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Conserved domains on  [gi|62078769|ref|NP_001014041|]
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heterogeneous nuclear ribonucleoprotein H2 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
 103-192 7.16e-66

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


:

Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 206.01  E-value: 7.16e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 103 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 182
Cdd:cd12731   1 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 80

                        90
                ....*....|
gi 62078769 183 IFKSSRAEVR 192
Cdd:cd12731  81 IFKSSRAEVR 90
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 10-88 1.75e-52

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


:

Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 170.73  E-value: 1.75e-52
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  10 GFVVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12729   1 GFVVKVRGLPWSCSADEVQNFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 289-364 5.38e-49

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: 161.75  E-value: 5.38e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST 364
Cdd:cd12734   1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST 76
zf-RNPHF pfam08080
RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. ...
 257-290 2.74e-17

RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076.


:

Pssm-ID: 429823  Cd Length: 36  Bit Score: 74.98  E-value: 2.74e-17
                          10        20        30
                  ....*....|....*....|....*....|....
gi 62078769   257 SDRFGRDLNYCFSGMSDHRYGDGGSSFQSTTGHC 290
Cdd:pfam08080   3 SDRFGRDLSYCLSGMSDHRYGDGESTFQSTTGHC 36
 
Name Accession Description Interval E-value
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
 103-192 7.16e-66

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


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 206.01  E-value: 7.16e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 103 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 182
Cdd:cd12731   1 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 80

                        90
                ....*....|
gi 62078769 183 IFKSSRAEVR 192
Cdd:cd12731  81 IFKSSRAEVR 90
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 10-88 1.75e-52

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


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 170.73  E-value: 1.75e-52
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  10 GFVVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12729   1 GFVVKVRGLPWSCSADEVQNFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 289-364 5.38e-49

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: 161.75  E-value: 5.38e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST 364
Cdd:cd12734   1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST 76
zf-RNPHF pfam08080
RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. ...
 257-290 2.74e-17

RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076.


Pssm-ID: 429823  Cd Length: 36  Bit Score: 74.98  E-value: 2.74e-17
                          10        20        30
                  ....*....|....*....|....*....|....
gi 62078769   257 SDRFGRDLNYCFSGMSDHRYGDGGSSFQSTTGHC 290
Cdd:pfam08080   3 SDRFGRDLSYCLSGMSDHRYGDGESTFQSTTGHC 36
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-182 1.67e-11

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: 59.55  E-value: 1.67e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769   113 VRLRGLPFGCSKEEIVQFFSGLEIVpNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE 182
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
113-183 1.45e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.14  E-value: 1.45e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    113 VRLRGLPFGCSKEEIVQFFSGLEIVPNgMTLPVDFQ-GRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI 183
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVES-VRLVRDKEtGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
290-359 2.56e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 53.37  E-value: 2.56e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    290 CVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAK-DKANMQHRYVEL 359
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKvESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
12-85 3.94e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.98  E-value: 3.94e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769     12 VVKVRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTRE-GRPSGEAFVELESEDEVKLALKKDRETM-GHRYVEV 85
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVES----VRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKElDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 293-347 3.98e-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: 3.98e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769   293 MRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPiKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEA 58
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 13-84 4.89e-06

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: 44.15  E-value: 4.89e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    13 VKVRGLPWSCSAEEVMRFFSDCkiqNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVE 84
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKF---GPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
15-79 7.92e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 41.24  E-value: 7.92e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  15 VRGLPWSCSAEEVMRFFSDCkiqnGT-SGVRFIYTRE-GRPSGEAFVELESEDEVKLALKK--DRETMG 79
Cdd:COG0724   6 VGNLPYSVTEEDLRELFSEY----GEvTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEAlnGAELMG 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 3-171 2.65e-03

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.90  E-value: 2.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769     3 LSTEGREGFVVKVRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTR-EGRPSGEAFVELESEDEVKLALKKDRETMGH 80
Cdd:TIGR01622 107 LTEDERDRRTVFVQQLAARARERDLYEFFSKVgKVRD----VQIIKDRnSRRSKGVGYVEFYDVDSVQAALALTGQKLLG 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769    81 RYVEVfKSNSVEMDWVLK---HTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSgleivPNGMTLPVDFQ-----GRST 152
Cdd:TIGR01622 183 IPVIV-QLSEAEKNRAARaatETSGHHPNSIPFHRLYVGNLHFNITEQDLRQIFE-----PFGEIEFVQLQkdpetGRSK 256

                         170
                  ....*....|....*....
gi 62078769   153 GEAFVQFASQEIAEKALKK 171
Cdd:TIGR01622 257 GYGFIQFRDAEQAKEALEK 275
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
112-171 8.13e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 35.46  E-value: 8.13e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSG------LEIVPNGMTlpvdfqGRSTGEAFVQFASQEIAEKALKK 171
Cdd:COG0724   5 YVG--NLPYSVTEEDLRELFSEygevtsVKLITDRET------GRSRGFGFVEMPDDEEAQAAIEA 62
 
Name Accession Description Interval E-value
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
 103-192 7.16e-66

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


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 206.01  E-value: 7.16e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 103 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 182
Cdd:cd12731   1 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 80

                        90
                ....*....|
gi 62078769 183 IFKSSRAEVR 192
Cdd:cd12731  81 IFKSSRAEVR 90
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
 93-188 3.52e-62

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: 196.68  E-value: 3.52e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  93 MDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 172
Cdd:cd12732   1 MDWVLKHNGPTDTENSSDGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKH 80

                        90
                ....*....|....*.
gi 62078769 173 KERIGHRYIEIFKSSR 188
Cdd:cd12732  81 KERIGHRYIEIFKSSR 96
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 10-88 1.75e-52

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


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 170.73  E-value: 1.75e-52
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  10 GFVVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12729   1 GFVVKVRGLPWSCSADEVQNFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
 111-187 1.29e-50

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: 165.99  E-value: 1.29e-50
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 111 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12504   1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 289-364 5.38e-49

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: 161.75  E-value: 5.38e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST 364
Cdd:cd12734   1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST 76
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
 289-363 8.88e-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: 158.30  E-value: 8.88e-48
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 363
Cdd:cd12506   1 HTVHMRGLPYRATENDIFEFFSPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
 289-363 6.86e-46

