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Conserved domains on  [gi|1567544023|ref|XP_011960563|]
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heterogeneous nuclear ribonucleoprotein H3 isoform X1 [Ovis aries]

Protein Classification

RNA-binding protein( domain architecture ID 10190819)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
42-134 1.19e-67

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: 208.62  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  42 MDWVMKHNGPNDA---SDGTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 118
Cdd:cd12732     1 MDWVLKHNGPTDTensSDGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 80
                          90
                  ....*....|....*.
gi 1567544023 119 KERIGHRYIEIFRSSR 134
Cdd:cd12732    81 KERIGHRYIEIFKSSR 96
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
236-310 1.74e-53

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: 171.73  E-value: 1.74e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12735     1 HFVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
 
Name Accession Description Interval E-value
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
42-134 1.19e-67

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: 208.62  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  42 MDWVMKHNGPNDA---SDGTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 118
Cdd:cd12732     1 MDWVLKHNGPTDTensSDGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 80
                          90
                  ....*....|....*.
gi 1567544023 119 KERIGHRYIEIFRSSR 134
Cdd:cd12732    81 KERIGHRYIEIFKSSR 96
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
236-310 1.74e-53

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: 171.73  E-value: 1.74e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12735     1 HFVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
59-128 9.64e-10

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: 54.55  E-value: 9.64e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVpNGITLTMDYQGRSTGEAFVQFASKEIAENAL-GKHKERIGHRYIE 128
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRDETGRSKGFAFVEFEDEEDAEKAIeALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
58-129 2.16e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 2.16e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023   58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENAL-GKHKERIGHRYIEI 129
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALeALNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
238-294 2.24e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 2.24e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023  238 VHMRGLPFRATENDIANFFSPLNPI-RVHIDIGAD-GRATGEADVEFVTHEDAVAAMSK 294
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRLVRDKEtGKSKGFAFVEFESEEDAEKALEA 60
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
240-305 3.11e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 47.23  E-value: 3.11e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 240 MRGLPFRATENDIANFFSPLNPIrVHIDI--GADGRATGEADVEFVTHEDAVAAmskdKNNMQHRYIE 305
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPI-KSIRLvrDETGRSKGFAFVEFEDEEDAEKA----IEALNGKELG 65
 
Name Accession Description Interval E-value
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
42-134 1.19e-67

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: 208.62  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  42 MDWVMKHNGPNDA---SDGTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 118
Cdd:cd12732     1 MDWVLKHNGPTDTensSDGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 80
                          90
                  ....*....|....*.
gi 1567544023 119 KERIGHRYIEIFRSSR 134
Cdd:cd12732    81 KERIGHRYIEIFKSSR 96
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
49-138 1.00e-55

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: 177.90  E-value: 1.00e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  49 NGPNDASDGTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIE 128
Cdd:cd12731     1 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 80
                          90
                  ....*....|
gi 1567544023 129 IFRSSRSEIK 138
Cdd:cd12731    81 IFKSSRAEVR 90
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
236-310 1.74e-53

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: 171.73  E-value: 1.74e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12735     1 HFVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
57-133 1.27e-52

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: 169.46  E-value: 1.27e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023  57 GTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12504     1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
236-310 6.65e-48

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: 157.15  E-value: 6.65e-48
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12506     1 HTVHMRGLPYRATENDIFEFFSPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
236-311 2.39e-42

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: 142.88  E-value: 2.39e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNST 311
Cdd:cd12734     1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST 76
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
236-310 3.25e-41

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: 139.90  E-value: 3.25e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12733     1 HFVHMRGLPFQANGQDIINFFAPLKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
58-130 1.58e-29

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: 108.80  E-value: 1.58e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 130
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
56-132 1.75e-29

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: 109.15  E-value: 1.75e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  56 DGTVRLRGLPFGCSKEEIVQFFQGLEIVpnGITLTMDYQG-RSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12505     1 DGVVRLRGLPYSCTEADIAHFFSGLDIV--DITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
56-132 1.75e-29

