RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 102 YRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRLIED 173
Cdd:cd12600     1 YRLIVENLSSRVSWQDLKDYMRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNGYGFVEFDDYRDADDAVYELNGKKLLGERVTVERARG 74
Cdd:cd12337     1 RVYIGRLPYRARERDVERFFRGYGRIRDINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 102 YRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRLIED 173
Cdd:cd12600     1 YRLIVENLSSRVSWQDLKDYMRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNGYGFVEFDDYRDADDAVYELNGKKLLGERVTVERARG 74
Cdd:cd12337     1 RVYIGRLPYRARERDVERFFRGYGRIRDINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70

Dual specificity phosphatase, catalytic domain; Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 313 LFLGSQDCCDLETLTNYKISFVLSVGIEAPTKYDNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRNVLVHCNAGV 392
Cdd:pfam00782   1 LYLGSKPTASDAFLSKLGITAVINVTREVDLYNSGILYLRIPVEDNHETNISKYLEEAVEFIDDARQKGGKVLVHCQAGI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1572956523 393 SRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQL 435
Cdd:pfam00782  81 SRSATLIIAYLMKTRNLSLNEAYSFVKERRPGISPNFGFKRQL 123

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDV-LIKN-------GYGFVEFDDYRDADDAVYELNGKKLLGERVTVERARgtP 76
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVkLITDretgrsrGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEAR--P 80

                  .
gi 1572956523  77 R 77
Cdd:COG0724    81 R 81

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1572956523  103 RLIVENLSSRISWQDLKDYMRQAGEVTYAD-----AHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRL 170
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRlvrdkETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   6 VYVGGLPYGTTERDLERFFRGYGRMRDV-LIKN-------GYGFVEFDDyRDADDAVYELNGKKLLGERVTVERARGTpr 77
Cdd:TIGR01622 117 VFVQQLAARARERDLYEFFSKVGKVRDVqIIKDrnsrrskGVGYVEFYD-VDSVQAALALTGQKLLGIPVIVQLSEAE-- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523  78 gRDQWSSRSDHRSHEryGPPTRTNYRLIVENLSSRISWQDLKDYMRQAGEVTYADAHK-----QHRNEGVVEFASYSDLK 152
Cdd:TIGR01622 194 -KNRAARAATETSGH--HPNSIPFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKdpetgRSKGYGFIQFRDAEQAK 270

                         170
                  ....*....|....*...
gi 1572956523 153 NAIEKLDDSELNGRRIRL 170
Cdd:TIGR01622 271 EALEKMNGFELAGRPIKV 288

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 103 RLIVENLSSRISWQDLKDYMRQAGEVTYAD-----AHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIR 169
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKlitdrETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   3 GSRVYVGGLPYGTTERDLERFFRGYGRM--RDVLIKN------GYGFVEFDDYRDADDAVYELNGKKLLG--ERVTVERA 72
Cdd:TIGR01661  89 GANLYVSGLPKTMTQHELESIFSPFGQIitSRILSDNvtglskGVGFIRFDKRDEADRAIKTLNGTTPSGctEPITVKFA 168

glycine-rich RNA-binding protein 4; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1572956523 103 RLIVENLSSRISWQDLKDYMRQAGEVTYADA-----HKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRL 170
Cdd:PLN03134   36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVivdreTGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV 108

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 102 YRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRLIED 173
Cdd:cd12600     1 YRLIVENLSSRVSWQDLKDYMRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72

RNA recognition motif 2 (RRM2) found found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subgroup corresponds to the RRM2 of SRSF6, also termed pre-mRNA-splicing factor SRp55, an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1572956523 102 YRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRLIEDK 174
Cdd:cd12766     1 YRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERTNEGVIEFRSYSDMKRALEKLDGTEINGRKIRLVEDK 73

dual specificity phosphatase domain of dual specificity protein phosphatase 19; Dual specificity protein phosphatase 19 (DUSP19), also called low molecular weight dual specificity phosphatase 3 (LMW-DSP3) or stress-activated protein kinase (SAPK) pathway-regulating phosphatase 1 (SKRP1), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP19 interacts with the MAPK kinase MKK7, a JNK activator, and inactivates the JNK MAPK pathway.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 307 AKITDYLFLGSQDCC-DLETLTNYKISFVLSVGIEAPTKY-DNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRNV 384
Cdd:cd14523     3 GVIKPWLLLSSQDVAhDLETLKKHKVTHILNVAYGVENAFpDDFTYKTISILDLPETDITSYFPECFEFIDEAKSQDGVV 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1572956523 385 LVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLKK 437
Cdd:cd14523    83 LVHCNAGVSRSASIVIGYLMATENLSFEDAFSLVKNARPSIRPNPGFMEQLKE 135

RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM2 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5), is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523  93 RYGPPTRTNYRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQHRNEGVVEFASYSDLKNAIEKLDDSELNGRRIRLIE 172
Cdd:cd12765     1 RNAPPMRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKLNEGVVEFASYSDLKNAIEKLSGKEINGRKIKLIE 80

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNGYGFVEFDDYRDADDAVYELNGKKLLGERVTVERARG 74
Cdd:cd12596     3 RVYIGRLSYHVREKDIQRFFSGYGKLLEVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHARG 72

Dual specificity phosphatase, catalytic domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523  306 PAKITDYLFLGSQDC-CDLETLTNYKISFVLSVGIEAPtKYDNVVYKFVHC--LDLPETNLQGILNESVSFIELAVLKQR 382
Cdd:smart00195   1 PSEILPHLYLGSYSDaLNLALLKKLGITHVINVTNEVP-NYNGSDFTYLGVpiDDNTETKISPYFPEAVEFIEDAESKGG 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1572956523  383 NVLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLKKL 438
Cdd:smart00195  80 KVLVHCQAGVSRSATLIIAYLMKTRNMSLNDAYDFVKDRRPIISPNFGFLRQLIEY 135

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNGYGFVEFDDYRDADDAVYELNGKKLLGERVTVERAR 73
Cdd:cd12595     1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCNERVTIEHAR 69

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 4 (SRSF4); This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   4 SRVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNGYGFVEFDDYRDADDAVYELNGKKLLGERVTVERARGTPRGRDQWS 83
Cdd:cd12594     2 PRVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARGPRRDGSYGS 81

                  ....*
gi 1572956523  84 SRSDH 88
Cdd:cd12594    82 GRSGY 86

dual specificity phosphatase domain of slingshot family phosphatases; The slingshot (SSH) family of dual specificity protein phosphatases is composed of Drosophila slingshot phosphatase and its vertebrate homologs: SSH1, SSH2 and SSH3. Its members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. In Drosophila, loss of ssh gene function causes prominent elevation in the levels of P-cofilin and filamentous actin and disorganized epidermal cell morphogenesis, including bifurcation phenotypes of bristles and wing hairs. SSH family phosphatases contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. In addition, many members contain a C-terminal tail. The SSH-N domain plays critical roles in P-cofilin recognition, F-actin-mediated activation, and subcellular localization of SSHs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGSQ-DCCDLETLTNYKISFVLSVGIEAPTKYDNVV-YKFVHCLDLPETNLQGILNESVSFIELAVLKQRN 383
Cdd:cd14513     1 ASKIFDHLYLGSEwNASNLEELQNNGVKYILNVTREIDNFFPGRFtYHNIRVWDEESTNLLPYWNETYRFIKEARRKGSK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 384 VLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQL 435
Cdd:cd14513    81 VLVHCKMGVSRSASTVIAYAMKEYGWSLEQALEHVKERRSCIKPNPGFLRQL 132

dual specificity protein phosphatase 22; Dual specificity protein phosphatase 22 (DUSP22), also called JNK-stimulatory phosphatase-1 (JSP-1), low molecular weight dual specificity phosphatase 2 (LMW-DSP2), mitogen-activated protein kinase phosphatase x (MKP-x) or VHR-related MKPx (VHX), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP22 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP22 negatively regulates the estrogen receptor-alpha-mediated signaling pathway and the IL6-leukemia inhibitory factor (LIF)-STAT3-mediated signaling pathway. It also regulates cell death by acting as a scaffold protein for the ASK1-MKK7-JNK signal transduction pathway independently of its phosphatase activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 308 KITDYLFLGS-QDCCDLETLTNYKISFVLSVGIEAPTKYDNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRNVLV 386
Cdd:cd14581     6 KVLPGLYLGNfKDARDREQLSKNNITHILSVHDSARPMLEGMTYLCIPAADSPSQNLTQHFKESIKFIHECRLRGEGCLV 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1572956523 387 HCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLKKLSSNFV 443
Cdd:cd14581    86 HCLAGVSRSVTLVVAYIMTVTDFGWEDALSAVKAARSCANPNMGFQRQLQEFEKHEV 142

