PBC domain; The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060  47 INDMLQKIMSIVNERLDDA--QERKHAFNSNK-------------------------DEPSDPQLMRLDNMLMAEGVSSN 99
Cdd:pfam03792   2 ISDLLQQIMKITDMSLDEAavNKLKHALNCHPmypalfsvlceikektvlsirmikeEEPPDNQLMRLDNMLLAEGVAGP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 100 sstavnavnastnvtGGNGNNLDSDSALEHSDYRAKLAQIRQIYHAELEKYEQHCNDFCSHVVTLLREQSQARPITAREI 179
Cdd:pfam03792  82 ---------------EKSGSAEAEDNGIDQSDYRAKLAQIRQIYHSELEKYEQACNEFTEHVRNLLREQSEFRPITPKEI 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2041616060 180 DRMVDIIRKKFSSIQLQLKQSTCEAVMILRSRFLD 214
Cdd:pfam03792 147 ERMVSIISKKFNKIQEQLKQSTCEAVMILRSRFLD 181

Homeodomain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 216 RRKRRNFSKTATEVLNEYFyshLSNPYPSEDAKEELARKCAISVSQVSNWFGNKRIRYKK 275
Cdd:pfam00046   1 RRKRTTFTPEQLEELEKEF---QENPYPSAEEREELAAQLGLTERQVKVWFQNRRAKWKR 57

PBC domain; The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060  47 INDMLQKIMSIVNERLDDA--QERKHAFNSNK-------------------------DEPSDPQLMRLDNMLMAEGVSSN 99
Cdd:pfam03792   2 ISDLLQQIMKITDMSLDEAavNKLKHALNCHPmypalfsvlceikektvlsirmikeEEPPDNQLMRLDNMLLAEGVAGP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 100 sstavnavnastnvtGGNGNNLDSDSALEHSDYRAKLAQIRQIYHAELEKYEQHCNDFCSHVVTLLREQSQARPITAREI 179
Cdd:pfam03792  82 ---------------EKSGSAEAEDNGIDQSDYRAKLAQIRQIYHSELEKYEQACNEFTEHVRNLLREQSEFRPITPKEI 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2041616060 180 DRMVDIIRKKFSSIQLQLKQSTCEAVMILRSRFLD 214
Cdd:pfam03792 147 ERMVSIISKKFNKIQEQLKQSTCEAVMILRSRFLD 181

Homeodomain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 216 RRKRRNFSKTATEVLNEYFyshLSNPYPSEDAKEELARKCAISVSQVSNWFGNKRIRYKK 275
Cdd:pfam00046   1 RRKRTTFTPEQLEELEKEF---QENPYPSAEEREELAAQLGLTERQVKVWFQNRRAKWKR 57

Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2041616060  216 RRKRRNFSKTATEVLNEYFyshLSNPYPSEDAKEELARKCAISVSQVSNWFGNKRIRYK 274
Cdd:smart00389   2 RRKRTSFTPEQLEELEKEF---QKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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 2041616060 357 DDTFEELFieleKKYGEIEEMNICDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIY 419
Cdd:pfam00076  12 EEDLKDLF----SKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|....*..
gi 2041616060 427 DFHEACCRQYQMGDCPRGGFCNFMHLK 453
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 341 KSMGDNLTEEkvQEHFDDTFEELFIELEKKYGEIEEMNICDNLSehlAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYA 420
Cdd:TIGR01622 405 SNMFDPATEE--EPNWDKEIEDDVREECSKYGGVVHIYVDDKNS---AGDIYLKFDSVQAAEAAIKALNGRYFGGKMITA 479

                          90
                  ....*....|..
gi 2041616060 421 ELSPVTDFHEAC 432
Cdd:TIGR01622 480 AFVVDAVYSKSR 491

PBC domain; The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060  47 INDMLQKIMSIVNERLDDA--QERKHAFNSNK-------------------------DEPSDPQLMRLDNMLMAEGVSSN 99
Cdd:pfam03792   2 ISDLLQQIMKITDMSLDEAavNKLKHALNCHPmypalfsvlceikektvlsirmikeEEPPDNQLMRLDNMLLAEGVAGP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 100 sstavnavnastnvtGGNGNNLDSDSALEHSDYRAKLAQIRQIYHAELEKYEQHCNDFCSHVVTLLREQSQARPITAREI 179
Cdd:pfam03792  82 ---------------EKSGSAEAEDNGIDQSDYRAKLAQIRQIYHSELEKYEQACNEFTEHVRNLLREQSEFRPITPKEI 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2041616060 180 DRMVDIIRKKFSSIQLQLKQSTCEAVMILRSRFLD 214
Cdd:pfam03792 147 ERMVSIISKKFNKIQEQLKQSTCEAVMILRSRFLD 181