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: 108.98  E-value: 1.75e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  56 DGTVRLRGLPFGCSKEEIVQFFQGLEIV---PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12508     1 QVIVRMRGLPFSATAADILAFFGGECPVtggKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
237-307 9.01e-26

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: 98.79  E-value: 9.01e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLN--PIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDipPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
59-132 1.23e-23

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: 93.22  E-value: 1.23e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIV--PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCRIKggENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
59-132 5.23e-23

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: 92.21  E-value: 5.23e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVP------NGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12741    20 IRMRGLPYDCTPKQVVEFFCTGDKIPhvldgaEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFRS 99
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
59-132 1.76e-22

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: 89.86  E-value: 1.76e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12507     2 VRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
59-132 2.39e-20

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: 84.44  E-value: 2.39e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIV--PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRS 132
Cdd:cd12729     4 VKVRGLPWSCSADEVQNFFSDCKIAngASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
59-136 1.71e-19

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: 81.88  E-value: 1.71e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRSE 136
Cdd:cd12738     2 VRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATGED 79
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
238-307 4.51e-19

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: 80.86  E-value: 4.51e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRVHID-----IGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12508     4 VRMRGLPFSATAADILAFFGGECPVTGGKDgilfvTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELF 78
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
59-138 7.18e-19

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: 81.25  E-value: 7.18e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFF-QGLEIV--PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRS 135
Cdd:cd12739    19 VRMRGLPFTATAEEVLAFFgQHCPVTggKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRSTAA 98

                  ...
gi 1567544023 136 EIK 138
Cdd:cd12739    99 EVQ 101
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
236-307 7.99e-19

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: 80.09  E-value: 7.99e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGAD--GRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12504     1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDrrGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIF 74
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
59-136 7.28e-18

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: 77.74  E-value: 7.28e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRSE 136
Cdd:cd12737     2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEE 79
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
59-138 3.45e-17

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: 76.56  E-value: 3.45e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFqGLEIVPNGIT---LTMDY-QGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSR 134
Cdd:cd12740    19 IRMRGLPFTATPEDVLGFL-GPECPVTGGTeglLFVKYpDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRSTA 97

                  ....
gi 1567544023 135 SEIK 138
Cdd:cd12740    98 AEVQ 101
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
59-133 4.06e-17

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: 75.82  E-value: 4.06e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12736    12 IRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKAT 86
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
58-133 4.81e-17

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: 75.10  E-value: 4.81e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEivPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12506     2 TVHMRGLPYRATENDIFEFFSPLN--PVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
238-307 4.61e-16

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: 72.42  E-value: 4.61e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNpIR-----VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12503     2 VRARGLPWSATAEDVLNFFTDCR-IKggengIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVF 75
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
236-307 7.63e-16

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: 71.68  E-value: 7.63e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 236 HFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12502     1 FTVKLRGAPFNVKEKQIREFFSPLKPVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
59-133 1.24e-15

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: 71.35  E-value: 1.24e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGL--EIVPNGITLTMDYQGRSTGEAFVQFASKEIA-ENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFArLAAQKRHKHHMGERYIEVFQCS 81
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
237-310 7.74e-15

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: 69.27  E-value: 7.74e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLN--PIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12731    10 FVRLRGLPFGCSKEEIVQFFSGLEivPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 85
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
59-133 1.58e-14

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: 67.87  E-value: 1.58e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLeiVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12733     3 VHMRGLPFQANGQDIINFFAPL--KPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
58-130 3.44e-14

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: 67.06  E-value: 3.44e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEivPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 130
Cdd:cd12502     2 TVKLRGAPFNVKEKQIREFFSPLK--PVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
59-136 4.22e-14

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: 67.08  E-value: 4.22e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVpnGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRSE 136
Cdd:cd12746     5 LFLRGMPYSATEDDVRNFFSGLKVD--GVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQ 80
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
59-133 9.14e-14

