NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species; The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension , found in Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA), Chironomus tentans hrp65 gene encoding protein Hrp65 and similar proteins. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 420 LRPCLVEPMEVNDDNDGLPEKALNKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLE 499
Cdd:cd12945     1 LRPCVVEPMEEIDDEDGLPEKSLNKKNPEFNKERSIGPRFAEPNSFEHEYGTRWKQLHELYKQKEEALKRELKMEEEKLE 80

                          90       100
                  ....*....|....*....|
gi 1810772822 500 AQMEYARYEQETELLRQELR 519
Cdd:cd12945    81 AQMEYARYEHETELLREQLR 100

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1810772822 274 RNRLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRF 344
Cdd:cd12332     1 RCRLFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGKGFGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71

NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species; The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension , found in Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA), Chironomus tentans hrp65 gene encoding protein Hrp65 and similar proteins. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 420 LRPCLVEPMEVNDDNDGLPEKALNKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLE 499
Cdd:cd12945     1 LRPCVVEPMEEIDDEDGLPEKSLNKKNPEFNKERSIGPRFAEPNSFEHEYGTRWKQLHELYKQKEEALKRELKMEEEKLE 80

                          90       100
                  ....*....|....*....|
gi 1810772822 500 AQMEYARYEQETELLRQELR 519
Cdd:cd12945    81 AQMEYARYEHETELLREQLR 100

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1810772822 274 RNRLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRF 344
Cdd:cd12332     1 RCRLFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGKGFGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1810772822  276 RLYVGNLTGDVTDDELREMFKPFGEIGEIF------SNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV 342
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRlvrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1810772822 275 NRLYVGNLTGDVTDDELREMFKPFGEIGEI------FSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRFA 345
Cdd:COG0724     2 MKIYVGNLPYSVTEEDLRELFSEYGEVTSVklitdrETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEA 78

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 264 EVPTEAKFSGrnrLYVGNLTGDVTDDELREMFKPFGEIGEIF-----SNVEKNFTFLKVDYHINAEKAKRALDGS----- 333
Cdd:TIGR01628 171 EAAPLKKFTN---LYVKNLDPSVNEDKLRELFAKFGEITSAAvmkdgSGRSRGFAFVNFEKHEDAAKAVEEMNGKkigla 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 334 ---------------------MRKGRQLRVRFAPNATI--LRVSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLG 390
Cdd:TIGR01628 248 kegkklyvgraqkraereaelRRKFEELQQERKMKAQGvnLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRG 327

                         170       180
                  ....*....|....*....|....
gi 1810772822 391 EGIVEFAKKSSASACLRLCNEKCF 414
Cdd:TIGR01628 328 FGFVCFSNPEEANRAVTEMHGRML 351

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1810772822  351 LRVSNLTPFVSNELLYKSFEIFGPIERASITVD-DRGKHLGEGIVEFAKKSSASACLRLCNEKCF 414
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDkETGKSKGFAFVEFESEEDAEKALEALNGKEL 66

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 481 KSKQDALKRELKMEEDKLEAQMEyaryEQETELLRQELRKREVDNERKKMEWEMREKQVEDMRKREEETMRRHQSEMQNH 560
Cdd:pfam02841 194 QTDQALTAKEKAIEAERAKAEAA----EAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREQLLAEQERMLEH 269

                          90       100
                  ....*....|....*....|....*..
gi 1810772822 561 MLRQEEDMRRRQQENTLFMQAQQLNSL 587
Cdd:pfam02841 270 KLQEQEELLKEGFKTEAESLQKEIQDL 296

PA2816 family glutamine-rich protein; Members of this family, including PA2816 from Pseudomonas aeruginosa, average about 140 amino acids in length, with an N-terminal signal peptide. The last 100 amino acids are extremely glutamine-rich. The family appears restricted to the genus Pseudomonas. The function is unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 508 EQETELLRQELRKREVDNERKKMEWEMREKQVEDMR-KREEETMRRhqsemQNHMLRQEEDMRRRQQENTLFMQAQQLNS 586
Cdd:NF041511   42 QRQQDSLRRQAEQRRRQQQDQRLQYEDQRLQMKQQQlKRQQDAQQR-----QRQQRRLQDQMIQRQQSDLQQFRLQQQQQ 116

