RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822983 184 KMLLVYDLHLSPKlwslatppkngrvqekVMEYLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEF 263
Cdd:cd12289    1 RTVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEF 64

                         90       100
                 ....*....|....*....|....*....
gi 157822983 264 EEVDAAIKAHEFMATESQGKENMKAVLIG 292
Cdd:cd12289   65 EEVEAARKAHELLGAEDDGKGGIKVVLLG 93

RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822983 184 KMLLVYDLHLSPKlwslatppkngrvqekVMEYLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEF 263
Cdd:cd12289    1 RTVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEF 64

                         90       100
                 ....*....|....*....|....*....
gi 157822983 264 EEVDAAIKAHEFMATESQGKENMKAVLIG 292
Cdd:cd12289   65 EEVEAARKAHELLGAEDDGKGGIKVVLLG 93

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 157822983   96 LVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALK 153
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 157822983  88 PDEELIRKLVDQIEFYFSDENLEKDAFLLKHVRrnKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVTLELNEDHRKV 167
Cdd:COG5193  266 PILLSIMAKKEQIEYYFSEENLKSDEFLRKKFK--KAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEVVQNKATNHLEIA 343

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 157822983 168 RRTTPVPLFPNENLPSKMllvYDLHLSPKLWSLATPPKNG 207
Cdd:COG5193  344 LGSIEDAQKNEAKDFSPG---KKYFIRKKEWSEWLMESNF 380

RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822983 184 KMLLVYDLHLSPKlwslatppkngrvqekVMEYLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEF 263
Cdd:cd12289    1 RTVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEF 64

                         90       100
                 ....*....|....*....|....*....
gi 157822983 264 EEVDAAIKAHEFMATESQGKENMKAVLIG 292
Cdd:cd12289   65 EEVEAARKAHELLGAEDDGKGGIKVVLLG 93

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 157822983  93 IRKLVDQIEFYFSDENLEKDAFLLKHVrrNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVTLELNEDHRKVRR 169
Cdd:cd07323    1 LEKIKKQVEYYFSDENLCKDRFLRSLM--DDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822983  90 EELIRKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVTLELNEDHRKVRR 169
Cdd:cd08032    3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR 82

La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, 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 157822983  91 ELIRKlvdQIEFYFSDENLEKDAFLLKhvRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVTLELNEDhrKVRR 169
Cdd:cd08034    2 EYIKK---QIEYYFSVDNLEKDFFLRR--KMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVDE--KVRC 73

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822983  91 ELIRKLVDQIEFYFSDENLEKDAFLLKHVRRNKlGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVT--LELNEDHRKVR 168
Cdd:cd08028    3 DLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDD-GWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSglIEVSEDKTKIR 81

                 .
gi 157822983 169 R 169
Cdd:cd08028   82 R 82

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 157822983  99 QIEFYFSDENLEKDAFLLKhvRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVTLELNEdhRKVRR 169
Cdd:cd08038    7 QIEYYFSTENLERDFFLRR--KMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVD--QKIRR 73

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 157822983  452 PLLSRKMQTADGLPVGVLRLPRGPDDTRGFH 482
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31

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 157822983 215 EYLLKLFGTFGVISSVRILKpgrelppDIRRISSRYsqvgtqecAIVEFEEVDAAIKAHEFM 276
Cdd:cd00590   13 EDLRELFSKFGEVVSVRIVR-------DRDGKSKGF--------AFVEFESPEDAEKALEAL 59

RNA recognition motif (RRM) found in plant proteins related to the La autoantigen; This subfamily corresponds to the RRM of plant La-like 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. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 157822983 214 MEYLLKLFGTFGVISSVRILKPGRElpPDIRRISSRYSQVGTQECAIVEFEEVDAAIKA 272
Cdd:cd12288   14 IQNLREIFGTVGSVKNVRVCDPGRV--GSGEKAKKPDTFVSNKLHALVEYETVEAAEKA 70