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: 65.80  E-value: 9.14e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEivPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12735     3 VHMRGLPFRATESDIANFFSPLN--PIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
238-307 1.09e-13

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: 65.62  E-value: 1.09e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRVHIDIGADG-RATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12505     4 VRLRGLPYSCTEADIAHFFSGLDIVDITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIF 74
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
59-133 1.71e-13

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: 65.21  E-value: 1.71e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFF--QGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGK-HKERIGHRYIEIFRSS 133
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLgeFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQCS 81
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
235-307 2.49e-13

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: 64.80  E-value: 2.49e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023 235 GHFVHMRGLPFRATENDIANFFSPLNPIR----VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12729     1 GFVVKVRGLPWSCSADEVQNFFSDCKIANgasgIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVF 77
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
238-307 2.69e-13

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: 64.55  E-value: 2.69e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023 238 VHMRGLPFRATENDIANFFS--PLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMsKDKNN--MQHRYIELF 307
Cdd:cd12515     3 VKMRNLPFKATIEDILDFFYgyRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAV-RELNNrpLGGRKVKLF 75
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
59-130 1.84e-12

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: 62.51  E-value: 1.84e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIV--PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 130
Cdd:cd12730     4 VRARGLPWSCTAEDVLSFFSDCRIRngEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVF 77
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
59-129 3.29e-12

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: 62.17  E-value: 3.29e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12512    12 VYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
238-307 5.89e-12

RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.


Pssm-ID: 410137 [Multi-domain]  Cd Length: 99  Bit Score: 61.39  E-value: 5.89e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIrVHIDIGA---------DGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12741    20 IRMRGLPYDCTPKQVVEFFCTGDKI-PHVLDGAegvlfvkkpDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELF 97
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
238-307 8.35e-12

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: 60.20  E-value: 8.35e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR--VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12507     2 VRARGLPWQSSDQDIAQFFRGLNIAKggVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVY 73
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
238-307 8.80e-12

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: 60.57  E-value: 8.80e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLN----PIRVHIDIGADGRATGEADVEFVTHEDAV-AAMSKDKNNMQHRYIELF 307
Cdd:cd12509     4 IRLRGLPYSATVEDILNFLGEFAkhiaPQGVHMVINAQGRPSGDAFIQMLSAEFARlAAQKRHKHHMGERYIEVF 78
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
59-130 1.47e-11

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: 59.49  E-value: 1.47e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIvpNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 130
Cdd:cd12511     2 LSLHGMPYSAMENDVRDFFHGLRV--DGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
237-306 2.57e-11

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: 59.38  E-value: 2.57e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIEL 306
Cdd:cd12746     4 YLFLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEV 73
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
56-130 6.16e-11

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: 6.16e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  56 DGTVRLRGLPFGCSKEEIVQFFQGLEIvpNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 130
Cdd:cd12747     1 DLYVHLHGMPFSATEADVRDFFHGLRI--DAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
59-134 1.08e-10

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: 57.42  E-value: 1.08e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSR 134
Cdd:cd12513     3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISR 78
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
58-130 1.63e-10

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: 56.85  E-value: 1.63e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGK-HKERIGHRYIEIF 130
Cdd:cd12515     2 VVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
238-307 2.18e-10

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: 56.55  E-value: 2.18e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR--VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12737     2 IRARGLPWQSSDQDIARFFKGLNIAKggVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVY 73
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
59-125 2.52e-10

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: 56.27  E-value: 2.52e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHR 125
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
238-307 7.67e-10

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: 55.76  E-value: 7.67e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRVHID-----IGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12740    19 IRMRGLPFTATPEDVLGFLGPECPVTGGTEgllfvKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELF 93
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
59-128 9.64e-10

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: 54.55  E-value: 9.64e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVpNGITLTMDYQGRSTGEAFVQFASKEIAENAL-GKHKERIGHRYIE 128
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRDETGRSKGFAFVEFEDEEDAEKAIeALNGKELGGRELK 70
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
59-133 1.17e-09

