Eukaryotic translation initiation factor 3 subunit G; This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with pfam00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083   18 APDITTNPDGTKTVITYRTNQDGKKVKITQKIKEVKVQERVHPLIAQRKNWKKYGKESKSPPGPDTSTTQLGEKVELKLG 97
Cdd:pfam12353   1 PPEIIENEDGTKTVIEYRINEDGKKVKVTRTIRRTKVKEKVNKAVAERKKWAKFGDEKGDPPGPNSATTTVGEEVFLKLS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 284018083   98 TSWKQQEKEEEEEKAENRAQKLSVqTIRCRTCGGDHYTSKCPFKDTL 144
Cdd:pfam12353  81 ANKKSTEKEEEEEDPKAKLKSKKK-LVKCRICKGDHWTSKCPYKDTL 126

Eukaryotic translation initiation factor 3 subunit G; This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with pfam00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083   18 APDITTNPDGTKTVITYRTNQDGKKVKITQKIKEVKVQERVHPLIAQRKNWKKYGKESKSPPGPDTSTTQLGEKVELKLG 97
Cdd:pfam12353   1 PPEIIENEDGTKTVIEYRINEDGKKVKVTRTIRRTKVKEKVNKAVAERKKWAKFGDEKGDPPGPNSATTTVGEEVFLKLS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 284018083   98 TSWKQQEKEEEEEKAENRAQKLSVqTIRCRTCGGDHYTSKCPFKDTL 144
Cdd:pfam12353  81 ANKKSTEKEEEEEDPKAKLKSKKK-LVKCRICKGDHWTSKCPYKDTL 126

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 189 TLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLEWS 265
Cdd:cd12408    1 TIRVTNLSEDATEEDLR-ELFRPFGPISRVYLAKDKETGQSKGFAFVTFETREDAERAIEKLNGFGYDNLILSVEWA 76

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 187 STTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLR-ELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGA 66

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083  163 GKYVPRHLRADAngnlPSKEgrddSTTLKVSQLNSFVDEDMLRnELFARFGPLQRVTlVRNRETGDSRGFAYVSFITEDM 242
Cdd:TIGR01628 162 GRFIKKHEREAA----PLKK----FTNLYVKNLDPSVNEDKLR-ELFAKFGEITSAA-VMKDGSGRSRGFAFVNFEKHED 231

                          90
                  ....*....|.
gi 284018083  243 AQRALDALNGK 253
Cdd:TIGR01628 232 AAKAVEEMNGK 242

Eukaryotic translation initiation factor 3 subunit G; This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with pfam00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083   18 APDITTNPDGTKTVITYRTNQDGKKVKITQKIKEVKVQERVHPLIAQRKNWKKYGKESKSPPGPDTSTTQLGEKVELKLG 97
Cdd:pfam12353   1 PPEIIENEDGTKTVIEYRINEDGKKVKVTRTIRRTKVKEKVNKAVAERKKWAKFGDEKGDPPGPNSATTTVGEEVFLKLS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 284018083   98 TSWKQQEKEEEEEKAENRAQKLSVqTIRCRTCGGDHYTSKCPFKDTL 144
Cdd:pfam12353  81 ANKKSTEKEEEEEDPKAKLKSKKK-LVKCRICKGDHWTSKCPYKDTL 126

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 189 TLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLEWS 265
Cdd:cd12408    1 TIRVTNLSEDATEEDLR-ELFRPFGPISRVYLAKDKETGQSKGFAFVTFETREDAERAIEKLNGFGYDNLILSVEWA 76

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 187 STTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLR-ELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGA 66

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 284018083  190 LKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRnRETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILH 261
Cdd:pfam00076   1 LFVGNLPPDTTEEDLK-DLFSKFGPIKSIRLVR-DETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 284018083 187 STTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:cd12363    1 SRCLGVFGLSLYTTERDLR-EVFSRYGPIEKVQVVYDQQTGRSRGFGFVYFESVEDAKEAKERLNG 65

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 284018083 189 TLKVSQLNSFVDEDMLRNElFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12236    3 TLFVARLSYDTTESKLRRE-FEKYGPIKRVRLVRDKKTGKSRGYAFIEFEHERDMKAAYKHADGK 66

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083 187 STTLKVSQLNSFVDEDMLRNElFARFGPLQRVTLVRNR---ETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLE 263
Cdd:cd12223    1 TTNLYVGNLPPSVTEEVLLRE-FGRFGPLASVKIMWPRteeERRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLG 79

                 ...
gi 284018083 264 WSK 266
Cdd:cd12223   80 WGK 82

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083 188 TTLKVSQLNSFVDEDMLrNELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLEWSKK 267
Cdd:cd12674    1 TTLFVRNLPFDVTLESL-TDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKP 79

                 .
gi 284018083 268 K 268
Cdd:cd12674   80 R 80

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 284018083 190 LKVSQLNSFVDEDMLRNeLFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:cd12284    1 LYVGSLHFNITEDMLRG-IFEPFGKIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKALEQLNG 62

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 284018083 207 ELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLEWSKKK 268
Cdd:cd12413   18 ELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 284018083 190 LKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12311    1 LKVDNLTYRTTPDDLR-RVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAIDAMDGA 63

