRngedgIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVF 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: 48.55 E-value: 1.36e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  94 LRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERI 155
Cdd:cd12748     5 VRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRF 66

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: 47.55 E-value: 3.11e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELF 348
Cdd:cd12511     1 YLSLHGMPYSAMENDVRDFFHGLRVDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71

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: 47.72 E-value: 3.83e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLpvdyQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSSRNEI 170
Cdd:cd12745     4 VIRLQGLPIVAGTMDIRHFFSGLTIPDGGVHI----VGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTEM 79


                  ....*....
gi 1951406064 171 KAYYELPRR 179
Cdd:cd12745    80 QNMIELSRR 88

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: 46.89 E-value: 4.70e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIvPNGitlPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12510     4 IRLQGLPWEAGSLDIRRFFSGLTI-PDG---GVHIIGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 46.82 E-value: 4.76e-07

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064    9 VVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAK-DRKYMGHRYIEV 64
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSkfgkvesvrlvrdketGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

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: 47.19 E-value: 5.07e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFS--GLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEK-ALGKHKERI----GHRYIEIFK 164
Cdd:cd12743     4 IRLRGLPYEAQVEHILEFLGdfAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASAcAQQRHNRYMvfgkKQRYIEVFQ 83


                  ..
gi 1951406064 165 SS 166
Cdd:cd12743    84 CS 85

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: 46.71 E-value: 5.38e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  10 VRIRGLPWSCTQEEVASFFSG--------------RPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12747     4 VHLHGMPFSATEADVRDFFHGlridaihmlkdhlgRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73

RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

Pssm-ID: 409933 [Multi-domain] Cd Length: 73 Bit Score: 46.78 E-value: 5.71e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  10 VRIRGLPWSCTQEEVASFFS--------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEVF 65
Cdd:cd12511     2 LSLHGMPYSAMENDVRDFFHglrvdgvhllkdhvGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71

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: 46.07 E-value: 9.14e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064 281 MRGLPFRATEGDIAKFFSPLNPLrVHIDVAP--NGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRdeTGRSKGFAFVEFEDEEDAEKAIEA 58

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: 44.58 E-value: 2.66e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS------------GRPSGEAFIELKTAEDFKNALAKDRK 55
Cdd:cd12510     3 VIRLQGLPWEAGSLDIRRFFSgltipdggvhiiGGEKGEAFIIFATDEDARLAMMRDGQ 61

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: 43.75 E-value: 5.67e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAK-DRKYMGHRYIEVF 65
Cdd:cd12515     2 VVKMRNLPFKATIEDILDFFYgyrvipdsvsirynddGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75

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: 43.80 E-value: 5.71e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLNPLR--VHIdvapNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNS 351
Cdd:cd12510     3 VIRLQGLPWEAGSLDIRRFFSGLTIPDggVHI----IGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 43.87 E-value: 6.07e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 281 MRGLPFRATEGDIAKFFSPLNPL-RVHIDV-APNGKSTGEADVEFRSHEDAVAAM-SKDKNHMQHRYIEL 347
Cdd:cd12316     4 VRNLPFTATEDELRELFEAFGKIsEVHIPLdKQTKRSKGFAFVLFVIPEDAVKAYqELDGSIFQGRLLHV 73

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.

Pssm-ID: 410081 [Multi-domain] Cd Length: 75 Bit Score: 43.76 E-value: 6.67e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 284 LPFRATEGDIAKFFSPLNPLR---VHIDvaPNGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:cd12680     8 LDFGVSDADIKELFAEFGTLKkaaVHYD--RSGRSLGTAEVVFERRADALKAMKQ 60

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

Pssm-ID: 409849 [Multi-domain] Cd Length: 83 Bit Score: 43.36 E-value: 1.00e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  94 LRGLPFGCSKEEIVQFFSGL------RIVPNGITlpvdyqGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12415     5 IRNLSFDTTEEDLKEFFSKFgevkyaRIVLDKDT------GHSKGTAFVQFKTKESADKCI 59