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: 54.28  E-value: 1.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEivPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12734     3 VHMRGLPYRATENDIYNFFSPLN--PVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNS 75
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
238-307 1.30e-09

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: 54.64  E-value: 1.30e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR--VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12736    12 IRARGLPWQSSDQDIARFFKGLNIAKggAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVY 83
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
235-306 1.39e-09

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: 54.85  E-value: 1.39e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023 235 GHFVHMRGLPFRATENDIANFFSPLNPIR--VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIEL 306
Cdd:cd12512     9 GFCVYLKGLPYEAENKHVIEFFKKLDIVEdsIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
238-307 2.78e-09

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: 53.38  E-value: 2.78e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR--VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12738     2 VRARGLPWQSSDQDIAKFFRGLNIAKggVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVY 73
RRM5_RBM12 cd12751
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
59-129 2.91e-09

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: 53.35  E-value: 2.91e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKER-IGHRYIEI 129
Cdd:cd12751     4 IKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAAVVDLNDRpIGSRKVKL 75
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
237-307 3.51e-09

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: 3.51e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12747     3 YVHLHGMPFSATEADVRDFFHGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
237-307 7.54e-09

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: 51.78  E-value: 7.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12511     1 YLSLHGMPYSAMENDVRDFFHGLRVDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
59-129 8.36e-09

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: 51.90  E-value: 8.36e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGL-EIVpnGITLTMDYQGRSTGEAFVQFASKEIAENAL-GKHKERIGHRYIEI 129
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFgEVV--SVRIVRDRDGKSKGFAFVEFESPEDAEKALeALNGTELGGRPLKV 71
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
238-307 1.08e-08

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


Pssm-ID: 410129 [Multi-domain]  Cd Length: 79  Bit Score: 51.72  E-value: 1.08e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNpIR-----VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12730     4 VRARGLPWSCTAEDVLSFFSDCR-IRngedgIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVF 77
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
238-307 1.51e-08

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: 52.36  E-value: 1.51e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR-----VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12739    19 VRMRGLPFTATAEEVLAFFGQHCPVTggkegILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELF 93
RRM smart00360
RNA recognition motif;
58-129 2.16e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 2.16e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023   58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENAL-GKHKERIGHRYIEI 129
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALeALNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
238-294 2.24e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 2.24e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023  238 VHMRGLPFRATENDIANFFSPLNPI-RVHIDIGAD-GRATGEADVEFVTHEDAVAAMSK 294
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRLVRDKEtGKSKGFAFVEFESEEDAEKALEA 60
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
59-138 4.38e-08

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: 49.82  E-value: 4.38e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTmdyqGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRSEIK 138
Cdd:cd12744     4 IRLQGLPVVAGSTDIRHFFTGLTIPDGGVHII----GGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEMQ 79
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
237-295 4.48e-08

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: 49.72  E-value: 4.48e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 237 FVHMRGLPFRATENDIANFFSP--LNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKD 295
Cdd:cd12514     1 FIRITNLPYDATPVDIQRFFEDhgVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLN 61
RRM5_RBM12B cd12750
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
59-129 6.10e-08

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: 49.42  E-value: 6.10e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKER-IGHRYIEI 129
Cdd:cd12750     3 VKLFNLPFKATVNEILDFFYGYRVIPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAVQDLNDRpIGPRKVKL 74
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
238-297 6.16e-08

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 49.20  E-value: 6.16e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPI-RVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKN 297
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVvSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNG 61
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
64-125 1.50e-07

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: 48.66  E-value: 1.50e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023  64 LPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHR 125
Cdd:cd12749     7 IPYNITKKDVLQFLEGIGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGR 68
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
59-133 1.87e-07

