La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114227  64 EAEVLKQVEFYFSDTNLPHDKFLWTTSQK-NDGWVPIQTIANFKRMRRFQPLEAIVNALRKSpELLEVDEAGEKVRR 139
Cdd:cd08029   1 PEEIRKQVEFYFSDSNLPTDKFLWTLTGGsNNGWVPIKTIASFKRMRRFQPLEAVVEALRES-ELLEVSEDGENVRR 76

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114227    67 VLKQVEFYFSDTNLPHDKFLWTTSQKN-DGWVPIQTIANFKRMRRFQP-LEAIVNALRK 123
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDpDGYVPISVIASFKRMKKLTTdIDLIAEALRE 59

La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114227  64 EAEVLKQVEFYFSDTNLPHDKFLWTTSQK-NDGWVPIQTIANFKRMRRFQPLEAIVNALRKSpELLEVDEAGEKVRR 139
Cdd:cd08029   1 PEEIRKQVEFYFSDSNLPTDKFLWTLTGGsNNGWVPIKTIASFKRMRRFQPLEAVVEALRES-ELLEVSEDGENVRR 76

LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114227  67 VLKQVEFYFSDTNLPHDKFLWTTSqKNDGWVPIQTIANFKRMRRFQP-LEAIVNALRKSPeLLEVDEAGEKVRR 139
Cdd:cd07323   4 IKKQVEYYFSDENLCKDRFLRSLM-DDDGWVPLSLLASFNRVKKLTTdVELILEALRDSS-VVEVSEDGTKVRR 75

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114227 155 SVYCKGFGdeKDDTQIALEKFFEEnAGPISAVRMRRD-DDKKFKGSVFVEFKEPDVANKFLEKvktAPLKWGEDELTIM 232
Cdd:cd12291   1 TVYVKGFP--LDATLDDIQEFFEK-KGKVENVRMRRDlDSKEFKGSVFVEFKTEEEAKKFLEK---EKLKYKGKELTIM 73

La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114227  65 AEVLKQVEFYFSDTNLPHDKFLWTTSQKN-DGWVPIQTIANFKRMRRF-QPLEAIVNALRKSpELLEVDEAGEKVRR 139
Cdd:cd08033   2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNkEGYVPIKLIASFKKVKALtRDWRVVAAALRRS-SKLVVSEDGKKVRR 77

La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114227  66 EVLK-QVEFYFSDTNLPHDKFLwtTSQKN-DGWVPIQTIANFKRMRRF-QPLEAIVNALRKSPeLLEVDEAGEKVR 138
Cdd:cd08031   2 ELLKrQLEYYFSRENLANDAYL--LSQMDsDQYVPIWTIANFNKIKKLtTDIDLIVEALRESP-NVQVDEKGEKVR 74

La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114227  65 AEVLKQVEFYFSDTNLPHDKFLWTTSQKN-DGWVPIQTIANFKRMRRFQPLEAIVNALRKSPELLEVDEAGEKVRR 139
Cdd:cd08032   7 ADIAKQVDFWFGDVNLHKDRFLREQIEKSrDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR 82

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 19114227 156 VYCKGFGDEKDDTQiaLEKFFEEnAGPISAVRMRRDDDKKFKGSVFVEFKEPDVANKFLEK 216
Cdd:cd00590   1 LFVGNLPPDTTEED--LRELFSK-FGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEA 58

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 19114227   156 VYCKGFGdeKDDTQIALEKFFEEnAGPISAVRMRRDDDKKFKGSVFVEFKEPDVANKFLEKV 217
Cdd:pfam00076   1 LFVGNLP--PDTTEEDLKDLFSK-FGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAL 59

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 19114227 156 VYCKGFGDEKDDTQiaLEKFFEEnAGPISAVRMRRDDDKKFKGSVFVEFKEPDVANKFLE 215
Cdd:cd12380   4 VYVKNFGEDVDDDE--LKELFEK-YGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVE 60

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 19114227 168 TQIALEKFFEEnAGPISAVRMRRD-DDKKFKGSVFVEFKEPDVANKFLEK 216
Cdd:cd12450  12 TQDDLENFFSD-CGEVVDVRIAMDrDDGRSKGFGHVEFASAESAQKALEK 60

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114227 153 ERSVYCKGFgdEKDDTQIALEKFFEENAGPISAVRMRRDDDKKFKGSvFVEFKEPDVANKFLE 215
Cdd:cd12460   4 ARTIYCTNI--DKKVTQDDVKAFFESLCGEVHRLRLLGDYVHSTRIA-FVEFVMAESAIAALN 63

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 19114227 166 DDTQIALEKFFEeNAGPISAVRMRRD-DDKKFKGSVFVEFKEPDVANKFLE 215
Cdd:cd12400  11 DTTAEDLKEHFK-KAGEPPSVRLLTDkKTGKSKGCAFVEFDNQKALQKALK 60

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 19114227 165 KDDTQIALEKFFEENAGPISAVRMRRDDDKKFKGSVFVEFKEPDVANKFLEK 216
Cdd:cd12267  10 KDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 61

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114227   156 VYCKGFGDEKDDTQiaLEKFFEEnAGPISAVRMRRDDDKKFKGSVFVEFKEPDVANKFLEKV 217
Cdd:TIGR01628 181 LYVKNLDPSVNEDK--LRELFAK-FGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239