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 284018083 190 LKVSQLNSFVDEDMLrNELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12449    3 LFVGGLSFDTNEQSL-EEVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGK 65

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 188 TTLKVSQLN-SFVDEDMlrNELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12393    2 STVYVSNLPfSLTNNDL--HQIFSKYGKVVKVTILKDKETRKSKGVAFVLFLDRESAHNAVRAMNNK 66

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 284018083 199 VDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALdALNGK 253
Cdd:cd12395   11 IEEEELR-KHFEDCGDVEAVRIVRDRETGIGKGFGYVLFKDKDSVDLAL-KLNGS 63

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 284018083 188 TTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNrETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12380    2 TNVYVKNFGEDVDDDELK-ELFEKYGKITSAKVMKD-DSGKSKGFGFVNFENHEAAQKAVEELNGK 65

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 284018083 190 LKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGK 253
Cdd:cd12231    3 LFIGGLPNYLNEDQVK-ELLQSFGKLKAFNLVKDSATGLSKGYAFCEYVDDNVTDQAIAGLNGM 65

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 284018083 190 LKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:cd12365    1 LHVGKLTRNVTKDHLK-EIFSVYGTVKNVDLPIDREPNLPRGYAYVEFESPEDAEKAIKHMDG 62

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 284018083 185 DDSTTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRA 246
Cdd:cd12237    2 DPRLTLFVGRLSLQTTEEKLK-EVFSRYGDIRRLRLVRDIVTGFSKRYAFIEYKEERDALHA 62

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 284018083 192 VSQLNSFVDEDMLRnELFARFGPLQRVTLVRNREtGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:cd12565    5 VKNLPKYVTEKRLK-EHFSKKGEITDVKVMRTKD-GKSRRFGFIGFKSEEEAQKAVKYFNK 63

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 284018083 188 TTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNReTGDSRGFAYVSFITEDMAQRALDALNGKGYHSLILHLE 263
Cdd:cd12418    1 TRVRVSNLHPDVTEEDLR-ELFGRVGPVKSVKINYDR-SGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVE 74

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284018083 178 LPSKEGrDDSTTLKVSQLNSFVDEDMLRNElFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKG 254
Cdd:cd21615   10 PHIADG-DPYKTLFVGRLDYSLTELELQKK-FSKFGEIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAFKEGNGLR 84

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 284018083  190 LKVSQLNSFVDEDMLRNeLFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:TIGR01622 217 LYVGNLHFNITEQDLRQ-IFEPFGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEKMNG 278

glycine-rich RNA-binding protein 4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083 175 NGNLP--SKEG--RDDSTTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDAL 250
Cdd:PLN03134  18 NGNVPvtSMLGslRLMSTKLFIGGLSWGTDDASLR-DAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

                 ...
gi 284018083 251 NGK 253
Cdd:PLN03134  97 DGK 99

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 284018083 201 EDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKG 254
Cdd:cd12366   16 EDDLR-EAFSPFGEIQDIWVVKDKQTKESKGIAYVKFAKSSQAARAMEEMHGKC 68

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284018083  156 GAGDNGPGKYVPRHLRADANGNLPSKEGRDDSTTLKVSqlnsFVDEDMLRNELFARF---GPLQRVTLVRNRETGDSRGF 232
Cdd:TIGR01659  76 GSMGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVN----YLPQDMTDRELYALFrtiGPINTCRIMRDYKTGYSFGY 151

                          90       100
                  ....*....|....*....|
gi 284018083  233 AYVSFITEDMAQRALDALNG 252
Cdd:TIGR01659 152 AFVDFGSEADSQRAIKNLNG 171

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 284018083 199 VDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNG 252
Cdd:cd12398   12 ATEEQLK-EIFSEVGPVVSFRLVTDRETGKPKGYGFCEFRDAETALSAVRNLNG 64

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 284018083 200 DEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDA----LNGK 253
Cdd:cd12325   11 TEESLR-EYFSKYGEVVDCVVMKDPATGRSRGFGFVTFKDPSSVDAVLAArphtLDGR 67

RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 284018083 197 SFVDEDmLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALD 248
Cdd:cd12367   11 SYTEED-LR-EKFKEFGDIEYCSIVKDKNTGESKGFGYVKFLKPSQAALAIE 60

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 284018083 189 TLKVSQLNSFVDEDMLRNELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALNGKGYHS 257
Cdd:cd12345    3 SLFVGDLAPDVTDYQLYETFSARYPSVRGAKVVMDPVTGRSKGYGFVRFGDESEQDRALTEMQGVYLGS 71

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 284018083 188 TTLKVSQLNSFVDEDMLRnELFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRA 246
Cdd:cd12235    4 NVLFVCKLNPVTTDEDLE-IIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKESCEEA 61

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 284018083 190 LKVSQLNSFVDEDMLRNeLFARFGPLQRVTLVRNRETGDSRGFAYVSFITEDMAQRALDALN 251
Cdd:cd12347    1 LYVGGLAEEVDEKVLHA-AFIPFGDIVDIQIPLDYETEKHRGFAFVEFEEAEDAAAAIDNMN 61