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: 48.35  E-value: 1.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQ--GLEIVPNGITLTMDYQGRSTGEAFVQFASKEIA-ENALGKHKERI----GHRYIEIFR 131
Cdd:cd12743     4 IRLRGLPYEAQVEHILEFLGdfAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSAsACAQQRHNRYMvfgkKQRYIEVFQ 83

                  ..
gi 1567544023 132 SS 133
Cdd:cd12743    84 CS 85
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
238-307 3.09e-07

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: 47.49  E-value: 3.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSP----LNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSK-DKNNMQHRYIELF 307
Cdd:cd12742     4 IRLRGLPYAATIEDILEFLGEfaadIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVF 78
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
240-305 3.11e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 47.23  E-value: 3.11e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 240 MRGLPFRATENDIANFFSPLNPIrVHIDI--GADGRATGEADVEFVTHEDAVAAmskdKNNMQHRYIE 305
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPI-KSIRLvrDETGRSKGFAFVEFEDEEDAEKA----IEALNGKELG 65
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
238-305 3.61e-07

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: 47.26  E-value: 3.61e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRvHIDIGADGRATgEADVEFVTHEDAVAAMSKDKNNMQHRYIE 305
Cdd:cd12296     3 VLVKNLPKSITENKIRQFFKDCGEIR-EVKILESGNGL-VAVIEFETEDEALAALTKDHKRIGGNEIS 68
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
59-122 5.45e-07

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: 46.62  E-value: 5.45e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERI 122
Cdd:cd12748     3 IYVRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRF 66
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
240-306 9.82e-07

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: 45.80  E-value: 9.82e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023 240 MRGLPFRATENDIANFFSPLNPI-RVHIDIGA-DGRATGEADVEFVTHEDAVAAM-SKDKNNMQHRYIEL 306
Cdd:cd12316     4 VRNLPFTATEDELRELFEAFGKIsEVHIPLDKqTKRSKGFAFVLFVIPEDAVKAYqELDGSIFQGRLLHV 73
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
237-306 1.21e-06

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: 45.85  E-value: 1.21e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 237 FVhmRGLPFRATENDIANFFS---PLNPIRVHIDiGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIEL 306
Cdd:cd12450     3 FV--GNLSWSATQDDLENFFSdcgEVVDVRIAMD-RDDGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
59-133 1.73e-06

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: 45.35  E-value: 1.73e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTmdyqGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12510     4 IRLQGLPWEAGSLDIRRFFSGLTIPDGGVHII----GGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
237-310 2.21e-06

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: 44.96  E-value: 2.21e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLNpIR---VHIdIGADgraTGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12510     3 VIRLQGLPWEAGSLDIRRFFSGLT-IPdggVHI-IGGE---KGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
58-125 4.86e-06

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: 43.76  E-value: 4.86e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGL-EIVPngITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHR 125
Cdd:cd12391     1 TVFVSNLDYSVPEDKIREIFSGCgEITD--VRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEGR 67
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
243-300 5.33e-06

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: 5.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 243 LPFRATENDIANFFSPLNPIR---VHIDigADGRATGEADVEFVTHEDAVAAMsKDKNNMQ 300
Cdd:cd12680     8 LDFGVSDADIKELFAEFGTLKkaaVHYD--RSGRSLGTAEVVFERRADALKAM-KQYNGVP 65
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
243-304 6.02e-06

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: 44.13  E-value: 6.02e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 243 LPFRATENDIANFFSPLNPIRVHIDI-GADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYI 304
Cdd:cd12402    10 LPYDVTEDDIEDFFRGLNISSVRLPReNGPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRI 72
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
238-297 7.30e-06

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: 43.38  E-value: 7.30e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR-VHIDIGADGRATGEADVEFVTHEDAVAAMSKDKN 297
Cdd:cd12320     3 LIVKNVPFEATRKEIRELFSPFGQLKsVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKS 63
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
238-310 7.54e-06

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: 43.66  E-value: 7.54e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIR--VHIdIGADgraTGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNS 310
Cdd:cd12744     4 IRLQGLPVVAGSTDIRHFFTGLTIPDggVHI-IGGE---LGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSS 74
RRM1_RBM12 cd12745
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
59-146 1.50e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgrup corresponds to the RRM1 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear.