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: 153.62  E-value: 6.86e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 363
Cdd:cd12735   1 HFVHMRGLPFRATESDIANFFSPLNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 289-363 2.40e-40

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: 138.74  E-value: 2.40e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 363
Cdd:cd12733   1 HFVHMRGLPFQANGQDIINFFAPLKPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
 12-88 4.51e-40

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: 138.29  E-value: 4.51e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12503   1 VVRARGLPWSATAEDVLNFFTDCRIKGGENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 112-184 1.11e-30

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: 113.04  E-value: 1.11e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12254   1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 11-87 2.31e-30

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: 112.20  E-value: 2.31e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFK 87
Cdd:cd12730   2 FIVRARGLPWSCTAEDVLSFFSDCRIRNGEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 12-86 1.04e-28

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: 107.65  E-value: 1.04e-28
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12254   1 VVRLRGLPFSATEEDIRDFFSGLDIPPD--GIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 110-186 2.06e-28

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: 106.84  E-value: 2.06e-28
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 110 DGFVRLRGLPFGCSKEEIVQFFSGLEIVpnGMTLPVDFQG-RSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 186
Cdd:cd12505   1 DGVVRLRGLPYSCTEADIAHFFSGLDIV--DITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 290-360 1.77e-27

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: 104.18  E-value: 1.77e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12254   1 VVRLRGLPFSATEEDIRDFFSGLDipPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 110-186 4.32e-27

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: 103.59  E-value: 4.32e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 110 DGFVRLRGLPFGCSKEEIVQFFSGLEIV---PNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 186
Cdd:cd12508   1 QVIVRMRGLPFSATAADILAFFGGECPVtggKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 12-88 2.63e-25

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: 98.58  E-value: 2.63e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSD-CKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12508   3 IVRMRGLPFSATAADILAFFGGeCPVTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
 11-88 1.03e-23

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: 93.96  E-value: 1.03e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12504   1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPN--GITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRS 76
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 113-186 4.95e-23

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: 92.17  E-value: 4.95e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 186
Cdd:cd12507   2 VRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
 113-186 1.94e-21

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: 88.74  E-value: 1.94e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVP------NGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 186
Cdd:cd12741  20 IRMRGLPYDCTPKQVVEFFCTGDKIPhvldgaEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFRS 99
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
 7-93 1.41e-20

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: 85.83  E-value: 1.41e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769   7 GREGFVvKVRGLPWSCSAEEVMRFFSDCKIQngTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12731   6 ANDGFV-RLRGLPFGCSKEEIVQFFSGLEIV--PNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 82


                ....*..
gi 62078769  87 KSNSVEM 93
Cdd:cd12731  83 KSSRAEV 89
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
 12-88 1.53e-19

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: 83.35  E-value: 1.53e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFS----DCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFK 87
Cdd:cd12741  19 IIRMRGLPYDCTPKQVVEFFCtgdkIPHVLDGAEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIELFR 98


                .
gi 62078769  88 S 88
Cdd:cd12741  99 S 99
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
 113-187 2.58e-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: 2.58e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12738   2 VRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKAT 76
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 291-360 5.02e-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: 81.25  E-value: 5.02e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIE-----IGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12508   4 VRMRGLPFSATAADILAFFGGECPVTGGKDgilfvTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELF 78
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 12-88 3.39e-18

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: 78.69  E-value: 3.39e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12507   1 VVRARGLPWQSSDQDIAQFFRGLNIAKG--GVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 12-97 4.51e-18

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: 79.71  E-value: 4.51e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSD-CKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSNS 90
Cdd:cd12739  18 IVRMRGLPFTATAEEVLAFFGQhCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRSTA 97


                ....*..
gi 62078769  91 VEMDWVL 97
Cdd:cd12739  98 AEVQQVL 104
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
 5-89 6.99e-18

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: 78.43  E-value: 6.99e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769   5 TEGREGFVVKVRGLPWSCSAEEVMRFFSDCKIQngTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVE 84
Cdd:cd12732  13 TENSSDGTVRLRGLPFGCSKEEIVQFFSGLEIV--PNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIE 90


                ....*
gi 62078769  85 VFKSN 89
Cdd:cd12732  91 IFKSS 95
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 109-192 7.17e-18

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: 78.94  E-value: 7.17e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 109 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG------MTLPvdfQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE 182
Cdd:cd12739  15 NQVIVRMRGLPFTATAEEVLAFFGQHCPVTGGkegilfVTYP---DSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIE 91

                        90
                ....*....|
gi 62078769 183 IFKSSRAEVR 192
Cdd:cd12739  92 LFRSTAAEVQ 101
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
 112-187 1.45e-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: 77.03  E-value: 1.45e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEivPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12506   2 TVHMRGLPYRATENDIFEFFSPLN--PVNVRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELFLNS 75
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 3-97 1.49e-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: 78.10  E-value: 1.49e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769   3 LSTEGRegFVVKVRGLPWSCSAEEVMRFFS-DCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHR 81
Cdd:cd12740  11 LSKENQ--VIIRMRGLPFTATPEDVLGFLGpECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKR 88

                        90
                ....*....|....*.
gi 62078769  82 YVEVFKSNSVEMDWVL 97
Cdd:cd12740  89 YIELFRSTAAEVQQVL 104
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
 12-86 1.65e-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: 76.64  E-value: 1.65e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNgtsgVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12506   2 TVHMRGLPYRATENDIFEFFSPLNPVN----VRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELF 72
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 109-192 2.00e-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: 77.72  E-value: 2.00e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 109 NDGFVRLRGLPFGCSKEEIVQFFsGLEIVPNGMTLPVDF----QGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12740  15 NQVIIRMRGLPFTATPEDVLGFL-GPECPVTGGTEGLLFvkypDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELF 93


                ....*...
gi 62078769 185 KSSRAEVR 192
Cdd:cd12740  94 RSTAAEVQ 101
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 109-187 2.54e-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: 76.98  E-value: 2.54e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 109 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12736   8 DNTVIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKAT 86
zf-RNPHF pfam08080
RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. ...
 257-290 2.74e-17

RNPHF zinc finger; This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076.