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 321 QTILMKNLYLS-LENSSQKADKsmGDNLTEEKVQEHFDDTFEELFIELeKKYGEIEEMNICDNLSEHLAGNCYVKFRFEE 399
Cdd:cd12539     1 PTILLSNMYQNpIMNAPLGAAQ--GIPLDPRELQEHFEDFYEDVFEEL-SKFGEVEALNVCDNLGDHMVGNVYVKFRDEE 77

                          90       100
                  ....*....|....*....|....*
gi 2041616060 400 DAEKAVGDLNNRWFDARAIYAELSP 424
Cdd:cd12539    78 HAAAALKALQGRFYAGRPIIVEFSP 102

Homeodomain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 216 RRKRRNFSKTATEVLNEYFyshLSNPYPSEDAKEELARKCAISVSQVSNWFGNKRIRYKK 275
Cdd:pfam00046   1 RRKRTTFTPEQLEELEKEF---QENPYPSAEEREELAAQLGLTERQVKVWFQNRRAKWKR 57

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 322 TILMKNLYLSL---ENSSQKADKSMGDNLTEEKVQEHFDDTFEELFIELeKKYGEIEEMNICDNLSEHLAGNCYVKFRFE 398
Cdd:cd12540     1 TLLIPNMFNTFgleQCKRDDYDTDAGLEYSEEDLYSDFLEFYEDVLPEF-KKFGKVVQFKVCCNSEPHLRGNVYVQYQSE 79

                          90       100
                  ....*....|....*....|....*.
gi 2041616060 399 EDAEKAVGDLNNRWFDARAIYAELSP 424
Cdd:cd12540    80 EEALKAFTSFNGRWYAGKQLQCEFSP 105

Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2041616060  216 RRKRRNFSKTATEVLNEYFyshLSNPYPSEDAKEELARKCAISVSQVSNWFGNKRIRYK 274
Cdd:smart00389   2 RRKRTSFTPEQLEELEKEF---QKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2041616060 361 EELFIELE-------KKYGEIEEMNICDNLSEhlaGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYAELSP 424
Cdd:cd12285    18 DNWDDEIKedvieecSKYGPVLHIYVDKNSPQ---GNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAYVP 85

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2041616060  345 DNLTEEKVQEHFddtfeelfieleKKYGEIEEMNIC-DNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIY 419
Cdd:smart00360   9 PDTTEEELRELF------------SKFGKVESVRLVrDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72

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 2041616060 357 DDTFEELFieleKKYGEIEEMNICDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIY 419
Cdd:pfam00076  12 EEDLKDLF----SKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|....*..
gi 2041616060 427 DFHEACCRQYQMGDCPRGGFCNFMHLK 453
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2041616060 352 VQEHFDDTFEElfIELE-KKYGEIEEMNIC--DNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYAELSP 424
Cdd:cd12374    12 PGEIDEDLKDE--IKEEcSKYGKVLNVIIHevASSEADDAVRVFVEFEDADEAIKAFRALNGRFFGGRKVKARFYD 85

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 2041616060 348 TEEKVQEHFDdtfeelfielekKYGEIEEMNI-CDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIY 419
Cdd:cd12316    12 TEDELRELFE------------AFGKISEVHIpLDKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLH 72

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2041616060 357 DDTFEELFIELEKKYGEIEEMNI--CDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYA 420
Cdd:cd12647    17 DEDLEPEVKEECEKYGKVTKVVIfeIPGAPDDEAVRIFVEFERVESAIKAVVDLNGRFFGGRTVKA 82

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 341 KSMGDNLTEEkvQEHFDDTFEELFIELEKKYGEIEEMNICDNLSehlAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYA 420
Cdd:TIGR01622 405 SNMFDPATEE--EPNWDKEIEDDVREECSKYGGVVHIYVDDKNS---AGDIYLKFDSVQAAEAAIKALNGRYFGGKMITA 479

                          90
                  ....*....|..
gi 2041616060 421 ELSPVTDFHEAC 432
Cdd:TIGR01622 480 AFVVDAVYSKSR 491

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2041616060 357 DDTFEELFieleKKYGEIEEMNICDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAIYA 420
Cdd:cd12380    15 DDELKELF----EKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2041616060 356 FDDTFEELFiELEKKYGEIEEMNI-CDNLSEHLAGNCYVKFRFEEDAEKAVGDLNNRWFDARAI 418
Cdd:cd12448     8 FSATQDALY-EAFSQHGSIVSVRLpTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPI 70

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2041616060 340 DKSMGDNLTEEKVQEHFddtfeelfieleKKYGEIEEMNI-CDNLSEHLAGNCYVKFRFEEDAEKAVgDLNNRWFDARAI 418
Cdd:cd12451     8 DASLGEDTIRDELREHF------------GECGEVTNVRIpTDRETGELKGFAYIEFSTKEAKEKAL-ELNGSDIAGGNL 74

                  ....*
gi 2041616060 419 YAELS 423
Cdd:cd12451    75 VVDEA 79