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 1102295114 193 QKIVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd08033     2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR 77

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 1102295114 193 QKIVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd08033     2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR 77

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 1102295114 195 IVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILR 252
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDPDGYVPISVIASFKRMKKLTTDIDLIAEALR 58

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 198 QVEFYFSDINLATTDHLIRIMFKDP-------EGYVPMSVVASFKKIKALTSSHALVAKILRASTK---LVVSEDGKKVR 267
Cdd:COG5193    78 QVEFYFSGSKDTDSNFPKDKFLKTTapknkkrDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDarvLEVSSSGSNKN 157

                          90
                  ....*....|....*.
gi 1102295114 268 RQFPLSEKDLEELQSR 283
Cdd:COG5193   158 RTEKLISNNNKSTSQM 173

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 1102295114 193 QKIVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd08033     2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR 77

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 1102295114 193 QKIVNQVEFYFSDINLATTDHLIRIMfkDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd07323     2 EKIKKQVEYYFSDENLCKDRFLRSLM--DDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75

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 1102295114 194 KIVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTsSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd08029     3 EIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQ-PLEAVVEALRESELLEVSEDGENVRR 76

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1102295114 193 QKIVNQVEFYFSDINLAtTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILRAS-TKLV-VSEDGKKVRR 268
Cdd:cd08028     6 KKIIRQIEYYFGDFNLP-RDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSkSGLIeVSEDKTKIRR 82

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 1102295114 195 IVNQVEFYFSDINLATTDHLIRIMFKDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRR 268
Cdd:cd08032     9 IAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR 82

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). 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 1102295114 198 QVEFYFSDINLATTDHLIRIMfkDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVR 267
Cdd:cd08035     7 QLEFCFSRENLSKDLYLISQM--DSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVR 74

La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related protein 2 (LARP2). 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 1102295114 195 IVNQVEFYFSDINLATTDHLIRIMfkDPEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEdgKKVRR 268
Cdd:cd08038     4 IKRQIEYYFSTENLERDFFLRRKM--DLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVD--QKIRR 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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 289 NLPEDHCHQNLMKIFSAVGSVKMIRTCQPqssnggassasRTGKSdstlystKLHAFVEYESVELAEKAVMELNdeNNWR 368
Cdd:cd00590     5 NLPPDTTEEDLRELFSKFGEVVSVRIVRD-----------RDGKS-------KGFAFVEFESPEDAEKALEALN--GTEL 64

                  ....*..
gi 1102295114 369 NGLKLRI 375
Cdd:cd00590    65 GGRPLKV 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1102295114 289 NLPEDHCHQNLMKIFSAVGSVKMIRTCQPQssnggassasrTGKSdstlystKLHAFVEYESVELAEKAVMELN 362
Cdd:pfam00076   5 NLPPDTTEEDLKDLFSKFGPIKSIRLVRDE-----------TGRS-------KGFAFVEFEDEEDAEKAIEALN 60

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 282 SRIVVAENLPEDHCHQN-LMKIFSAVGSVKMirtCQpqssnggasSASRTGKSdstlystKLHAFVEYESVELAEKAVME 360
Cdd:cd12390     2 SKCLFVDRLPKDFRDGSeLRKLFSQVGKPTF---CQ---------LAMGNGVP-------RGFAFVEFASAEDAEEAQQL 62

                          90       100
                  ....*....|....*....|....*.
gi 1102295114 361 LNDENnwRNGLKLRILNRCTGKSGQN 386
Cdd:cd12390    63 LNGHD--LQGSPIRVSFGNPGRPGAS 86

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 193 QKIVNQVEFYFSDINLaTTDHLIRIMFKDpEGYVPMSVVASFKKIKALTSSHALVAKILRASTKLVVSEDGKKVRRQFPL 272
Cdd:COG5193   272 MAKKEQIEYYFSEENL-KSDEFLRKKFKK-AGFIPLSFIGKFYRNLSFGGDKNLILAAMKEVVQNKATNHLEIALGSIED 349

                          90
                  ....*....|.
gi 1102295114 273 SEKDLEELQSR 283
Cdd:COG5193   350 AQKNEAKDFSP 360

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 289 NLPEDHCHQNLMKIFSAVGSVKMIRTCqpqssnggasSASRTGKSDSTlystklhAFVEYESVELAEKAVMELNDENNwR 368
Cdd:cd12415     7 NLSFDTTEEDLKEFFSKFGEVKYARIV----------LDKDTGHSKGT-------AFVQFKTKESADKCIEAANDESE-D 68

                          90
                  ....*....|.
gi 1102295114 369 NGLKL--RILN 377
Cdd:cd12415    69 GGLVLdgRKLI 79

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102295114 284 IVVAENLPEDHCHQNLMKIFSAVGSVKMIRTCQPQssnggassasrtgksdstlysTKLHAFVEYESVELAEKAVMELND 363
Cdd:cd12422     3 LVTVTNLLYPVTVDVLHQVFSPYGAVEKIVIFEKG---------------------TGVQALVQFDSVESAEAAKKALNG 61

                          90
                  ....*....|..
gi 1102295114 364 ENNWRNGLKLRI 375
Cdd:cd12422    62 RNIYDGCCTLDI 73