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: 43.27 E-value: 1.03e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLR--VHIdvapNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIELFLNSTA 353
Cdd:cd12744     4 IRLQGLPVVAGSTDIRHFFTGLTIPDggVHI----IGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKA 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: 42.78 E-value: 1.13e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHR 60
Cdd:cd12514     1 FIRITNLPYDATPVDIQRFFEdhgvrpedvhllrnkkGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68

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: 43.04 E-value: 1.19e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  10 VRIRGLPWSCTQEEVASFFS---------------GRPSGEAFIELKTAEDFKNALAK-DRKYMGHRYIEV 64
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSkfgevvsvrivrdrdGKSKGFAFVEFESPEDAEKALEAlNGTELGGRPLKV 71

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: 42.98 E-value: 1.25e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  97 LPFGCSKEEIVQFFSGLRIVpnGITLPVDY-QGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEI 162
Cdd:cd12402    10 LPYDVTEDDIEDFFRGLNIS--SVRLPRENgPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74

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: 42.31 E-value: 1.72e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  10 VRIRGLPWSCTQEEVASFF----------------SGRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEV 64
Cdd:cd12271     1 VYVGGIPYYSTEAEIRSYFsscgevrsvdlmrfpdSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

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: 42.15 E-value: 2.25e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  94 LRGLPFGCSKEEIVQFFSglrivPNG----ITLPVDYQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12414     4 VRNLPFKCTEDDLKKLFS-----KFGkvleVTIPKKPDGKLRGFAFVQFTNVADAAKAI 57

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

Pssm-ID: 409737 [Multi-domain] Cd Length: 71 Bit Score: 41.87 E-value: 2.61e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLRvHIDVAPNGKSTgEADVEFRSHEDAVAAMSKDK 337
Cdd:cd12296     3 VLVKNLPKSITENKIRQFFKDCGEIR-EVKILESGNGL-VAVIEFETEDEALAALTKDH 59

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: 42.11 E-value: 3.28e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 280 HMRGLPFRATEGDIAKFFS--PLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAA 332
Cdd:cd12749     3 HISNIPYNITKKDVLQFLEgiGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKA 57

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: 41.44 E-value: 3.39e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  97 LPFGCSKEEIVQFFSGLRIVPNgITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHR 158
Cdd:cd12391     7 LDYSVPEDKIREIFSGCGEITD-VRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEGR 67

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: 41.45 E-value: 3.99e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  10 VRIRGLPWSCTQEEVASFFS---------------GRPSGEAFIELKTAEDFKNAL-AKDRKYMGHRYIE 63
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSkfgpiksirlvrdetGRSKGFAFVEFEDEEDAEKAIeALNGKELGGRELK 70

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409982 [Multi-domain] Cd Length: 79 Bit Score: 41.63 E-value: 4.15e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064 281 MRGLPFRATEGDIAKFFSPLNPL-RVH--IDVApNGKSTGEADVEFRSHEDAVAAMSK-DKNHMQHRYI 345
Cdd:cd12566     7 LRNLPYSTKEDDLQKLFSKFGEVsEVHvpIDKK-TKKSKGFAYVLFLDPEDAVQAYNElDGKVFQGRLI 74

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

Pssm-ID: 409847 [Multi-domain] Cd Length: 79 Bit Score: 41.04 E-value: 6.32e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064 278 FVhmRGLPFRATEGDIAKFFSPLNPLRvHIDVAPN---GKSTGEADVEFRSHEDAVAAMSKDKN 338
Cdd:cd12413     3 FV--RNLPYDTTDEQLEELFSDVGPVK-RCFVVKDkgkDKCRGFGYVTFALAEDAQRALEEVKG 63

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409759 [Multi-domain] Cd Length: 76 Bit Score: 40.68 E-value: 6.82e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPLR-VHIDVAPNGKSTGEADVEFRSHEDAVAAMskdkNHMQH 342
Cdd:cd12320     3 LIVKNVPFEATRKEIRELFSPFGQLKsVRLPKKFDGSHRGFAFVEFVTKQEAQNAM----EALKS 63

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

Pssm-ID: 409852 [Multi-domain] Cd Length: 75 Bit Score: 40.64 E-value: 6.85e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLNPL-RVHIDVAPNGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:cd12418     3 VRVSNLHPDVTEEDLRELFGRVGPVkSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQ 60

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.

