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 1894684306  70 RVKQVLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRI 149
Cdd:cd08032     1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRI 80

                  ..
gi 1894684306 150 RR 151
Cdd:cd08032    81 RR 82

RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins; This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306 503 GVIVKIISTEPLPGRKQIKDALAVLADVAYVDMLERDTECHVRFKTPEDAQIVMKSYKeiqiKNNWKFEVLAGDHEQRYW 582
Cdd:cd12542     1 GVIVKIILTEPLPGRKQFKDELKPLSDVAYVDILEGDTEAYVRFKTPEAAQKVVEQKK----KHNWKLEILSGDEEQRYW 76

                  ..
gi 1894684306 583 QK 584
Cdd:cd12542    77 QK 78

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 1894684306  70 RVKQVLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRI 149
Cdd:cd08032     1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRI 80

                  ..
gi 1894684306 150 RR 151
Cdd:cd08032    81 RR 82

RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins; This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306 503 GVIVKIISTEPLPGRKQIKDALAVLADVAYVDMLERDTECHVRFKTPEDAQIVMKSYKeiqiKNNWKFEVLAGDHEQRYW 582
Cdd:cd12542     1 GVIVKIILTEPLPGRKQFKDELKPLSDVAYVDILEGDTEAYVRFKTPEAAQKVVEQKK----KHNWKLEILSGDEEQRYW 76

                  ..
gi 1894684306 583 QK 584
Cdd:cd12542    77 QK 78

Domain in the RNA-binding Lupus La protein; unknown function;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1894684306   78 IAKQVDFWFGDVNLHKDRFLREQIEKSrDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRIRRR 152
Cdd:smart00715   7 IKKQVEYYFSDENLPRDKFLRKKMDKN-DGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1894684306  166 TVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG 63

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1894684306 164 SRTVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNG 65

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 1894684306  49 DKAMEEESTEQKKEREKKKRSRVKQVLADIAKQVDFWF-----GDVNLHKDRFLREQIEKS--RDGYVDISLLVSFNKMK 121
Cdd:COG5193    46 VIPVEELTESSKSKKEDKNPSKLTSNTKWTLKQVEFYFsgskdTDSNFPKDKFLKTTAPKNkkRDKWVPIKTIATFNRMK 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306 122 KLTTDGKLIARAVKSSS---VVELDLEGTRIRRRQPL---GEQPKDVDSRTVYVELLPKN--------VNHSWIERVFGK 187
Cdd:COG5193   126 NSGSPVSAVSGALRKSLdarVLEVSSSGSNKNRTEKLisnNNKSTSQMQRDVYQNGFGKEdvnnasrpEQQEDLEIQFPP 205

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1894684306 188 C--GNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAI-EFLNNPP-EEAPRKPGIFP 241
Cdd:COG5193   206 HyhAPPSQIRNRRDWLNKNFRGSVFVEFKYFREAQRFNnGFYRNKKyPNDPETVYYYS 263

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 1894684306  70 RVKQVLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRI 149
Cdd:cd08032     1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRI 80

                  ..
gi 1894684306 150 RR 151
Cdd:cd08032    81 RR 82

RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins; This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306 503 GVIVKIISTEPLPGRKQIKDALAVLADVAYVDMLERDTECHVRFKTPEDAQIVMKSYKeiqiKNNWKFEVLAGDHEQRYW 582
Cdd:cd12542     1 GVIVKIILTEPLPGRKQFKDELKPLSDVAYVDILEGDTEAYVRFKTPEAAQKVVEQKK----KHNWKLEILSGDEEQRYW 76

                  ..
gi 1894684306 583 QK 584
Cdd:cd12542    77 QK 78

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 1894684306  75 LADIAKQVDFWFGDVNLHKDRFLREQIEKsrDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRIRR 151
Cdd:cd07323     1 LEKIKKQVEYYFSDENLCKDRFLRSLMDD--DGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75

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 1894684306  78 IAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKS 136
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDPDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59

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 1894684306  73 QVLADIAKQVDFWFGDVNLHKDRFLREQIEKSrDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSS--VVELDLEGTRIR 150
Cdd:cd08028     3 DLEKKIIRQIEYYFGDFNLPRDKFLKEQIKED-DGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKsgLIEVSEDKTKIR 81

                  .
gi 1894684306 151 R 151
Cdd:cd08028    82 R 82

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 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRyKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVR-DETGRSKGFAFVEFEDEEDAEKAIEALNG 61

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 1894684306  75 LADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLtTDGKLIARAVKSSSVVELDLEGTRIRR 151
Cdd:cd08029     1 PEEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRESELLEVSEDGENVRR 76

La-motif domain of plant proteins similar to the La autoantigen; This domain is found in 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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306  76 ADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDG------------KLIARAVKSSSVVELD 143
Cdd:cd08030     3 EKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGggkpedvpedtlKAVAEALRTSTLLKVS 82

                  ....*...
gi 1894684306 144 LEGTRIRR 151
Cdd:cd08030    83 EDGKRVGR 90

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 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLN 227
Cdd:cd12448     1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALG 61

