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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158519843  22 GYSAIPIKF----SEKQQSSHYLYVREHKVREgTKSPWPPKRTLFVLNVPPYCTEECLLRLLSP-CGPVQSV 88
Cdd:cd12293    5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGLgGGRIESV 75

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158519843  22 GYSAIPIKF----SEKQQSSHYLYVREHKVREgTKSPWPPKRTLFVLNVPPYCTEECLLRLLSP-CGPVQSV 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.

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                  ....*....|....*....|....*....|
gi 158519843   61 LFVLNVPPYCTEECLLRLLSPCGPVQSVEL 90
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRL 30

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158519843  59 RTLFVLNVPPYCTEECLLRLLSPCGPVQSVELQEKPelAESPKEPP-----SKFFHPKPVPgfQVAYVLFQKPGSVSAAL 133
Cdd:cd12394    1 RTVFVGNLPVTVKKKALKKLFKEFGKIESVRFRSVA--VANPKLPKkvaviKKKFHPKRDS--MNAYVVFKEEESAQKAL 76

                 ....*..
gi 158519843 134 ALKGPLL 140
Cdd:cd12394   77 KLNGTEF 83

RNA recognition motif;

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158519843    60 TLFVLNVPPYCTEECLLRLLSPCGPVQSVELqekpelaesPKEPPSKffHPKpvpGFqvAYVLFQKPGSVSAALAL 135
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRL---------VRDKETG--KSK---GF--AFVEFESEEDAEKALEA 60

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are 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. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158519843  62 FVLNVPPYCTEECLLRLLSPCGPVQSVELqekpelaespkePPSKFF-HPKpvpGFqvAYVLFQKPGSVSAALALKGPLL 140
Cdd:cd12306    3 YVGNVDYGTTPEELQAHFKSCGTINRVTI------------LCDKFTgQPK---GF--AYIEFVDKSSVENALLLNESEF 65

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158519843  60 TLFVLNVPPYCTEECLLRLLSPCGPVQSVELqekpelaespkepPSKFFHPKPvpgfQVAYVLFQKPGSVSAALALKGPL 139
Cdd:cd12297    2 TLWVTNFPPSYDERSIRDLFGDYGVILSVRL-------------PSLRYNTSR----RFCYIDFTSPESARAAVELLNGL 64

                 ....
gi 158519843 140 LVST 143
Cdd:cd12297   65 LEEG 68

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent 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.

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                 ....*....|....*....|....*....|.
gi 158519843  60 TLFVLNVPPYCTEECLLRLLSPCGPVQSVEL 90
Cdd:cd12377    1 CIFVYNLAPDADESLLWQLFGPFGAVQNVKI 31

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.

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                 ....*....|....*....|....*....|....*..
gi 158519843  59 RTLFVLNVPPYCTEECLLRLLSPCGPVQSVELQEKPE 95
Cdd:cd12275    2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISE 38