Pssm-ID: 410003 [Multi-domain] Cd Length: 80 Bit Score: 40.76 E-value: 7.27e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  92 LRLRGL-PFgCSKEEIVQFFSGLRIVPNGITLpVDYQGRSTGEAFVQFASKEIAEKALGK 150
Cdd:cd12590     2 LSVRNLsPY-VSNELLEEAFSQFGPIERAVVI-VDDRGRSTGKGIVEFASKPAARKAFER 59

RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins; This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response.

Pssm-ID: 409886 [Multi-domain] Cd Length: 83 Bit Score: 40.96 E-value: 7.74e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064  90 CMLRLRGLPFGCSKEEIVQFFSGLRIVPNGI-TLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIFKSS 166
Cdd:cd12452     1 KILYMNGLPHDTTQSELESWFTQHGVRPVAFwTLKTPEQIKPSGSGFAVFQSHEEAAESLALNGRALGDRAIEVQPSS 78

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

Pssm-ID: 409847 [Multi-domain] Cd Length: 79 Bit Score: 40.65 E-value: 9.08e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  91 MLRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGK 150
Cdd:cd12413     1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEE 60

RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.

Pssm-ID: 410002 [Multi-domain] Cd Length: 80 Bit Score: 39.98 E-value: 1.40e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLpVDYQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12589     2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVI-VDDRGRPTGKGFVEFAAKPPARKAL 57

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: 39.84 E-value: 1.73e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 282 RGLPFRATEGDIAKFFSPLNP-LRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:cd12414     5 RNLPFKCTEDDLKKLFSKFGKvLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKG 59

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410077 [Multi-domain] Cd Length: 107 Bit Score: 40.49 E-value: 1.78e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 278 FVhmRGLPFRATEGDIAKFFSPLNPL---RVHIDVApNGKSTGEADVEFRSHEDAVAAMS 334
Cdd:cd12676     5 FV--RNLPFDATEDELYSHFSQFGPLkyaRVVKDPA-TGRSKGTAFVKFKNKEDADNCLS 61

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: 39.31 E-value: 2.62e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064 279 VHMRGLPFRATEGDIAKFFS--PLNPLRVHIDVAPNGKSTGEADVEFRSHEDAVAAMSkdKNHMQHRYIELFL 349
Cdd:cd12748     3 IYVRNLPFDVTKVEVQDFFEgfALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAER--LNGQRFLGTEVLL 73

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.

Pssm-ID: 409747 [Multi-domain] Cd Length: 73 Bit Score: 39.21 E-value: 2.64e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  99 FGCSKEEIVQFFSGLRIVpNGITLPVD-YQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12306     9 YGTTPEELQAHFKSCGTI-NRVTILCDkFTGQPKGFAYIEFVDKSSVENAL 58

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409759 [Multi-domain] Cd Length: 76 Bit Score: 39.14 E-value: 3.03e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVpNGITLPVDYQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12320     3 LIVKNVPFEATRKEIRELFSPFGQL-KSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58

RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.

