RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins; This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1516 ERRVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCFGGRR 1595
Cdd:cd12624     1 ERRVVYIGKIRGRMTRSELKDRFSVFGEIEECTIHFREEGDNYGFVTYRYTEDAFAAIENGHKLRRPDELPFDLCFGGRR 80

                          90
                  ....*....|.
gi 564333910 1596 QFCKRSYSDLD 1606
Cdd:cd12624    81 QFCKSSYADLD 91

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  379 DPALQLLMPAMEPGTEDGVPKVAPCPDQELPLSSACLLEPRDIMESLAPKEPRNLPANASEGSQRVPRKGRKKKKKEQPT 458
Cdd:PHA03247 2550 DPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPP 2629

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  459 AclegcTRRLRSSSRGQSTVATEVNSQAGNLQKQPQEELQRETAAPqsrGKPRAWARAWAAALEKTGSEDPEDQNAGQDS 538
Cdd:PHA03247 2630 S-----PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL---GRAAQASSPPQRPRRRAARPTVGSLTSLADP 2701

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  539 PAEEDVLELRPKLVETSQADPTLSLNDSARADSIPVNSVEgDSTAVDTAVPVDQASSCTElvgSLSGGPILSSPVLDDRT 618
Cdd:PHA03247 2702 PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAGPATPGGPARPARP---PTTAGPPAPAPPAAPAA 2777

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  619 GVEPAVAIPTSNHLSPADAILANPGTADPAPNGLAPGDPVLVKCRPTDPRRAAAAATAAQGPRPSLEPSDHPKVITPEVK 698
Cdd:PHA03247 2778 GPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVA 2857

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  699 dAGGPLKVEGST--SATTQEARPRPLSLSEYRQRRRQRQIEAEDRNSQPPAGKWPSLPETPKGLADIPCLVPSAPTKKTA 776
Cdd:PHA03247 2858 -PGGDVRRRPPSrsPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP 2936

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333910  777 PQRSPIAVPETcsvsvgsnpvSPTPEPSASKLMVSTHSEQVSSHEMPLP-VRLPPPTLQSMAPAGPTPS 844
Cdd:PHA03247 2937 PRPQPPLAPTT----------DPAGAGEPSGAVPQPWLGALVPGRVAVPrFRVPQPAPSREAPASSTPP 2995

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins; This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1516 ERRVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCFGGRR 1595
Cdd:cd12624     1 ERRVVYIGKIRGRMTRSELKDRFSVFGEIEECTIHFREEGDNYGFVTYRYTEDAFAAIENGHKLRRPDELPFDLCFGGRR 80

                          90
                  ....*....|.
gi 564333910 1596 QFCKRSYSDLD 1606
Cdd:cd12624    81 QFCKSSYADLD 91

RNA recognition motif;

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910   1519 VVFIGKIPGRMTRSELKQRFSVFGEIEECTIHF---RVQGDNYGFVTYRYAEEAFAAIES-------GHKLR 1580
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdkeTGKSKGFAFVEFESEEDAEKALEAlngkeldGRPLK 72

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  379 DPALQLLMPAMEPGTEDGVPKVAPCPDQELPLSSACLLEPRDIMESLAPKEPRNLPANASEGSQRVPRKGRKKKKKEQPT 458
Cdd:PHA03247 2550 DPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPP 2629

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  459 AclegcTRRLRSSSRGQSTVATEVNSQAGNLQKQPQEELQRETAAPqsrGKPRAWARAWAAALEKTGSEDPEDQNAGQDS 538
Cdd:PHA03247 2630 S-----PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL---GRAAQASSPPQRPRRRAARPTVGSLTSLADP 2701

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  539 PAEEDVLELRPKLVETSQADPTLSLNDSARADSIPVNSVEgDSTAVDTAVPVDQASSCTElvgSLSGGPILSSPVLDDRT 618
Cdd:PHA03247 2702 PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAGPATPGGPARPARP---PTTAGPPAPAPPAAPAA 2777

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  619 GVEPAVAIPTSNHLSPADAILANPGTADPAPNGLAPGDPVLVKCRPTDPRRAAAAATAAQGPRPSLEPSDHPKVITPEVK 698
Cdd:PHA03247 2778 GPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVA 2857

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  699 dAGGPLKVEGST--SATTQEARPRPLSLSEYRQRRRQRQIEAEDRNSQPPAGKWPSLPETPKGLADIPCLVPSAPTKKTA 776
Cdd:PHA03247 2858 -PGGDVRRRPPSrsPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP 2936