dual specificity phosphatase domain of mitogen-activated protein kinase phosphatase; Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs, which are involved in gene regulation, cell proliferation, programmed cell death and stress responses, as an important feedback control mechanism that limits MAPK cascades. MKPs, also referred to as typical DUSPs, function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGS-QDCCDLETLTNYKISFVLSVGIEAPTKYDNVV--YKFVHCLDLPETNLQGILNESVSFIELAVLKQR 382
Cdd:cd14512     1 PTRILPNLYLGSqRDSLNLELMQQLGIGYVLNVSNTCPNPDFIGLfhYKRIPVNDSFCQNISPWFDEAIEFIEEAKASNG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1572956523 383 NVLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQL 435
Cdd:cd14512    81 GVLVHCLAGISRSATIAIAYLMKRMRMSLDEAYDFVKEKRPTISPNFNFMGQL 133

dual specificity phosphatase domain of class III mitogen-activated protein kinase phosphatase; Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs and function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). Class III MKPs consist of DUSP8, DUSP10/MKP-5 and DUSP16/MKP-7, and are JNK/p38-selective phosphatases, which are found in both the cell nucleus and cytoplasm. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGSQ-DCCDLETLTNYKISFVLSVGIEAPtKYDNVVYKfvHCLDLPET-----NLQGILNESVSFIELAVL 379
Cdd:cd14568     1 PTRILPHLYLGSQrDVLDKDLMQRNGISYVLNVSNTCP-KPDFIPDS--HFLRIPVNdsyceKLLPWLDKAVEFIEKARA 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1572956523 380 KQRNVLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQL 435
Cdd:cd14568    78 SNKRVLVHCLAGISRSATIAIAYIMKHMRMSLDDAYRFVKEKRPTISPNFNFLGQL 133

dual specificity phosphatase domain of class I mitogen-activated protein kinase phosphatase; Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs and function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). Class I MKPs consist of DUSP1/MKP-1, DUSP2 (PAC1), DUSP4/MKP-2 and DUSP5. They are all mitogen- and stress-inducible nuclear MKPs. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGSQ-DCCDLETLTNYKISFVLSVGIEAP-TKYDNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRN 383
Cdd:cd14565     1 PVEILPFLYLGSAyHASRREVLKALGITAVLNVSRNCPnHFEDHFQYKSIPVEDSHNADISSWFEEAIGFIDKVKASGGR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1572956523 384 VLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLKKLSS 440
Cdd:cd14565    81 VLVHCQAGISRSATICLAYLMTTRRVRLNEAFDYVKQRRSVISPNFNFMGQLLQYES 137

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523   6 VYVGGLPYGTTERDLERFFRGYGRMRDVLIKN-------GYGFVEFDDYRDADDAVYELNGKKLLGERVT 68
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrskGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins; This subfamily corresponds to the RRM2 of serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. SRSF1, also termed ASF-1, is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9, also termed SRp30C, has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1572956523 102 YRLIVENLSSRISWQDLKDYMRQAGEVTYADAHKQhrNEGVVEFASYSDLKNAIEKLDDSE 162
Cdd:cd12601     1 YRVIVSGLPPTGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFLRYEDMKYAVRKLDDSK 59

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1572956523   5 RVYVGGLPYGTTERDLERFFRGYGRMRDVLIKNG-----YGFVEFDDYRDADDAVYELNGKKLLGERVTVE 70
Cdd:cd12338     1 RIYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRrrgppFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVE 71