Pssm-ID: 241189 [Multi-domain]  Cd Length: 92  Bit Score: 43.10  E-value: 1.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTmdyqGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSSRSEIK 138
Cdd:cd12745     5 IRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIV----GGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTEMQ 80

                  ....*...
gi 1567544023 139 GFYDPPRR 146
Cdd:cd12745    81 NMIELSRR 88
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
58-115 1.53e-05

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: 42.97  E-value: 1.53e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGL------EIVPNGITltmdyqGRSTGEAFVQFASKEIAENAL 115
Cdd:cd12415     2 TVFIRNLSFDTTEEDLKEFFSKFgevkyaRIVLDKDT------GHSKGTAFVQFKTKESADKCI 59
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
237-297 1.79e-05

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: 42.45  E-value: 1.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023 237 FVhmRGLPFRATENDIANFFSPLNPIRvHIDIGAD---GRATGEADVEFVTHEDAVAAMSKDKN 297
Cdd:cd12674     4 FV--RNLPFDVTLESLTDFFSDIGPVK-HAVVVTDpetKKSRGYGFVSFSTHDDAEEALAKLKN 64
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
237-297 3.87e-05

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: 41.42  E-value: 3.87e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1567544023 237 FVhmRGLPFRATENDIANFFSPLNPIR---VHIDIGADgRATGEADVEFVTHEDAVAAMSKDKN 297
Cdd:cd12413     3 FV--RNLPYDTTDEQLEELFSDVGPVKrcfVVKDKGKD-KCRGFGYVTFALAEDAQRALEEVKG 63
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
238-294 5.26e-05

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: 41.02  E-value: 5.26e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNP-IRVHIDIGADGRATGEADVEFVTHEDAVAAMSK 294
Cdd:cd12418     3 VRVSNLHPDVTEEDLRELFGRVGPvKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQ 60
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
66-115 6.61e-05

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: 40.75  E-value: 6.61e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1567544023  66 FGCSKEEIVQFFQGLEIVpNGITLTMD-YQGRSTGEAFVQFASKEIAENAL 115
Cdd:cd12306     9 YGTTPEELQAHFKSCGTI-NRVTILCDkFTGQPKGFAYIEFVDKSSVENAL 58
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
58-129 7.16e-05

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: 40.85  E-value: 7.16e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVpNGITLTMDYQ-GRSTGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12450     1 TLFVGNLSWSATQDDLENFFSDCGEV-VDVRIAMDRDdGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
58-117 7.84e-05

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: 7.84e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGK 117
Cdd:cd12413     1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEE 60
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
237-293 8.26e-05

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: 41.64  E-value: 8.26e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023 237 FVhmRGLPFRATENDIANFFSPLNPI---RVHIDiGADGRATGEADVEFVTHEDAVAAMS 293
Cdd:cd12676     5 FV--RNLPFDATEDELYSHFSQFGPLkyaRVVKD-PATGRSKGTAFVKFKNKEDADNCLS 61
RRM5_RBM12B cd12750
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
238-298 1.48e-04

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: 39.79  E-value: 1.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLN--PIRVHIDIGADGRATGEADVEFVTHEDAVAAMsKDKNN 298
Cdd:cd12750     3 VKLFNLPFKATVNEILDFFYGYRviPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAV-QDLND 64
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
241-294 1.58e-04

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: 1.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 241 RGLPFRATENDIANFFSPLNPI-RVHIDIGADGRATGEADVEFVTHEDAVAAMSK 294
Cdd:cd12414     5 RNLPFKCTEDDLKKLFSKFGKVlEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKG 59
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
58-129 2.32e-04