Pssm-ID: 410004 [Multi-domain] Cd Length: 80 Bit Score: 39.13 E-value: 3.19e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLpVDYQGRSTGEAFVQFASKEIAEKALGKHKE 153
Cdd:cd12591     2 LTVKNLPQFVSNELLEEAFSVFGQVERAVVI-VDDRGRPTGKGIVEFSGKPAARKALDRCSD 62

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: 39.13 E-value: 3.21e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1951406064 284 LPFRATEGDIAKFFSPLN--PLRVHIDVAPnGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYI 345
Cdd:cd12402    10 LPYDVTEDDIEDFFRGLNisSVRLPRENGP-GRLRGFGYVEFEDRESLIQALSLNEESLKNRRI 72

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: 39.10 E-value: 3.53e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064  10 VRIRGLPWSCTQEEVASFF------------------SGRPSGEAFIELKTAED-FKNALAKDRKYM----GHRYIEVFK 66
Cdd:cd12743     4 IRLRGLPYEAQVEHILEFLgdfakmivfqgvhmvynaQGQPSGEAFIQMDSEQSaSACAQQRHNRYMvfgkKQRYIEVFQ 83

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410075 [Multi-domain] Cd Length: 80 Bit Score: 38.98 E-value: 3.59e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064 278 FVhmRGLPFRATEGDIAKFFSPLNPLR--VHIDVAPNGKSTGEADVEFRSHEDAVAAMSKDKN 338
Cdd:cd12674     4 FV--RNLPFDVTLESLTDFFSDIGPVKhaVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKN 64

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: 38.65 E-value: 4.45e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFSGR--PSG----------EAFIELKTAEDFKNALAKDRKYMGHRYIEVFKSNRSEM 72
Cdd:cd12744     3 VIRLQGLPVVAGSTDIRHFFTGLtiPDGgvhiiggelgEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEM 78

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410077 [Multi-domain] Cd Length: 107 Bit Score: 39.33 E-value: 5.28e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  89 GCMLRLRGLPFGCSKEEIVQFFSGL------RIVPNGITlpvdyqGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12676     1 GRTLFVRNLPFDATEDELYSHFSQFgplkyaRVVKDPAT------GRSKGTAFVKFKNKEDADNCL 60

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409884 [Multi-domain] Cd Length: 78 Bit Score: 38.15 E-value: 5.78e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVpNGITLPVDYQ-GRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEI 162
Cdd:cd12450     2 LFVGNLSWSATQDDLENFFSDCGEV-VDVRIAMDRDdGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409826 [Multi-domain] Cd Length: 81 Bit Score: 38.08 E-value: 6.44e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  12 IRGLPWSCTQEEVASFF---------------SGRPSGEAFIELKTAEDFKNALAK-DRKYMGHRYIEVFKSN 68
Cdd:cd12392     7 VKGLPFSCTKEELEELFkqhgtvkdvrlvtyrNGKPKGLAYVEYENEADASQAVLKtDGTEIKDHTISVAISN 79

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 38.09 E-value: 6.67e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNgITLPVDYQ-GRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12316     2 LFVRNLPFTATEDELRELFEAFGKISE-VHIPLDKQtKRSKGFAFVLFVIPEDAVKAY 58

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409884 [Multi-domain] Cd Length: 78 Bit Score: 38.15 E-value: 7.39e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064 278 FVhmRGLPFRATEGDIAKFFS---PLNPLRVHIDvAPNGKSTGEADVEFRSHEDAVAAMSKDKNHMQHRYIEL 347
Cdd:cd12450     3 FV--GNLSWSATQDDLENFFSdcgEVVDVRIAMD-RDDGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

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: 37.69 E-value: 8.46e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064 278 FVHMRGLPFRATEGDIAKFFSPLNPL-RVHIDVAPNGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:cd21607     4 TIYCSNLPLSTAESDLYDLFETIGKVnNAELKYDETGDPTGSAVVEYENLDDADVCISK 62

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: 37.31 E-value: 9.54e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  96 GLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEI 162
Cdd:cd12271     5 GIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

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: 37.20 E-value: 1.10e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064   8 YVVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEV 64
Cdd:cd12400     1 YILFVGNLPYDTTAEDLKEHFKkageppsvrlltdkktGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73

RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

Pssm-ID: 409677 [Multi-domain] Cd Length: 82 Bit Score: 37.53 E-value: 1.27e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064 283 GLPFRATEGDIAKFF-----------SPLNPLrVHIDVAPNGKStgeADVEFRSHEDAVAAMSKD 336
Cdd:cd12230     8 NIPPGITEEELMDFFnqamraagltqAPGNPV-LAVQINPDKNF---AFVEFRSVEETTAALALD 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: 37.20 E-value: 1.27e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  97 LPFGCSKEEIVQFFSGLRIVPNgITLPVDYQ-GRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEI 162
Cdd:cd12400     8 LPYDTTAEDLKEHFKKAGEPPS-VRLLTDKKtGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409884 [Multi-domain] Cd Length: 78 Bit Score: 37.38 E-value: 1.33e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064   9 VVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAKDRKYMGHRYIEV 64
Cdd:cd12450     1 TLFVGNLSWSATQDDLENFFSdcgevvdvriamdrddGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

Pssm-ID: 409838 [Multi-domain] Cd Length: 77 Bit Score: 37.02 E-value: 1.43e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064  90 CMLRLRGLPFGCSKEEIVQFFsglrivPNG--ITLPVDYQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12404     4 RTLFVKNLPYSTTQDELKEVF------EDAvdIRIPMGRDGRSKGIAYIEFKSEAEAEKAL 58

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.

Pssm-ID: 409957 [Multi-domain] Cd Length: 77 Bit Score: 36.86 E-value: 1.64e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  89 GCMLRLRGLPFGCSKEEIVQFFSglrivPNGITLPVDYQgRSTGEAFVQFASKEIAEKALGKHKERI 155
Cdd:cd12541     1 GCILHFSGVGEQTSREDLKEAFE-----KHGEVAWIDFA-RGQTEGYVRFKEEDAAKEALEKAKEAK 61

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.

Pssm-ID: 409711 [Multi-domain] Cd Length: 78 Bit Score: 37.02 E-value: 1.68e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064 279 VHMRGLPFRATEGDIAKFF-SPLNPL-RVHIDVAPNGKSTGEADVEFRSHEDAVAAMSK 335
Cdd:cd12267     3 VIVSNLPKDVTEAQIREYFvSQIGPIkRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 61

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.

Pssm-ID: 409833 [Multi-domain] Cd Length: 75 Bit Score: 36.73 E-value: 2.17e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064  15 LPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALAK-DRKYMGHRYIEV 64
Cdd:cd12399     6 LPYSASEEQLKSLFGqfgavfdvklpmdretKRPRGFGFVELQEEESAEKAIAKlDGTDFMGRTIRV 72

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410075 [Multi-domain] Cd Length: 80 Bit Score: 36.67 E-value: 2.62e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLPVDYQGRSTGEAFVQFASKEIAEKALGKHKERI--GHR 158
Cdd:cd12674     3 LFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKlsGHI 71

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.

Pssm-ID: 409829 [Multi-domain] Cd Length: 73 Bit Score: 36.32 E-value: 2.80e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1951406064  97 LPFGCSKEEIVQFFS------GLRIVPNGITlpvdyqGRSTGEAFVQFASKEIAEKALGKHKERIGHRYIEIF 163
Cdd:cd12395     7 LPFDIEEEELRKHFEdcgdveAVRIVRDRET------GIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410077 [Multi-domain] Cd Length: 107 Bit Score: 37.02 E-value: 2.97e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1951406064   7 GYVVRIRGLPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALA 51
Cdd:cd12676     1 GRTLFVRNLPFDATEDELYSHFSqfgplkyarvvkdpatGRSKGTAFVKFKNKEDADNCLS 61

RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.