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 1894684306  78 IAKQVDFWFGDVNLHKDRFLREQIEKsrDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDleGTRIRR 151
Cdd:cd08034     4 IKKQIEYYFSVDNLEKDFFLRRKMDP--EGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELV--DEKVRC 73

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12365     1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDREPNLPRGYAYVEFESPEDAEKAIKHMDG 62

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12651     5 LYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKLTGRPRGVAFVRYDKREEAQAAISALNG 66

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNNPPEEAPRKP 237
Cdd:cd12376     3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGASEP 73

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1894684306 166 TVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNNP 229
Cdd:cd12450     1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRDDGRSKGFGHVEFASAESAQKALEKSGQD 64

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1894684306 164 SRTVYVELLPKN-VNHSWIERVFGKCGNVVY--ISIprykSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12390     2 SKCLFVDRLPKDfRDGSELRKLFSQVGKPTFcqLAM----GNGVPRGFAFVEFASAEDAEEAQQLLNG 65

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12334     1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDRVTQQHQGYGFVEFLSEEDADYAIKIMNM 62

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 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 1894684306 166 TVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12447     1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSG 63

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).

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1894684306 165 RTVYVELLPKNVNHSWIERVFGKCGNVVYISI---PRYKS--TGDPKGF-------AFVEFETKEQAEKAIEFLNNP 229
Cdd:cd12288     1 RTVVVENLPEDHSIQNLREIFGTVGSVKNVRVcdpGRVGSgeKAKKPDTfvsnklhALVEYETVEAAEKAVTELNNE 77

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1894684306 165 RTVYVELLPKNVNHSWIERVFGKCGNVVyisipRYK----STGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12446     1 TTVFVGNIPDDVSDDFIRQLLEKCGKVL-----SWKrvqdPSGKLKAFGFCEFEDPEGALRALRLLNG 63

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.

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                  ....*....|....*....|....*....|....*....|....
gi 1894684306 181 IERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIE 224
Cdd:cd12311    15 LRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAID 58

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1894684306  78 IAKQVDFWFGDVNLHKDRFLREQIEKSrdGYVDISLLVSFNKMKKLTTDGKLIARAVKSSsvVELDLEGTRIRR 151
Cdd:cd08038     4 IKRQIEYYFSTENLERDFFLRRKMDLQ--GFLPISLIAGFYRVQALTTNVDLILEALKDS--TEVEIVDQKIRR 73

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

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                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEF 225
Cdd:cd12271     1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRALAL 59

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKS---TGDPKGFAFVEFETKEQAEKAIEFLN 227
Cdd:cd12355     2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKTgplKGQPRGYCFVTFETKEEAEKAIECLN 65

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain 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.

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gi 1894684306 166 TVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLN 227
Cdd:cd12312     2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYIQFEDVRDAEDALYYLD 63

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 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. NAM8 also contains three RRMs.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1894684306 166 TVYVELLPKNVNHSWIERVFGKCG-NVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNNPPeeAPRKPGIF 240
Cdd:cd12344     1 TLWMGDLEPWMDEAYISSCFAKTGeEVVSVKIIRNKQTGKSAGYCFVEFATQEAAEQALEHLNGKP--IPNTQQRF 74

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1894684306 167 VYVELLPKNVNHSWIERVFGKCGNVVYISIPRykstgDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12373     2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVAR-----NPPGFAFVEFEDPRDAEDAVRALDG 58

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1894684306 163 DSRTVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKStGDPKGFAFVEFETKEQAEKAI 223
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRN-GKPKGLAYVEYENEADASQAV 60

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894684306 168 YVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNNppeeapRKPGIF--PKTVK 245
Cdd:cd12652     4 YVSGLPKTMTQKELEQLFSQFGRIITSRILCDNVTGLSRGVGFIRFDKRVEAERAIKALNG------TIPPGAtePITVK 77

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

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gi 1894684306 166 TVYVELLPKNVNHSWIERVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEFLNN 228
Cdd:cd12307     1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFEDPEVAKIVAETMNN 63

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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gi 1894684306 183 RVFGKCGNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIeFLNNPPEEAPRK 236
Cdd:cd12670    18 RYFGKCGAIESVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LLNEKPTMKGRK 70

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1894684306 166 TVYVELLPKNVNHSWIERVFGKCgNVVYISIPRYKSTGDPKGFAFVEFETKEQAEKAIEfLNNP 229
Cdd:cd12402     4 TAYLGNLPYDVTEDDIEDFFRGL-NISSVRLPRENGPGRLRGFGYVEFEDRESLIQALS-LNEE 65

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1894684306 163 DSRTVYVELLPKNVNHSWIERVFGKCgnvVYISIPRYKsTGDPKGFAFVEFETKEQAEKAIE 224
Cdd:cd12404     2 DARTLFVKNLPYSTTQDELKEVFEDA---VDIRIPMGR-DGRSKGIAYIEFKSEAEAEKALE 59