Pssm-ID: 429823  Cd Length: 36  Bit Score: 74.98  E-value: 2.74e-17
                          10        20        30
                  ....*....|....*....|....*....|....
gi 62078769   257 SDRFGRDLNYCFSGMSDHRYGDGGSSFQSTTGHC 290
Cdd:pfam08080   3 SDRFGRDLSYCLSGMSDHRYGDGESTFQSTTGHC 36
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
 289-360 3.83e-17

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: 75.86  E-value: 3.83e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12504   1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDrrGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIF 74
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 113-190 4.86e-17

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: 75.81  E-value: 4.86e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE 190
Cdd:cd12737   2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEE 79
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 113-187 1.58e-16

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: 74.05  E-value: 1.58e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGL--EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK-ALKKHKERIGHRYIEIFKSS 187
Cdd:cd12509   4 IRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFARLaAQKRHKHHMGERYIEVFQCS 81
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 12-88 5.27e-16

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: 72.56  E-value: 5.27e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIqngtSGVRFIYTREG-RPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12505   3 VVRLRGLPYSCTEADIAHFFSGLDI----VDITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 13-87 8.99e-16

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


Pssm-ID: 409931 [Multi-domain]  Cd Length: 81  Bit Score: 72.12  E-value: 8.99e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELES-EDEVKLALKKDRETMGHRYVEVFK 87
Cdd:cd12509   4 IRLRGLPYSATVEDILNFLGEFAKHIAPQGVHMVINAQGRPSGDAFIQMLSaEFARLAAQKRHKHHMGERYIEVFQ 79
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 290-360 1.06e-15

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: 71.48  E-value: 1.06e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 290 CVHMRGLPYRATENDIYNFFS--PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-DKANMQHRYVELF 360
Cdd:cd12515   2 VVKMRNLPFKATIEDILDFFYgyRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 11-86 1.45e-15

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: 71.29  E-value: 1.45e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCKIqngtSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12502   1 FTVKLRGAPFNVKEKQIREFFSPLKP----VAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
 112-187 9.40e-15

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: 68.88  E-value: 9.40e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEivPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12735   2 FVHMRGLPFRATESDIANFFSPLN--PIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELFLNS 75
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 110-190 1.83e-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: 68.62  E-value: 1.83e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 110 DGFVRLRGLPFGCSKEEIVQFFSGLEIVpnGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRA 189
Cdd:cd12746   2 DVYLFLRGMPYSATEDDVRNFFSGLKVD--GVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEE 79


                .
gi 62078769 190 E 190
Cdd:cd12746  80 Q 80
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 112-187 2.29e-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: 2.29e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLeiVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12733   2 FVHMRGLPFQANGQDIINFFAPL--KPVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELFLNS 75
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
 291-360 2.64e-14

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: 67.80  E-value: 2.64e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR----VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12503   2 VRARGLPWSATAEDVLNFFTDCRIKGgengIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVF 75
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 12-88 4.16e-14

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: 67.73  E-value: 4.16e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12736  11 VIRARGLPWQSSDQDIARFFKGLNIAKG--GAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVYKA 85
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 12-92 4.81e-14

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: 67.34  E-value: 4.81e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSNSV 91
Cdd:cd12737   1 VIRARGLPWQSSDQDIARFFKGLNIAKG--GVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGE 78


                .
gi 62078769  92 E 92
Cdd:cd12737  79 E 79
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
 13-87 5.96e-14

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: 66.75  E-value: 5.96e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVEVFK 87
Cdd:cd12742   4 IRLRGLPYAATIEDILEFLGEFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQ 79
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 113-184 8.73e-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: 66.29  E-value: 8.73e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEivPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12502   3 VKLRGAPFNVKEKQIREFFSPLK--PVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
 12-88 1.22e-13

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: 66.09  E-value: 1.22e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12738   1 VVRARGLPWQSSDQDIAKFFRGLNIAKG--GVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKA 75
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 289-360 1.23e-13

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: 65.52  E-value: 1.23e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 289 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12502   1 FTVKLRGAPFNVKEKQIREFFSPLKPVAIRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
 113-187 3.97e-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: 64.44  E-value: 3.97e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 113 VRLRGLPFGCSKEEIVQFFS--GLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSS 187
Cdd:cd12742   4 IRLRGLPYAATIEDILEFLGefAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQCS 81
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 288-360 8.12e-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: 63.64  E-value: 8.12e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 288 GHCVHMRGLPYRATENDIYNFFSPL----NPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12729   1 GFVVKVRGLPWSCSADEVQNFFSDCkianGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVF 77
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 290-360 1.40e-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: 62.88  E-value: 1.40e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLN----PMRVHIEIGPDGRVTGEADVEFATHEDAV-AAMAKDKANMQHRYVELF 360
Cdd:cd12509   3 CIRLRGLPYSATVEDILNFLGEFAkhiaPQGVHMVINAQGRPSGDAFIQMLSAEFARlAAQKRHKHHMGERYIEVF 78
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 291-359 2.13e-12

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: 62.46  E-value: 2.13e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVEL 359
Cdd:cd12746   5 LFLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEV 73
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 291-360 2.77e-12

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: 62.16  E-value: 2.77e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDG-RVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12505   4 VRLRGLPYSCTEADIAHFFSGLDIVDITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIF 74
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 112-179 2.95e-12

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: 61.66  E-value: 2.95e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHR 179
Cdd:cd12514   1 FIRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
 279-360 3.07e-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: 62.55  E-value: 3.07e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 279 GGSS-----FQSTTGHC-VHMRGLPYRATENDIYNFFSPLNPMrVHIEIG---------PDGRVTGEADVEFATHEDAVA 343
Cdd:cd12741   2 GGESneaqnFLSKGGQViIRMRGLPYDCTPKQVVEFFCTGDKI-PHVLDGaegvlfvkkPDGRATGDAFVLFETEEVAEK 80

                        90
                ....*....|....*..
gi 62078769 344 AMAKDKANMQHRYVELF 360
Cdd:cd12741  81 ALEKHRQHIGSRYIELF 97
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 112-184 6.08e-12

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


Pssm-ID: 409933 [Multi-domain]  Cd Length: 73  Bit Score: 61.03  E-value: 6.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEIvpNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12511   1 YLSLHGMPYSAMENDVRDFFHGLRV--DGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 288-359 9.56e-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: 61.40  E-value: 9.56e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 288 GHCVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVEL 359
Cdd:cd12512   9 GFCVYLKGLPYEAENKHVIEFFKKLDIVEdsIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 110-184 1.41e-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: 59.81  E-value: 1.41e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 110 DGFVRLRGLPFGCSKEEIVQFFSGLEIvpNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12747   1 DLYVHLHGMPFSATEADVRDFFHGLRI--DAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-182 1.67e-11

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: 59.55  E-value: 1.67e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769   113 VRLRGLPFGCSKEEIVQFFSGLEIVpNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE 182
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPI-KSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 113-202 2.32e-11

RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; This subfamily corresponds to the RRM3 of RBM12. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear.