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: 39.51  E-value: 2.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVpnGITLTMDY-QGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12402     4 TAYLGNLPYDVTEDDIEDFFRGLNIS--SVRLPRENgPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
240-304 4.07e-04

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: 38.55  E-value: 4.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 240 MRGLPFRATENDIANFFSPLNPI-RVHIDIGAD-GRATGEADVEFVTHEDAVAAMSK-DKNNMQHRYI 304
Cdd:cd12566     7 LRNLPYSTKEDDLQKLFSKFGEVsEVHVPIDKKtKKSKGFAYVLFLDPEDAVQAYNElDGKVFQGRLI 74
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
58-115 4.70e-04

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: 4.70e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGItLTMDY-QGRSTGEAFVQFASKEIAENAL 115
Cdd:cd12676     3 TLFVRNLPFDATEDELYSHFSQFGPLKYAR-VVKDPaTGRSKGTAFVKFKNKEDADNCL 60
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
238-295 6.25e-04

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 38.21  E-value: 6.25e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIrVHIDIGADGRATGEADVEFVTHEDAVAAMSKD 295
Cdd:cd12225     3 IHVGGIDGSLSEDELADYFSNCGEV-TQVRLCGDRVHTRFAWVEFATDASALSALNLD 59
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
63-129 1.12e-03

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: 1.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023  63 GLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12271     5 GIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM_ARP_like cd12452
RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins; ...
59-133 1.13e-03

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: 37.50  E-value: 1.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGLEIVPNGI-TLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFRSS 133
Cdd:cd12452     3 LYMNGLPHDTTQSELESWFTQHGVRPVAFwTLKTPEQIKPSGSGFAVFQSHEEAAESLALNGRALGDRAIEVQPSS 78
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
61-115 1.46e-03

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: 37.21  E-value: 1.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  61 LRGLPFGCSKEEIVQFFQGL-EIVPNGITLTMDyqGRSTGEAFVQFASKEIAENAL 115
Cdd:cd12320     5 VKNVPFEATRKEIRELFSPFgQLKSVRLPKKFD--GSHRGFAFVEFVTKQEAQNAM 58
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
238-293 1.71e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 36.78  E-value: 1.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRVHIDIgadgRATGEADVEFVTHEDAVAAMS 293
Cdd:cd12421     2 VHIRNLPPDATEADLVALGLPFGKVTNVLLL----KGKNQALVEMEDVESASSMVN 53
RRM1_U2AF65 cd12230
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
63-115 2.29e-03

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: 36.76  E-value: 2.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1567544023  63 GLPFGCSKEEIVQFF------QGLEIVPNGITL--TMDYQGRStgeAFVQFASKEIAENAL 115
Cdd:cd12230     8 NIPPGITEEELMDFFnqamraAGLTQAPGNPVLavQINPDKNF---AFVEFRSVEETTAAL 65
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
242-304 2.37e-03

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 36.38  E-value: 2.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1567544023 242 GLPFRATENDIANFFSPLNPIrVHIDIGAD---GRATGEADVEFVTHEDAVAAMSK-DKNNMQHRYI 304
Cdd:cd21608     6 NLSWDTTEDDLRDLFSEFGEV-ESAKVITDretGRSRGFGFVTFSTAEAAEAAIDAlNGKELDGRSI 71
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
61-115 2.37e-03

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: 36.38  E-value: 2.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023  61 LRGLPFGCSKEEIVQFFQGLEIVPNgITLTMDYQGRSTGEAFVQFASKEIAENAL 115
Cdd:cd12414     4 VRNLPFKCTEDDLKKLFSKFGKVLE-VTIPKKPDGKLRGFAFVQFTNVADAAKAI 57
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
239-291 2.73e-03

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: 36.72  E-value: 2.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 239 HMRGLPFRATENDIANFFS--PLNPIRVHIDIGADGRATGEADVEFVTHEDAVAA 291
Cdd:cd12749     3 HISNIPYNITKKDVLQFLEgiGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKA 57
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
58-129 2.80e-03