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333910  777 PQRSPIAVPETcsvsvgsnpvSPTPEPSASKLMVSTHSEQVSSHEMPLP-VRLPPPTLQSMAPAGPTPS 844
Cdd:PHA03247 2937 PRPQPPLAPTT----------DPAGAGEPSGAVPQPWLGALVPGRVAVPrFRVPQPAPSREAPASSTPP 2995

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333910  1515 EERRVVFIGKIPGRMTRSELKQRFSVFGEIEECT-IHFRVQGDN--YGFVTYRYAEEAFAAIESGHKLR 1580
Cdd:TIGR01661    1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKlVRDKVTGQSlgYGFVNYVRPEDAEKAVNSLNGLR 69

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910   707 EGSTSATTQEARPRPLSLSEYRQRRRQRQIEAEDRNSQPPAGKWPSLPETPKGLADIPCLVPSAPTKKTAP--------Q 778
Cdd:pfam03154  157 DSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPhtliqqtpT 236

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910   779 RSPIAVPETCSVSVGSNPVSPTPEPSASKLMVSTHSEQVSSheMPLPVRLPPPTLQSMAPAGPTPSTVPTPLPFPPSLPP 858
Cdd:pfam03154  237 LHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPP--MPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPS 314

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910   859 LLPLPASGPGVPSLPPPPLQPPGLPVSMRQMPPDPYTQ-------YAPVPPWPCYPS-------VSPSGY---SCLPPPP 921
Cdd:pfam03154  315 PAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMphikpppTTPIPQLPNPQShkhpphlSGPSPFqmnSNLPPPP 394

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910   922 AM----------------PIVSGTPGTYAVPPTCNVPWVPPPAPVSPYSSSSAYGSLGWGPGLQQPPFWSTVSPPPLSSA 985
Cdd:pfam03154  395 ALkplsslsthhppsahpPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPP 474

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910   986 STGRAVPPPSVEPSNSSAGPPED-----TLPVPVTPSLSSRPAS-PIAPPAEPTKLEAQPVPV-SPQPKHKV 1050
Cdd:pfam03154  475 ITPPSGPPTSTSSAMPGIQPPSSasvssSGPVPAAVSCPLPPVQiKEEALDEAEEPESPPPPPrSPSPEPTV 546

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins; This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1516 ERRVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCFGGRR 1595
Cdd:cd12624     1 ERRVVYIGKIRGRMTRSELKDRFSVFGEIEECTIHFREEGDNYGFVTYRYTEDAFAAIENGHKLRRPDELPFDLCFGGRR 80

                          90
                  ....*....|.
gi 564333910 1596 QFCKRSYSDLD 1606
Cdd:cd12624    81 QFCKSSYADLD 91

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins; This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1516 ERRVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCFGGRR 1595
Cdd:cd12623     1 ERRVIYVGKIRPDITRTELKRRFEVFGEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNEPDFELCFGGRK 80

                          90
                  ....*....|.
gi 564333910 1596 QFCKRSYSDLD 1606
Cdd:cd12623    81 QFCKSNYADLD 91

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).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDN--YGFVTYRYAEEAFAAIESGH 1577
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSkgFAFVEFESPEDAEKALEALN 60

RNA recognition motif;

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910   1519 VVFIGKIPGRMTRSELKQRFSVFGEIEECTIHF---RVQGDNYGFVTYRYAEEAFAAIES-------GHKLR 1580
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdkeTGKSKGFAFVEFESEEDAEKALEAlngkeldGRPLK 72

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDN--YGFVTYRYAEEAFAAIESGHKLR 1580
Cdd:cd12412     5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSkgYGFVTFETQEDAEKIQKWGANLV 67

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEECT-IHFRVQGDN--YGFVTYRYAEEAFAAIE 1574
Cdd:cd21608     2 LYVGNLSWDTTEDDLRDLFSEFGEVESAKvITDRETGRSrgFGFVTFSTAEAAEAAID 59

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEEC-TIHFRVQGDN--YGFVTYRYAEEAFAAIE 1574
Cdd:cd12384     3 IFVGGLPYHTTDDSLREYFEQFGEIEEAvVITDRQTGKSrgYGFVTMADREAAERACK 60

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910 1518 RVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYG--FVTYRYAEEAFAAIESGH 1577
Cdd:cd12635     2 RKLFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGcaFVKFSSHAEAQAAINALH 63