Pssm-ID: 409934 [Multi-domain]  Cd Length: 101  Bit Score: 60.25  E-value: 2.32e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 192
Cdd:cd12512  12 VYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQVHPITKKAML 91

                        90
                ....*....|
gi 62078769 193 THYDPPRKLM 202
Cdd:cd12512  92 EKIDMIRKRL 101
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 291-365 5.28e-11

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: 59.23  E-value: 5.28e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIE-----IGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA 365
Cdd:cd12740  19 IRMRGLPFTATPEDVLGFLGPECPVTGGTEgllfvKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELFRSTAA 98
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 12-86 9.26e-11

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: 57.62  E-value: 9.26e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGTsgVRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVEVF 86
Cdd:cd12515   2 VVKMRNLPFKATIEDILDFFYGYRVIPDS--VSIRYNDDGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 113-184 1.17e-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: 57.23  E-value: 1.17e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF 184
Cdd:cd12515   3 VKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRElNNRPLGGRKVKLF 75
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 13-96 1.30e-10

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.


Pssm-ID: 410140 [Multi-domain]  Cd Length: 86  Bit Score: 57.45  E-value: 1.30e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIqngtSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSNsvE 92
Cdd:cd12746   5 LFLRGMPYSATEDDVRNFFSGLKV----DGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTT--E 78


                ....
gi 62078769  93 MDWV 96
Cdd:cd12746  79 EQWI 82
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 113-183 1.52e-10

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: 56.91  E-value: 1.52e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGL-EIVpnGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI 183
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFgEVV--SVRIVRDRDGKSKGFAFVEFESPEDAEKALEAlNGTELGGRPLKV 71
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 113-187 2.82e-10

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: 56.21  E-value: 2.82e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEivPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12734   3 VHMRGLPYRATENDIYNFFSPLN--PVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNS 75
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
 290-360 3.80e-10

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: 55.97  E-value: 3.80e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12507   1 VVRARGLPWQSSDQDIAQFFRGLNIAKggVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVY 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 13-85 4.29e-10

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: 55.75  E-value: 4.29e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVEV 85
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFgEVVS----VRIVRDRDGKSKGFAFVEFESPEDAEKALEAlNGTELGGRPLKV 71
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 13-86 5.29e-10

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: 55.54  E-value: 5.29e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKiqngTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12733   3 VHMRGLPFQANGQDIINFFAPLK----PVRITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 113-188 6.49e-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: 55.50  E-value: 6.49e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR 188
Cdd:cd12513   3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIYPISR 78
RRM smart00360
RNA recognition motif;
113-183 1.45e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.14  E-value: 1.45e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    113 VRLRGLPFGCSKEEIVQFFSGLEIVPNgMTLPVDFQ-GRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI 183
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVES-VRLVRDKEtGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
290-359 2.56e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 53.37  E-value: 2.56e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    290 CVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAK-DKANMQHRYVEL 359
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKvESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 291-360 3.32e-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: 53.33  E-value: 3.32e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12511   2 LSLHGMPYSAMENDVRDFFHGLRVDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 118-179 3.53e-09

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: 53.67  E-value: 3.53e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 118 LPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHR 179
Cdd:cd12749   7 IPYNITKKDVLQFLEGIGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAERLHRKKLNGR 68
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
 290-360 3.63e-09

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: 53.26  E-value: 3.63e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLNPMR----VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12730   3 IVRARGLPWSCTAEDVLSFFSDCRIRNgedgIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVF 77
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
 290-360 3.78e-09

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: 53.27  E-value: 3.78e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 290 CVHMRGLPYRATENDIYNFFSP----LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-DKANMQHRYVELF 360
Cdd:cd12742   3 CIRLRGLPYAATIEDILEFLGEfaadIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVF 78
RRM smart00360
RNA recognition motif;
12-85 3.94e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.98  E-value: 3.94e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769     12 VVKVRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTRE-GRPSGEAFVELESEDEVKLALKKDRETM-GHRYVEV 85
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVES----VRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKElDGRPLKV 73
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 291-360 8.42e-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: 52.10  E-value: 8.42e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12747   4 VHLHGMPFSATEADVRDFFHGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM5_RBM12 cd12751
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 113-183 1.06e-08

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: 51.81  E-value: 1.06e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER-IGHRYIEI 183
Cdd:cd12751   4 IKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAAVVDLNDRpIGSRKVKL 75
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
 291-360 1.09e-08

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: 51.84  E-value: 1.09e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12738   2 VRARGLPWQSSDQDIAKFFRGLNIAKggVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVY 73
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 12-88 1.28e-08

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: 51.51  E-value: 1.28e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIytreGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKS 88
Cdd:cd12510   3 VIRLQGLPWEAGSLDIRRFFSGLTIPDG--GVHII----GGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLS 73
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 290-348 1.47e-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: 51.26  E-value: 1.47e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769 290 CVHMRGLPYRATENDIYNFFSP--LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 348
Cdd:cd12514   1 FIRITNLPYDATPVDIQRFFEDhgVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLN 61
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 291-365 1.73e-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: 1.73e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR-----VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA 365
Cdd:cd12739  19 VRMRGLPFTATAEEVLAFFGQHCPVTggkegILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELFRSTAA 98
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 113-192 1.77e-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: 51.36  E-value: 1.77e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIvPNGmtlPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 192
Cdd:cd12744   4 IRLQGLPVVAGSTDIRHFFTGLTI-PDG---GVHIIGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKAEMQ 79
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
 13-81 1.85e-08