Pssm-ID: 409770 [Multi-domain] Cd Length: 80 Bit Score: 36.14 E-value: 3.03e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1951406064  92 LRLRGLPFGCSKEEIVQFFSGLRIVPNGITLpVDYQGRSTGEAFVQFASKEIAEKALGKHKE 153
Cdd:cd12333     2 LRVKNLSPYVSNELLEQAFSQFGDVERAVVI-VDDRGRSTGEGIVEFSRKPGAQAALKRCSE 62

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.

Pssm-ID: 409720 [Multi-domain] Cd Length: 84 Bit Score: 36.02 E-value: 3.90e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1951406064 115 IVPNGITLPVDYQGRSTGEAFVQFASKEIAEKAL 148
Cdd:cd12278    34 GKIVGIYMPVDETGKTKGFAFVEYATPEEAKKAV 67

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: 35.94 E-value: 3.94e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1951406064 279 VHMRGLPFRATEGDIAKFFSPLN--PLRVHIDVAPNGKSTGEADVEFRSHEDAVAAM 333
Cdd:cd12750     3 VKLFNLPFKATVNEILDFFYGYRviPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAV 59

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409826 [Multi-domain] Cd Length: 81 Bit Score: 35.77 E-value: 4.91e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1951406064 278 FVhmRGLPFRATEGDIAKFFSPLNPLR-VHIDVAPNGKSTGEADVEFRSHEDAVAAMSK-DKNHMQHRYI 345
Cdd:cd12392     6 FV--KGLPFSCTKEELEELFKQHGTVKdVRLVTYRNGKPKGLAYVEYENEADASQAVLKtDGTEIKDHTI 73

RNA recognition motif 1 (RRM1) 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 first RRM motif.

Pssm-ID: 410184 [Multi-domain] Cd Length: 77 Bit Score: 35.35 E-value: 5.59e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  97 LPFGCSKEEIVQFFSGL-RIVPNGItlpVDYQGRSTGEAFVQFASKEIAEKALGK 150
Cdd:cd21605     9 LPFDCTWEDLKDHFSQVgEVIRADI---VTSRGRHRGMGTVEFTNKEDVDRAISK 60

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.

Pssm-ID: 409720 [Multi-domain] Cd Length: 84 Bit Score: 35.25 E-value: 7.22e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064 293 IAKFFSPLNPLRV---HIDVAPNGKSTGEADVEFRSHEDAVAAMSK------DKNH 339
Cdd:cd12278    24 LTKIFSKFGSGKIvgiYMPVDETGKTKGFAFVEYATPEEAKKAVKAlngyklDKKH 79

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

Pssm-ID: 409882 [Multi-domain] Cd Length: 73 Bit Score: 35.08 E-value: 8.10e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1951406064  15 LPWSCTQEEVASFFS----------------GRPSGEAFIELKTAEDFKNALakdrKYMGHRYIE 63
Cdd:cd12448     6 LPFSATQDALYEAFSqhgsivsvrlptdretGQPKGFGYVDFSTIDSAEAAI----DALGGEYID 66

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

Pssm-ID: 409882 [Multi-domain] Cd Length: 73 Bit Score: 34.69 E-value: 8.34e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1951406064  97 LPFGCSKEEIVQFFSGLRIVpNGITLPVDYQ-GRSTGEAFVQFASKEIAEKALgkhkERIGHRYIE 161
Cdd:cd12448     6 LPFSATQDALYEAFSQHGSI-VSVRLPTDREtGQPKGFGYVDFSTIDSAEAAI----DALGGEYID 66

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

Pssm-ID: 440488 [Multi-domain] Cd Length: 85 Bit Score: 35.07 E-value: 8.83e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1951406064  95 RGLPFGCSKEEIVQFFSG------LRIVPNGITlpvdyqGRSTGEAFVQFASKEIAEKA 147
Cdd:COG0724     7 GNLPYSVTEEDLRELFSEygevtsVKLITDRET------GRSRGFGFVEMPDDEEAQAA 59