                  ....*
gi 1810772822 587 LLDQQ 591
Cdd:NF041511  117 QLDQQ 121

NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species; The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension , found in Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA), Chironomus tentans hrp65 gene encoding protein Hrp65 and similar proteins. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 420 LRPCLVEPMEVNDDNDGLPEKALNKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLE 499
Cdd:cd12945     1 LRPCVVEPMEEIDDEDGLPEKSLNKKNPEFNKERSIGPRFAEPNSFEHEYGTRWKQLHELYKQKEEALKRELKMEEEKLE 80

                          90       100
                  ....*....|....*....|
gi 1810772822 500 AQMEYARYEQETELLRQELR 519
Cdd:cd12945    81 AQMEYARYEHETELLREQLR 100

NOPS domain, including C-terminal helical extension region, in the p54nrb/PSF/PSP1 family; All members in this family contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRM1 and RRM2), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain with a long helical C-terminal extension. The NOPS domain specifically binds to RRM2 domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. PSF has an additional large N-terminal domain that differentiates it from other family members. The p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein 1 (PSP1), which are ubiquitously expressed and are well conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1, also termed PSPC1, is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species. For instance, the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 421 RPCLVEPMEVNDDNDGLPEKALnKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLEA 500
Cdd:cd12931     2 RPVVVEPLEQRDEEDGLPERNV-KKNAGYQKEREVGPRFAPPGSFEYEFGQRWKALYELEKQQREQLEKELKEAREKLEA 80

                          90
                  ....*....|
gi 1810772822 501 QMEYARYEQE 510
Cdd:cd12931    81 EMEAARYEHQ 90

NOPS (NUC059) domain; This domain is found at the C-terminus of NONA and PSP1 proteins adjacent to 1 or 2 pfam00076 domains.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1810772822 422 PCLVEPMEVNDDNDGLPEKALNKKmPEFNQERSVGPRFADINSFEHEYGSRWK 474
Cdd:pfam08075   1 PVIVEPLEQEDDEDGLPEKSLPKN-PDFQKEREVGPRFAQPGSFEHEYGQRWK 52

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1810772822 351 LRVSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLGEGIVEFAKKSSASACLRLCNEKCFFLTASLRPCLVEPME 429
Cdd:cd12589     2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPPARKALERCSDGAFLLTTTPRPVIVEPME 80

NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins; The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, found in the p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Members in the family include 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein component 1 (PSPC1 or PSP1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSPC1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSPC1 remains unknown currently. PSF has an additional large N-terminal domain that differentiates it from other family members.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 421 RPCLVEPMEVNDDNDGLPEKaLNKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLEA 500
Cdd:cd12946     2 RPVIVEPMEQLDDEDGLPEK-LAQKNQQYHKEREQPPRFAQPGTFEYEYAQRWKALDEMEKQQREQVDRNIKEAKEKLES 80

                          90
                  ....*....|...
gi 1810772822 501 QMEYARYEQETEL 513
Cdd:cd12946    81 EMEAARHEHQAML 93

NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins; This model contains the NOPS (NONA and PSP1) domain PSF (also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex), with a long helical C-terminal extension. PSF is a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also single-stranded DNA (ssDNA) as well as double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Additionally, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. As an RNA-binding component of spliceosomes, PSF binds to the insulin-like growth factor response element (IGFRE), and acts as an independent negative regulator of the transcriptional activity of the porcine P-450 cholesterol side-chain cleavage enzyme gene (P450scc) IGFRE. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. In addition, PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NONO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 421 RPCLVEPMEVNDDNDGLPEKaLNKKMPEFNQERSVGPRFADINSFEHEYGSRWKQLHDLYKSKQDALKRELKMEEDKLEA 500
Cdd:cd12948     2 RPVIVEPLEQLDDEDGLPEK-LAQKNPMYQKERETPPRFAQPGTFEYEYSQRWKSLDEMEKQQREQVEKNMKEAKEKLES 80

