RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725 151 GIHKWISDYADSVPDPEALRVEVDTFMEAYDQKIAEEEAKAKEEeGVPDEEGWVKVTRRGRRPVLPRTEAASLRVLERER 230
Cdd:cd12951   1 GLKKWVEEYNASIPDPAELQSEIDEYMEEYDKEEEEEKEEKEKE-AEPDEDGWVTVTKKGRRPKTARKESVAAKAAEKEK 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 25092725 231 RKRSRKELLNFYAWQHRESKMEHLAQLRKKFEEDKQRIELLRAQRKFRPY 280
Cdd:cd12951  80 KKKKKKELKNFYRFQIRESKRNELAELRKKFEEDKKRIALLKAARKFKPY 129

RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725 151 GIHKWISDYADSVPDPEALRVEVDTFMEAYDQKIAEEEAKAKEEeGVPDEEGWVKVTRRGRRPVLPRTEAASLRVLERER 230
Cdd:cd12951   1 GLKKWVEEYNASIPDPAELQSEIDEYMEEYDKEEEEEKEEKEKE-AEPDEDGWVTVTKKGRRPKTARKESVAAKAAEKEK 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 25092725 231 RKRSRKELLNFYAWQHRESKMEHLAQLRKKFEEDKQRIELLRAQRKFRPY 280
Cdd:cd12951  80 KKKKKKELKNFYRFQIRESKRNELAELRKKFEEDKKRIALLKAARKFKPY 129

deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 25092725  22 GYAAIPIKF----SEKQQASHYLYVRAHGVRQgTKSTWPQKRTLFVLNVPPYCTEESLSRLLS-TCGLVQSV 88
Cdd:cd12293   5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGlGGGRIESV 75

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 25092725    61 LFVLNVPPYCTEESLSRLLSTCGLVQSVELQEKPDlaespkeSRSKFFhpkpvpgfqvAYVVFQKPSGVSAALA 134
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDET-------GRSKGF----------AFVEFEDEEDAEKAIE 57

RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725 151 GIHKWISDYADSVPDPEALRVEVDTFMEAYDQKIAEEEAKAKEEeGVPDEEGWVKVTRRGRRPVLPRTEAASLRVLERER 230
Cdd:cd12951   1 GLKKWVEEYNASIPDPAELQSEIDEYMEEYDKEEEEEKEEKEKE-AEPDEDGWVTVTKKGRRPKTARKESVAAKAAEKEK 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 25092725 231 RKRSRKELLNFYAWQHRESKMEHLAQLRKKFEEDKQRIELLRAQRKFRPY 280
Cdd:cd12951  80 KKKKKKELKNFYRFQIRESKRNELAELRKKFEEDKKRIALLKAARKFKPY 129

Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain; RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725   162 SVPDPEALRVEVDTFMEAYDQKIAEEEAKAKEEEGVPDEEGWVKVTRRGrrPVLPRTEAASLRVLERERRKRSRKELLNF 241
Cdd:pfam12923   3 SRPDPEALQQEVDEYMEEFDAEEEEEKRERKKARNEPDEDGFVTVTRGG--PGGARKEAAEEKIAKKEKKKKKKKELLDF 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 25092725   242 YAWQHRESKMEHLAQLRKKFEEDKQRIELLRAQRKFRPY 280
Cdd:pfam12923  81 YRFQIREKKKNELAELRKKFEEDKEKIEKLKESRKFKPY 119

deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 25092725  22 GYAAIPIKF----SEKQQASHYLYVRAHGVRQgTKSTWPQKRTLFVLNVPPYCTEESLSRLLS-TCGLVQSV 88
Cdd:cd12293   5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGlGGGRIESV 75

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 25092725  61 LFVLNVPPYCTEESLSRLLSTCGLVQSVELQEKPDlaespkeSRSKFFhpkpvpgfqvAYVVFQKPSgvSAALALK 136
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRD-------GKSKGF----------AFVEFESPE--DAEKALE 57

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 25092725    61 LFVLNVPPYCTEESLSRLLSTCGLVQSVELQEKPDlaespkeSRSKFFhpkpvpgfqvAYVVFQKPSGVSAALA 134
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDET-------GRSKGF----------AFVEFEDEEDAEKAIE 57

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is 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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725  60 TLFVLNVPPYCTEESLSRLLSTCGLVQSVEL-QEKpdlaespKESRSKffhpkpvpgfQVAYVVFQKPSGVSAALALKGP 138
Cdd:cd12283   1 TVFVMQLSLKARERDLYEFFSKAGKVRDVRLiMDR-------NSRRSK----------GVAYVEFYDVESVPLALALTGQ 63

                ..
gi 25092725 139 LL 140
Cdd:cd12283  64 RL 65

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725  59 RTLFVLNVPPYCTEESLSRLLSTCGLVQSVELqekpdlaesPKESRSKFFHPKpvPGFqvAYVVFQKPSGVSAALALKGP 138
Cdd:cd12298   1 REIRVRNLDFELDEEALRGIFEKFGEIESINI---------PKKQKNRKGRHN--NGF--AFVTFEDADSAESALQLNGT 67

                ..
gi 25092725 139 LL 140
Cdd:cd12298  68 LL 69

Rrp7 RRM-like N-terminal domain; This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25092725    22 GYAAIPIKF----SEKQQASHYLYVRAHgvrQGTKSTWPQKRTLFVLNVPPYCTEESLSRLLSTCGLVQSVELQEKPDLA 97
Cdd:pfam17799   4 GFHVLPVRLppspSLPKKATHYIYFKKH---QTKNNDEASSRSLFLVNLPINTNFATLKKFFGTVALGATIESFVSSLLT 80

                  ....*.
gi 25092725    98 ESPKES 103
Cdd:pfam17799  81 DEQEDV 86

RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1; This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 25092725  63 VLNVPPYCTEESLSRLLSTCGLVQSVELQEKPDLAespkesrskffhpkpvpgfQVAYVVFQKPSGVSAALALKGPLLV 141
Cdd:cd12269   3 VTNVSPLATERDLHEFFSFSGDIEHIEIQREGEQS-------------------RIAFVTFKDPYALETAVLLSGATIV 62

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 25092725  63 VLNVPPYCTEESLSRLLSTCGLVQSVELQekPDLAeSPKESRSKffhpkpvpgfqVAYVVFQKPSGVSAALALKGPLLV 141
Cdd:cd12259   4 VTNVSPQATEEQMRTLFGFIGKIEELRLY--PSED-DLAPVLSK-----------VCFVKYEDPEDVAVALHLTNTVFI 68