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: 51.07  E-value: 1.85e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCK-IQNgtsgVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHR 81
Cdd:cd12391   2 VFVSNLDYSVPEDKIREIFSGCGeITD----VRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEGR 67
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
 15-89 2.76e-08

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


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 50.79  E-value: 2.76e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769  15 VRGLPWSCSAEEVMRFFSdckiQNGT-SGVRFIYTREGRPSGEAFVELESEDEVKLA-LKKDRETMGHRYVEVFKSN 89
Cdd:cd12392   7 VKGLPFSCTKEELEELFK----QHGTvKDVRLVTYRNGKPKGLAYVEYENEADASQAvLKTDGTEIKDHTISVAISN 79
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
 13-86 4.10e-08

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: 50.00  E-value: 4.10e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKiqngTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12735   3 VHMRGLPFRATESDIANFFSPLN----PIRVHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELF 72
RRM5_RBM12B cd12750
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 113-183 4.35e-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: 50.19  E-value: 4.35e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER-IGHRYIEI 183
Cdd:cd12750   3 VKLFNLPFKATVNEILDFFYGYRVIPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAVQDLNDRpIGPRKVKL 74
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 112-187 4.45e-08

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: 49.97  E-value: 4.45e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRLRGLPFGCSKEEIVQFFSGLEIvPNGmtlPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12510   3 VIRLQGLPWEAGSLDIRRFFSGLTI-PDG---GVHIIGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 13-86 4.66e-08

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: 49.86  E-value: 4.66e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQngtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12511   2 LSLHGMPYSAMENDVRDFFHGLRVD----GVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 291-347 4.73e-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: 49.97  E-value: 4.73e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 291 VHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFgEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEA 58
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
 13-87 5.88e-08

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: 49.89  E-value: 5.88e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETM-----GHRYVEVFK 87
Cdd:cd12743   4 IRLRGLPYEAQVEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYmvfgkKQRYIEVFQ 83
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 10-85 5.89e-08

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: 50.62  E-value: 5.89e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  10 GFVVKVRGLPWSCSAEEVMRFFSDCKIQNGTsgVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12512   9 GFCVYLKGLPYEAENKHVIEFFKKLDIVEDS--IYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 113-176 7.07e-08

RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM4 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.


Pssm-ID: 410142 [Multi-domain]  Cd Length: 76  Bit Score: 49.32  E-value: 7.07e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERI 176
Cdd:cd12748   3 IYVRNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKAERLNGQRF 66
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 12-85 9.81e-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: 48.95  E-value: 9.81e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDckIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12514   1 FIRITNLPYDATPVDIQRFFED--HGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREAVV 72
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 11-86 1.33e-07

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: 48.63  E-value: 1.33e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCKIQngtsGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12747   2 LYVHLHGMPFSATEADVRDFFHGLRID----AIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 12-81 1.79e-07

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: 48.55  E-value: 1.79e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCkiqNGTSGVRFIYTRE-GRPSGEAFVELESEDEVKLALKKDRETMGHR 81
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDC---GEVVDVRIAMDRDdGRSKGFGHVEFASAESAQKALEKSGQDLGGR 68
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
 113-187 2.92e-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: 47.96  E-value: 2.92e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 113 VRLRGLPFGCSKEEIVQFFS--GLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERI-----GHRYIEIFK 185
Cdd:cd12743   4 IRLRGLPYEAQVEHILEFLGdfAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYmvfgkKQRYIEVFQ 83


                ..
gi 62078769 186 SS 187
Cdd:cd12743  84 CS 85
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
 291-360 3.50e-07

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: 47.69  E-value: 3.50e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12737   2 IRARGLPWQSSDQDIARFFKGLNIAKggVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVY 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 293-347 3.98e-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: 3.98e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769   293 MRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPiKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEA 58
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
 13-86 5.06e-07

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: 46.96  E-value: 5.06e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQNgtsgVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12734   3 VHMRGLPYRATENDIYNFFSPLNPVR----VHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELF 72
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 294-366 1.13e-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: 46.24  E-value: 1.13e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 294 RGLPYRATENDIYNFFS---PLNPMRVHIEIGpDGRVTGEADVEFATHEDAVAAMAKDKANMQHRyvELFLNSTAG 366
Cdd:cd12450   5 GNLSWSATQDDLENFFSdcgEVVDVRIAMDRD-DGRSKGFGHVEFASAESAQKALEKSGQDLGGR--EIRLDLANE 77
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
 15-72 1.17e-06

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


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 45.88  E-value: 1.17e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769  15 VRGLPWSCSAEEVMRFFSDCKiqngtsGVRFIYTREGRPSGEAFVELESEDEVKLALK 72
Cdd:cd12404   8 VKNLPYSTTQDELKEVFEDAV------DIRIPMGRDGRSKGIAYIEFKSEAEAEKALE 59
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
 291-360 1.18e-06

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: 46.55  E-value: 1.18e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12736  12 IRARGLPWQSSDQDIARFFKGLNIAKggAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYIEVY 83
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
 291-363 1.60e-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: 45.73  E-value: 1.60e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGrvtgEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 363
Cdd:cd12510   4 IRLQGLPWEAGSLDIRRFFSGLTIPDggVHIIGGEKG----EAFIIFATDEDARLAMMRDGQTIKGSKVKLFLSS 74
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 13-85 1.70e-06

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: 45.34  E-value: 1.70e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCkiqnGTsgVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12296   3 VLVKNLPKSITENKIRQFFKDC----GE--IREVKILESGNGLVAVIEFETEDEALAALTKDHKRIGGNEISV 69
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 115-171 1.80e-06

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: 45.62  E-value: 1.80e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 115 LRGLPFGCSKEEIVQFFSGLEIVPNgMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 171
Cdd:cd12414   4 VRNLPFKCTEDDLKKLFSKFGKVLE-VTIPKKPDGKLRGFAFVQFTNVADAAKAIKG 59
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 291-349 2.91e-06