dual specificity phosphatase domain of slingshot homolog 1; Dual specificity protein phosphatase slingshot homolog 1 (SSH1), also called SSH-like protein 1, is part of the slingshot (SSH) family, whose members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. SSH1 links NOD1 signaling to actin remodeling, facilitating the changes that leads to NF-kappaB activation and innate immune responses. There are at least two human SSH1 isoforms reported: hSSH-1L (long) and hSSH-1S (short). As SSH family phosphatases, they contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. They also contain C-terminal tails, differing in the lengths of the tail.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGSQ-DCCDLETLTNYKISFVLSVGIEAPTKYDNV-VYKFVHCLDLPETNLQGILNESVSFIELAVLKQRN 383
Cdd:cd14570     4 ASLIFDHLYLGSEwNASNLEELQGSGVGYILNVTREIDNFFPGLfAYHNIRVYDEETTDLLAHWNDAYHFINKAKKNHSK 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1572956523 384 VLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQL 435
Cdd:cd14570    84 CLVHCKMGVSRSASTVIAYAMKEFGWSLEKAYNFVKQKRSITRPNAGFMRQL 135

dual specificity phosphatase-like domain of serine/threonine/tyrosine-interacting protein; Serine/threonine/tyrosine-interacting protein (STYX), also called protein tyrosine phosphatase-like protein, is a catalytically inactive member of the protein tyrosine phosphatase family that plays an integral role in regulating pathways by competing with active phosphatases for binding to MAPKs. It acts as a nuclear anchor for MAPKs, affecting their nucleocytoplasmic shuttling.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 313 LFLGSQDCC---DLETLTNYKISFVLSV--GIEA----PTKYDNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRN 383
Cdd:cd14522    12 LYLGPYSAAmksKLEVLLKHGITHIVCVrqNIEAnfikPNFPDHFRYLVLDVADNPTENIIRHFPTVKEFIDDCLQTGGK 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1572956523 384 VLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLK 436
Cdd:cd14522    92 VLVHGNAGISRSAALVIAYIMETYGLSYRDAFAYVQQRRFCINPNEGFVHQLK 144

dual specificity phosphatase domain of dual specificity protein phosphatase 15; Dual specificity protein phosphatase 15 (DUSP15), also called Vaccinia virus VH1-related dual-specific protein phosphatase Y (VHY) or VH1-related member Y, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). DUSP15 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It is highly expressed in the testis and is located in the plasma membrane in a myristoylation-dependent manner. It may be involved in the regulation of meiotic signal transduction in testis cells. It is also expressed in the brain and has been identified as a regulator of oligodendrocyte differentiation. DUSP15 contains an N-terminal catalytic dual specificity phosphatase domain and a short C-terminal tail.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 308 KITDYLFLGS-QDCCDLETLTNYKISFVLSVGiEAPTKY-DNVVYKFVHCLDLPETNLQGILNESVSFIELAVLKQRNVL 385
Cdd:cd14582     7 KVLPGLYLGNfIDAKDLEQLSRNKITHIISIH-ESPQPLlQDITYLRIPLPDTPEAPIKKHFKECISFIHQCRLNGGNCL 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1572956523 386 VHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLKKLS 439
Cdd:cd14582    86 VHCLAGISRSTTIVVAYVMAVTELSWQEVLEAIRAVRPIANPNPGFKQQLEEFG 139

dual specificity phosphatase domain of fungal YVH1-like dual specificity protein phosphatase; This family is composed of Saccharomyces cerevisiae dual specificity protein phosphatase Yvh1 and similar fungal proteins. Yvh1 could function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It regulates cell growth, sporulation, and glycogen accumulation. It plays an important role in ribosome assembly. Yvh1 associates transiently with late pre-60S particles and is required for the release of the nucleolar/nuclear pre-60S factor Mrt4, which is necessary to construct a translation-competent 60S subunit and mature ribosome stalk. Yvh1 contains an N-terminal catalytic dual specificity phosphatase domain and a C-terminal tail.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 306 PAKITDYLFLGSqdccdLETLTN------YKISFVLSV--GIEAPTKYDNVVYKFVHCLDLPETNLQGILNESVSFIELA 377
Cdd:cd14518     1 LSRILGGLYLGG-----IEPLNRnrllkaENITHILSVipGDVPEEYFKGYEHKQIEIDDVEDENILQHFPETNRFIDSA 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1572956523 378 -----------VLKQRNVLVHCNAGVSRSASVVIGYLILVCHFSYCNAYLTVKNARSCIRPNDGFVEQLK 436
Cdd:cd14518    76 lfgngkdedeeKKHGGAVLVHCAMGKSRSVTVVIAYLMYKYNLSVSQALHAVRRKRPIAEPNDGFMEQLE 145