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910 1520 VFIGKIP-GRMTRSELKQRFSVFGEIEECTIHfrvqgDNYGFVTYRYAEEAFAAIeSGHKLRQADEQPFDLC 1590
Cdd:cd12341     3 IFVGNLPtDQMTKEDLEEIFSKYGKILGISLH-----KGYGFVQFDNEEDARAAV-AGENGRTIKGQRLDIN 68

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEECTIHF-----RVQGdnYGFVTYRYAEEAFAAIESG-HKL--RQAD 1583
Cdd:cd12325     1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKdpatgRSRG--FGFVTFKDPSSVDAVLAARpHTLdgRTID 70

DNA polymerase III subunit gamma/tau;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  918 PPPPAMPIVSGTPGTYAVPPTCNVPWVPPPAPVSPYSSSSAYGSLGWGPGLQQPPFWSTVSPPPLSSASTGRAVPPPSVE 997
Cdd:PRK12323  375 ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAP 454

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  998 PSNSSAGPPEDTLPVPVTPSLSSRPASPIAPPAEPTkleaqPVPVSPQPKHKVSPVVQSPQikvlPTLSAEGVAIGESES 1077
Cdd:PRK12323  455 AAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPA-----PADDDPPPWEELPPEFASPA----PAQPDAAPAGWVAES 525

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 564333910 1078 ERLKPETQENRPREKPISTATKAVLLPKQSTVAKLPAVHPARLRRLSFLPT 1128
Cdd:PRK12323  526 IPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDM 576

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 564333910 1519 VVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFR--VQGDNYGFVTYRYAEEAFA 1571
Cdd:cd12226     1 RLFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKkdAPDRGFAYIDLRTSEAALQ 55

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333910 1518 RVVFIGKIPGRMTRSELKQRFSVFGEIEECTIHFRVQGDNYG--FVTYRYAEEAFAAIESGH 1577
Cdd:cd12636     2 RKLFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGcaFVTFTSRQCAVNAIKAMH 63

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 564333910 1520 VFIGKIPGRMTRSELKQRFSVFGEIEECTIhFRVQGdnYGFVTYRYAEEAFAAI 1573
Cdd:cd12354     3 VYVGNITKGLTEALLQQTFSPFGQILEVRV-FPDKG--YAFIRFDSHEAATHAI 53

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 564333910 1521 FIGKIPGRMTRSELKQRFSVFGEIEECTIhfrVQGDNYGFVTYRYAEEAFAAIESGH 1577
Cdd:cd12340     3 FVRPFPPDTSESAIREIFSPYGPVKEVKM---LSDSNFAFVEFEELEDAIRAKDSVH 56

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910  978 SPPPLSSASTGRA----VPPPS------VEPSNSSAGPPEDTLPVPVTPSLSSRPASPIAPPAEPTKLEAQPVPVSPQPK 1047
Cdd:PHA03247 2574 APRPSEPAVTSRArrpdAPPQSarprapVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1048 HKVSPVVQSPQIKVlptlSAEGVAIGESESERlKPETQENRPREKPISTATKAVLLPKQ------STVAKLPAVHPARLR 1121
Cdd:PHA03247 2654 DDPAPGRVSRPRRA----RRLGRAAQASSPPQ-RPRRRAARPTVGSLTSLADPPPPPPTpepaphALVSATPLPPGPAAA 2728

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1122 RLSFLPTPRAQGSEDVVQAFISEIGiEASDLSSLLEQFEKSEAKKECPL--PAPADSVAVGNSGSIDTPQEKKPLD--RL 1197
Cdd:PHA03247 2729 RQASPALPAAPAPPAVPAGPATPGG-PARPARPPTTAGPPAPAPPAAPAagPPRRLTRPAVASLSESRESLPSPWDpaDP 2807

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1198 HAPELANVAGLTPPATPPHQLWKPLAAV---SLLAKAKSPKSTAQEGTLKPEGITEAKPPAaaclqegvRGPSPVHVgsg 1274
Cdd:PHA03247 2808 PAAVLAPAAALPPAASPAGPLPPPTSAQptaPPPPPGPPPPSLPLGGSVAPGGDVRRRPPS--------RSPAAKPA--- 2876

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333910 1275 dhdycVRSRTPPKKMPALVISEMGSRWNVKRHQditIKPVLSLGSAAPPLPCTTTSQEPLDHRTSSEQADPSAPcFAPST 1354
Cdd:PHA03247 2877 -----APARPPVRRLARPAVSRSTESFALPPDQ---PERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPP-LAPTT 2947

                  ....*...
gi 564333910 1355 LLSPEASP 1362
Cdd:PHA03247 2948 DPAGAGEP 2955