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: 44.57  E-value: 2.91e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRvHIEIGPDGRVTgEADVEFATHEDAVAAMAKDK 349
Cdd:cd12296   3 VLVKNLPKSITENKIRQFFKDCGEIR-EVKILESGNGL-VAVIEFETEDEALAALTKDH 59
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
 296-355 3.17e-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: 44.90  E-value: 3.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62078769 296 LPYRATENDIYNFFSPLNPMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKDKANMQHR 355
Cdd:cd12402  10 LPYDVTEDDIEDFFRGLNISSVRLPRENGpGRLRGFGYVEFEDRESLIQALSLNEESLKNR 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 13-84 4.89e-06

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: 44.15  E-value: 4.89e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769    13 VKVRGLPWSCSAEEVMRFFSDCkiqNGTSGVRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVE 84
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKF---GPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM5_RBM12 cd12751
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 12-71 5.64e-06

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: 44.11  E-value: 5.64e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGTsgVRFIYTREGRPSGEAFVELESEDEVKLAL 71
Cdd:cd12751   3 VIKVQNMPFTVSVDEILDFFYGYQVIPGS--VCLKYNEKGMPTGEAMVAFESRDEAMAAV 60
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 11-86 6.24e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM3 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.


Pssm-ID: 409935 [Multi-domain]  Cd Length: 81  Bit Score: 43.94  E-value: 6.24e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCKIQNgtSGVRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12513   1 FCVHLKNLSYSVDKRDIRNFFRDLDISD--DQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 291-365 7.49e-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: 44.04  E-value: 7.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPmrvhieigPDGRV------TGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST 364
Cdd:cd12744   4 IRLQGLPVVAGSTDIRHFFTGLTI--------PDGGVhiiggeLGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSK 75


                .
gi 62078769 365 A 365
Cdd:cd12744  76 A 76
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 293-359 1.11e-05

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


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 43.10  E-value: 1.11e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 293 MRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVEL 359
Cdd:cd12316   4 VRNLPFTATEDELRELFEAFGKIsEVHIPLDKqTKRSKGFAFVLFVIPEDAVKAYqELDGSIFQGRLLHV 73
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 15-85 1.37e-05

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


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 42.89  E-value: 1.37e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769  15 VRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTRE-GRPSGEAFVELESEDEVKLALKK-DRETMGHRYVEV 85
Cdd:cd12399   3 VGNLPYSASEEQLKSLFGQFgAVFD----VKLPMDREtKRPRGFGFVELQEEESAEKAIAKlDGTDFMGRTIRV 72
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 112-171 1.79e-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: 42.58  E-value: 1.79e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 171
Cdd:cd12413   3 FVR--NLPYDTTDEQLEELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEE 60
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 13-85 3.33e-05

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: 41.93  E-value: 3.33e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769  13 VKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTreGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDS--GNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 18-86 3.73e-05

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


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 41.71  E-value: 3.73e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769  18 LPWSCSAEEVMRFFSDCkiqnGT-SGVRFIYTRE---GRpsGEAFVELESEDEVKLALKKDRETMGHRYVEVF 86
Cdd:cd12395   7 LPFDIEEEELRKHFEDC----GDvEAVRIVRDREtgiGK--GFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
 118-179 3.89e-05

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


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 41.44  E-value: 3.89e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 118 LPFGCSKEEIVQFFSGL-EIVPngMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHR 179
Cdd:cd12391   7 LDYSVPEDKIREIFSGCgEITD--VRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEGR 67
RRM1_RBM12 cd12745
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 113-200 5.14e-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: 41.94  E-value: 5.14e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIvPNGmtlPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 192
Cdd:cd12745   5 IRLQGLPIVAGTMDIRHFFSGLTI-PDG---GVHIVGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSSKTEMQ 80


                ....*...
gi 62078769 193 THYDPPRK 200
Cdd:cd12745  81 NMIELSRR 88
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
 11-85 5.51e-05

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: 41.05  E-value: 5.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  11 FVVKVRGLPWSCSAEEVMRFFSDCkiqNGTSGVRFIYTRE-GRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12400   1 YILFVGNLPYDTTAEDLKEHFKKA---GEPPSVRLLTDKKtGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 290-359 6.48e-05

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: 41.34  E-value: 6.48e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 290 CVHMRGLPYRATENDIYNFFS--PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAA--MAKDKANMQHRYVEL 359
Cdd:cd12749   1 CAHISNIPYNITKKDVLQFLEgiGLDENSVQVLVDNNGQGLGQALVQFKSEDDARKAerLHRKKLNGRDAFLHL 74
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 291-356 6.54e-05

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: 40.77  E-value: 6.54e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPD-GRVTGEADVEFATHEDAVAAMAKDKANMQHRY 356
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRsVDLMRFPDsGNFRGIAFITFKTEEAAKRALALDGEMLGNRF 68
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
 291-347 6.60e-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: 6.60e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVkSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQ 60
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 117-183 7.29e-05

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: 40.77  E-value: 7.29e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 117 GLPFGCSKEEIVQFFS--GLEIVPNGMTLPVDfqGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI 183
Cdd:cd12271   5 GIPYYSTEAEIRSYFSscGEVRSVDLMRFPDS--GNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
15-79 7.92e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 41.24  E-value: 7.92e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  15 VRGLPWSCSAEEVMRFFSDCkiqnGT-SGVRFIYTRE-GRPSGEAFVELESEDEVKLALKK--DRETMG 79
Cdd:COG0724   6 VGNLPYSVTEEDLRELFSEY----GEvTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEAlnGAELMG 70
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 15-74 1.11e-04

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 40.67  E-value: 1.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769  15 VRGLPWSCSAEEVMRFFS------DCKIqngtsgvrfIYTREGRPSGEAFVELESEDEVKLALKKD 74
Cdd:cd12412   7 VGGIDWDTTEEELREFFSkfgkvkDVKI---------IKDRAGVSKGYGFVTFETQEDAEKIQKWG 63
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
 115-171 1.50e-04

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


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 39.91  E-value: 1.50e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 115 LRGLPFGCSKEEIVQFFSGL-EIVpnGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 171
Cdd:cd12320   5 VKNVPFEATRKEIRELFSPFgQLK--SVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 115-170 2.08e-04

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: 39.89  E-value: 2.08e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62078769 115 LRGLPFGCSKEEIVQFFSGL------EIVPNGMTlpvdfqGRSTGEAFVQFASQEIAEKALK 170
Cdd:cd12415   5 IRNLSFDTTEEDLKEFFSKFgevkyaRIVLDKDT------GHSKGTAFVQFKTKESADKCIE 60
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 290-360 2.08e-04