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


Pssm-ID: 409737 [Multi-domain]  Cd Length: 71  Bit Score: 36.09  E-value: 2.80e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNgITLTMDYQGRStgeAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12296     2 TVLVKNLPKSITENKIRQFFKDCGEIRE-VKILESGNGLV---AVIEFETEDEALAALTKDHKRIGGNEISV 69
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
58-125 3.10e-03

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: 36.29  E-value: 3.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1567544023  58 TVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERI--GHR 125
Cdd:cd12674     2 TLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKlsGHI 71
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
238-307 3.26e-03

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: 36.41  E-value: 3.26e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPI----RVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNM-----QHRYIELF 307
Cdd:cd12743     4 IRLRGLPYEAQVEHILEFLGDFAKMivfqGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYmvfgkKQRYIEVF 82
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
238-307 4.28e-03

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: 35.85  E-value: 4.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIRVHIDIGAD--GRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELF 307
Cdd:cd12513     3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDkyGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74
RRM1_U2AF65 cd12230
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
242-295 4.37e-03

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: 35.99  E-value: 4.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1567544023 242 GLPFRATENDIANFF-----------SPLNPIrVHIDIGADGRAtgeADVEFVTHEDAVAAMSKD 295
Cdd:cd12230     8 NIPPGITEEELMDFFnqamraagltqAPGNPV-LAVQINPDKNF---AFVEFRSVEETTAALALD 68
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
59-129 7.71e-03

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 34.93  E-value: 7.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  59 VRLRGLPFGCSKEEIVQFFQGL-EI----VPNGITLTMDYQGRstGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12298     3 IRVRNLDFELDEEALRGIFEKFgEIesinIPKKQKNRKGRHNN--GFAFVTFEDADSAESALQLNGTLLDNRKISV 76
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
243-292 8.06e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 34.90  E-value: 8.06e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 243 LPFRATENDIANFFSPLNPIRvHIDIGAD---GRATGEADVEFVTHEDAVAAM 292
Cdd:cd12283     7 LSLKARERDLYEFFSKAGKVR-DVRLIMDrnsRRSKGVAYVEFYDVESVPLAL 58
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
247-309 8.10e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 34.79  E-value: 8.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 247 ATENDIANFFSPLNPI-RVHIdigADGRATGE----ADVEFVTHEDAVAAMSKDKNnmqHRYIELFLN 309
Cdd:cd12408    11 ATEEDLRELFRPFGPIsRVYL---AKDKETGQskgfAFVTFETREDAERAIEKLNG---FGYDNLILS 72
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
238-293 8.30e-03

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: 35.07  E-value: 8.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1567544023 238 VHMRGLPFRATENDIANFFS--PLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMS 293
Cdd:cd12748     3 IYVRNLPFDVTKVEVQDFFEgfALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAER 60
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
64-129 8.72e-03

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: 34.89  E-value: 8.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1567544023  64 LPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEI 129
Cdd:cd12400     8 LPYDTTAEDLKEHFKKAGEPPSVRLLTDKKTGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
237-294 8.74e-03

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: 34.99  E-value: 8.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1567544023 237 FVHMRGLPFRATENDIANFFSPLNPI-RVHIDIGADGRATGEADVEFVTHEDAVAAMSK 294
Cdd:cd21607     4 TIYCSNLPLSTAESDLYDLFETIGKVnNAELKYDETGDPTGSAVVEYENLDDADVCISK 62
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
238-307 8.82e-03

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 34.89  E-value: 8.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1567544023 238 VHMRGLPFRATENDIANFFSPLNPIrVHIDIGAD---GRATGEADVEFVTHEDAVAAMskdkNNMQhrYIELF 307
Cdd:cd12347     1 LYVGGLAEEVDEKVLHAAFIPFGDI-VDIQIPLDyetEKHRGFAFVEFEEAEDAAAAI----DNMN--ESELF 66
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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