                          90
                  ....*....|....*..
gi 1810772822 501 QMEYARYEQETELLRQE 517
Cdd:cd12948    81 EMEDAYHEHQANLLRQD 97

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1810772822 274 RNRLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRF 344
Cdd:cd12587     1 RCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRVRF 71

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1810772822 274 RNRLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRF 344
Cdd:cd12586     1 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF 71

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1810772822 351 LRVSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLGEGIVEFAKKSSASACLRLCNEKCF 414
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKEL 64

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 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVE-----KNFTFLKVDYHINAEKAKRALDGSMRKGRQLR 341
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetgrsKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1810772822 278 YVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLR 341
Cdd:cd12354     4 YVGNITKGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAIVSVNGTIINGQAVK 67

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIF------SNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV 342
Cdd:cd12311     1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYiprdryTRESRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVeKNFTFLKVDYH-I-NAEKAKRALDGSMRKGRQLRVRFA 345
Cdd:cd12524     4 LFVRNINSSVEDEELRALFEQFGEIRTLYTAC-KHRGFIMVSYYdIrAAQSAKRALQGTELGGRKLDIHFS 73

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 1810772822 351 LRVSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLGEGIVEFAKKSSASACLRLCNEKCFF 415
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELG 65

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1810772822 276 RLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVE------KNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV 342
Cdd:cd12316     1 RLFVRNLPFTATEDELRELFEAFGKISEVHIPLDkqtkrsKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIF----SNVEKNFTFLKVDY--HINAEKAKRALDGSMRKGRQLRVRFAPNATI 350
Cdd:TIGR01628   3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRvcrdSVTRRSLGYGYVNFqnPADAERALETMNFKRLGGKPIRIMWSQRDPS 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1810772822 351 LR--------VSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLGEGIVEFAKKSSASA 404
Cdd:TIGR01628  83 LRrsgvgnifVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKA 144

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1810772822  351 LRVSNLTPFVSNELLYKSFEIFGPIERASITVD-DRGKHLGEGIVEFAKKSSASACLRLCNEKCF 414
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDkETGKSKGFAFVEFESEEDAEKALEALNGKEL 66

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1810772822 276 RLYVGNLTGDVTDDELREMFKPFGEIGEifSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV 342
Cdd:cd12343     1 KIFVGNLPDAATSEELRALFEKYGKVTE--CDIVKNYAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). 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. 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 first RRM motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1810772822 276 RLYVGNLTGDVTDDELREMFKPFG--EIGEIFSNVE----KNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRFA 345
Cdd:cd21609     1 RLYVGNIPRNVTSEELAKIFEEAGtvEIAEVMYDRYtgrsRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNIT 76

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins; This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRF 344
Cdd:cd12331     6 LFIGGVTLNMKEWDLRSVFKRFGEVQSVILNNSRRHAFVKMYSRHEAENALQAMEKVPDGDLPLRTRW 73

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVE------KNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRFA 345
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDretkrpRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNEA 75

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKA-KRALDGSMRKGRQLRVR 343
Cdd:cd12224     4 LYVGGLGDKITEKDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAaERTFNKLIIKGRRLKVK 71

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1810772822 277 LYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLR 341
Cdd:cd12346     4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIR 68

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1810772822 276 RLYVGNLTGDVTDDELREMFKPFGEIGEIFSNVEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV 342
Cdd:cd12340     1 RLFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 269 AKFSGRNRLYVGNLTGDVTDDELREMFKPFGEI--GEIFSNVE---KNFTFLKVDYHINAEKAKRALDGSMRKGRQLRV- 342
Cdd:TIGR01628  83 LRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNIlsCKVATDENgksRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVg 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1810772822 343 RF----------APNATILRVSNLTPFVSNELLYKSFEIFGPIERASITVDDRGKHLGEGIVEFAKKSSASACLRLCNEK 412
Cdd:TIGR01628 163 RFikkhereaapLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGK 242