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: 39.70  E-value: 2.08e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 360
Cdd:cd12513   2 CVHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDkyGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 112-183 2.18e-04

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: 39.69  E-value: 2.18e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSGLEIVpNGMTLPVDFQ-GRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI 183
Cdd:cd12450   3 FVG--NLSWSATQDDLENFFSDCGEV-VDVRIAMDRDdGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
 291-347 2.19e-04

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: 39.62  E-value: 2.19e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMrVHIEIGPD--GRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd21607   5 IYCSNLPLSTAESDLYDLFETIGKV-NNAELKYDetGDPTGSAVVEYENLDDADVCISK 62
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 112-179 2.50e-04

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: 39.76  E-value: 2.50e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERI--GHR 179
Cdd:cd12674   4 FVR--NLPFDVTLESLTDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKlsGHI 71
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
 118-183 2.65e-04

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: 39.13  E-value: 2.65e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 118 LPFGCSKEEIVQFFSGLEIVPNgMTLPVDFQ-GRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI 183
Cdd:cd12400   8 LPYDTTAEDLKEHFKKAGEPPS-VRLLTDKKtGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73
RRM5_RBM12B cd12750
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 291-345 5.76e-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: 38.64  E-value: 5.76e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM 345
Cdd:cd12750   3 VKLFNLPFKATVNEILDFFYGYRviPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAV 59
RRM1_U2AF65 cd12230
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
 295-348 7.45e-04

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: 38.30  E-value: 7.45e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 295 GLPYRATENDIYNFF-----------SPLNPMrVHIEIGPDGRVtgeADVEFATHEDAVAAMAKD 348
Cdd:cd12230   8 NIPPGITEEELMDFFnqamraagltqAPGNPV-LAVQINPDKNF---AFVEFRSVEETTAALALD 68
RRM_ARP_like cd12452
RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins; ...
 113-187 7.62e-04

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: 38.27  E-value: 7.62e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGLEIVPNGM-TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 187
Cdd:cd12452   3 LYMNGLPHDTTQSELESWFTQHGVRPVAFwTLKTPEQIKPSGSGFAVFQSHEEAAESLALNGRALGDRAIEVQPSS 78
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
 120-169 7.77e-04

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: 38.05  E-value: 7.77e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 62078769 120 FGCSKEEIVQFFSGLEIVpNGMTLPVD-FQGRSTGEAFVQFASQEIAEKAL 169
Cdd:cd12306   9 YGTTPEELQAHFKSCGTI-NRVTILCDkFTGQPKGFAYIEFVDKSSVENAL 58
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 294-349 7.80e-04

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: 37.96  E-value: 7.80e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 294 RGLPYRATENDIYNFFSPLNPMR---VHIEIGPDgRVTGEADVEFATHEDAVAAMAKDK 349
Cdd:cd12413   5 RNLPYDTTDEQLEELFSDVGPVKrcfVVKDKGKD-KCRGFGYVTFALAEDAQRALEEVK 62
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 112-171 1.07e-03

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 37.59  E-value: 1.07e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSGL------EIVpngmtlpVDFQGRSTGEAFVQFASQEIAEKALKK 171
Cdd:cd12412   6 FVG--GIDWDTTEEELREFFSKFgkvkdvKII-------KDRAGVSKGYGFVTFETQEDAEKIQKW 62
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 115-170 1.18e-03

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: 37.32  E-value: 1.18e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 115 LRGLPFGCSKEEIVQFFSGLEIVPNgMTLPVDFQ-GRSTGEAFVQFASQEIAEKALK 170
Cdd:cd12316   4 VRNLPFTATEDELRELFEAFGKISE-VHIPLDKQtKRSKGFAFVLFVIPEDAVKAYQ 59
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 294-346 1.32e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 37.63  E-value: 1.32e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 294 RGLPYRATENDIYNFFSPLNPMRVH-IEIGPDgRVTGE----ADVEFATHEDAVAAMA 346
Cdd:cd12313   8 RGLDVLTTEEDILSALQAHADLPIKdVRLIRD-KLTGTsrgfAFVEFSSLEDATQVMD 64
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 296-346 1.40e-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: 37.21  E-value: 1.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 62078769 296 LPYRATENDIYNFFSPLNPMRvHIEIGPD---GRVTGEADVEFATHEDAVAAMA 346
Cdd:cd12283   7 LSLKARERDLYEFFSKAGKVR-DVRLIMDrnsRRSKGVAYVEFYDVESVPLALA 59
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 293-355 1.55e-03

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: 37.40  E-value: 1.55e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 293 MRGLPYRATENDIYNFFSPLNPM-RVHIEIGPD-GRVTGEADVEFATHEDAVAAMAK-DKANMQHR 355
Cdd:cd12566   7 LRNLPYSTKEDDLQKLFSKFGEVsEVHVPIDKKtKKSKGFAYVLFLDPEDAVQAYNElDGKVFQGR 72
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 294-347 1.59e-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: 37.15  E-value: 1.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 294 RGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd12414   5 RNLPFKCTEDDLKKLFSKFGKVlEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKG 59
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
 290-360 1.77e-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: 37.18  E-value: 1.77e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769 290 CVHMRGLPYRATENDIYNFFSPLNPM----RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANM-----QHRYVELF 360
Cdd:cd12743   3 CIRLRGLPYEAQVEHILEFLGDFAKMivfqGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYmvfgkKQRYIEVF 82
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
 296-345 1.79e-03

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: 36.82  E-value: 1.79e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 62078769 296 LPYRATENDIYNFFSPLNPMR---VHIeiGPDGRVTGEADVEFATHEDAVAAM 345
Cdd:cd12680   8 LDFGVSDADIKELFAEFGTLKkaaVHY--DRSGRSLGTAEVVFERRADALKAM 58
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
 118-183 1.90e-03

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: 37.20  E-value: 1.90e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 118 LPFGCSKEEIVQFFSGLEIVpnGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI 183
Cdd:cd12402  10 LPYDVTEDDIEDFFRGLNIS--SVRLPREnGPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 115-174 1.97e-03

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


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 37.79  E-value: 1.97e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 115 LRGLPFGCSKEEIVQFFS---GLE---IVPNGMTlpvdfqGRSTGEAFVQFASQEIAEKALKKHKE 174
Cdd:cd12676   6 VRNLPFDATEDELYSHFSqfgPLKyarVVKDPAT------GRSKGTAFVKFKNKEDADNCLSAAPE 65
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 291-345 2.23e-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: 2.23e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIgpdgRVTGEADVEFATHEDAVAAM 345
Cdd:cd12421   2 VHIRNLPPDATEADLVALGLPFGKVTNVLLL----KGKNQALVEMEDVESASSMV 52
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 293-347 2.39e-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: 36.67  E-value: 2.39e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 293 MRGLPYRATENDIYNFFSPLNPMRvHIEIGPD---GRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd12674   5 VRNLPFDVTLESLTDFFSDIGPVK-HAVVVTDpetKKSRGYGFVSFSTHDDAEEALAK 61
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 3-171 2.65e-03

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 39.90  E-value: 2.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769     3 LSTEGREGFVVKVRGLPWSCSAEEVMRFFSDC-KIQNgtsgVRFIYTR-EGRPSGEAFVELESEDEVKLALKKDRETMGH 80
Cdd:TIGR01622 107 LTEDERDRRTVFVQQLAARARERDLYEFFSKVgKVRD----VQIIKDRnSRRSKGVGYVEFYDVDSVQAALALTGQKLLG 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769    81 RYVEVfKSNSVEMDWVLK---HTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSgleivPNGMTLPVDFQ-----GRST 152
Cdd:TIGR01622 183 IPVIV-QLSEAEKNRAARaatETSGHHPNSIPFHRLYVGNLHFNITEQDLRQIFE-----PFGEIEFVQLQkdpetGRSK 256

                         170
                  ....*....|....*....
gi 62078769   153 GEAFVQFASQEIAEKALKK 171
Cdd:TIGR01622 257 GYGFIQFRDAEQAKEALEK 275
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 118-184 3.25e-03

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


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 36.32  E-value: 3.25e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62078769 118 LPFGCSKEEIVQFFS------GLEIVPNGMTlpvdFQGRstGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 184
Cdd:cd12395   7 LPFDIEEEELRKHFEdcgdveAVRIVRDRET----GIGK--GFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
 18-85 3.85e-03

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


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 36.04  E-value: 3.85e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769  18 LPWSCSAEEVMRFFSDCKIQNgtsgVRFIYTRE-GRPSGEAFVELESEDEVKLALKKDRETMGHRYVEV 85
Cdd:cd12402  10 LPYDVTEDDIEDFFRGLNISS----VRLPRENGpGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
 115-170 3.91e-03

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


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 36.25  E-value: 3.91e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 62078769 115 LRGLPFGCSKEEIVQFFS-GLEIvpngmTLPVDFQGRSTGEAFVQFASQEIAEKALK 170
Cdd:cd12404   8 VKNLPYSTTQDELKEVFEdAVDI-----RIPMGRDGRSKGIAYIEFKSEAEAEKALE 59
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
 291-347 4.34e-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: 36.06  E-value: 4.34e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHEDAVAAMAK 347
Cdd:cd12320   3 LIVKNVPFEATRKEIRELFSPFGQLKsVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 291-341 4.85e-03

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: 36.64  E-value: 4.85e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPD-GRVTGEADVEFATHEDA 341
Cdd:cd12676   4 LFVRNLPFDATEDELYSHFSQFGPLKyARVVKDPAtGRSKGTAFVKFKNKEDA 56
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 135-171 4.86e-03

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


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 36.02  E-value: 4.86e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 62078769 135 EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 171
Cdd:cd12278  33 SGKIVGIYMPVDETGKTKGFAFVEYATPEEAKKAVKA 69
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 290-355 4.90e-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: 35.84  E-value: 4.90e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62078769 290 CVHMRGLPYRATENDIYNFFS--PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAmakdkANMQHR 355
Cdd:cd12748   2 CIYVRNLPFDVTKVEVQDFFEgfALAEDDIILLYDDKGVGLGEALVKFKSEEEAMKA-----ERLNGQ 64
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
 12-93 5.61e-03

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: 35.57  E-value: 5.61e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078769  12 VVKVRGLPWSCSAEEVMRFFSDCKIQNGtsGVRFIytreGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSNSV 91
Cdd:cd12744   3 VIRLQGLPVVAGSTDIRHFFTGLTIPDG--GVHII----GGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLSSKA 76


                ..
gi 62078769  92 EM 93
Cdd:cd12744  77 EM 78
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 291-349 5.71e-03

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 35.64  E-value: 5.71e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNP-----MRVHIEigpDGRVTGEADVEFATHEDAVAAMAKDK 349
Cdd:cd12291   2 VYVKGFPLDATLDDIQEFFEKKGKvenvrMRRDLD---SKEFKGSVFVEFKTEEEAKKFLEKEK 62
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 113-183 7.15e-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: 35.31  E-value: 7.15e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 113 VRLRGLPFGCSKEEIVQFFSGL-EIvpNGMTLPV---DFQGRST-GEAFVQFASQEIAEKALKKHKERIGHRYIEI 183
Cdd:cd12298   3 IRVRNLDFELDEEALRGIFEKFgEI--ESINIPKkqkNRKGRHNnGFAFVTFEDADSAESALQLNGTLLDNRKISV 76
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
112-171 8.13e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 35.46  E-value: 8.13e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62078769 112 FVRlrGLPFGCSKEEIVQFFSG------LEIVPNGMTlpvdfqGRSTGEAFVQFASQEIAEKALKK 171
Cdd:COG0724   5 YVG--NLPYSVTEEDLRELFSEygevtsVKLITDRET------GRSRGFGFVEMPDDEEAQAAIEA 62
RRM1_RBM12 cd12745
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
 291-363 8.26e-03

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: 35.78  E-value: 8.26e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62078769 291 VHMRGLPYRATENDIYNFFSPLNPmrvhieigPDGRV------TGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 363
Cdd:cd12745   5 IRLQGLPIVAGTMDIRHFFSGLTI--------PDGGVhivggeLGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSS 75
 
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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