RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. 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. Rrp7A, also termed gastric cancer antigen Zg14, is the Rrp7p homolog mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Both Rrp7p and Rrp7A harbor 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 1860672248 195 GLSHYLTLYDSLRPPLDIVQAYVDSAMELYEFEIAKSKQKSKyrKGEAIVDEDGFTLVTRGGAYGQTLGGGVTVASKKFQ 274
Cdd:cd12950     1 GLARYRAHYRRLRPPLEALQESVDSFMALFEAREEERKRERK--RLRNEPDEDGFVTVVRGGRKGPAAGEEAGKAAEEEK 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1860672248 275 ESGEASERGRKRKkksakdkESFYAFQKAEKQRKGLLELKKNWELDKAKVEKLKASR 331
Cdd:cd12950    79 KEKEKKKKKKKEL-------EDFYRFQLREKKKEEQADLLKKFEEDKERVEKMKEKR 128

RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly. Rrp7p contains 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 1860672248 195 GLSHYLTLYDSLRPPLDIVQAYVDSAMELYEFEIAKSKQKSKyrKGEAIVDEDGFTLVTRGGAYGQTLGGGVTVASKKFQ 274
Cdd:cd12950     1 GLARYRAHYRRLRPPLEALQESVDSFMALFEAREEERKRERK--RLRNEPDEDGFVTVVRGGRKGPAAGEEAGKAAEEEK 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1860672248 275 ESGEASERGRKRKkksakdkESFYAFQKAEKQRKGLLELKKNWELDKAKVEKLKASR 331
Cdd:cd12950    79 KEKEKKKKKKKEL-------EDFYRFQLREKKKEEQADLLKKFEEDKERVEKMKEKR 128

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 1860672248   8 LINGFQVLPI------AYSTSSTHYIYVRAHnASKKTSNNLwPNRRTLFLVNVPPDATERDLILLFKP-YGTVEKVV 77
Cdd:cd12293     2 EINGFLVLPVtvpspsASPEKTTHYLYIRKH-ASKNPAETL-PASRTLFLVNLPVDSTERHLRKLFGLgGGRIESVL 76

RNA recognition motif;

                           10        20        30
                   ....*....|....*....|....*....|....
gi 1860672248   48 TLFLVNVPPDATERDLILLFKPYGTVEKVVFDLD 81
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRD 34

RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly. Rrp7p contains 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 1860672248 195 GLSHYLTLYDSLRPPLDIVQAYVDSAMELYEFEIAKSKQKSKyrKGEAIVDEDGFTLVTRGGAYGQTLGGGVTVASKKFQ 274
Cdd:cd12950     1 GLARYRAHYRRLRPPLEALQESVDSFMALFEAREEERKRERK--RLRNEPDEDGFVTVVRGGRKGPAAGEEAGKAAEEEK 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1860672248 275 ESGEASERGRKRKkksakdkESFYAFQKAEKQRKGLLELKKNWELDKAKVEKLKASR 331
Cdd:cd12950    79 KEKEKKKKKKKEL-------EDFYRFQLREKKKEEQADLLKKFEEDKERVEKMKEKR 128

RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. 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. Rrp7A, also termed gastric cancer antigen Zg14, is the Rrp7p homolog mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Both Rrp7p and Rrp7A harbor 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 1860672248 195 GLSHYLTLYDSLRPPLDIVQAYVDSAMELYEFEIAKSKQKSKyrKGEAIVDEDGFTLVTRGGAYGQTLGGGVTVASKKFQ 274
Cdd:cd12932     1 GLKKWVAEYKRSRPDPAELQSEVDEYMEEFDKREEEEKEEAK--EARNEPDEDGFVTVTRGGRKGKTAREEAVEAKAKEK 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1860672248 275 ESGEASERGRkrkkksakdkESFYAFQKAEKQRKGLLELKKNWELDKAKV 324
Cdd:cd12932    79 EKKKKKKKEL----------EDFYRFQIREKKKEELAELRKKFEEDKKRI 118

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 1860672248   8 LINGFQVLPI------AYSTSSTHYIYVRAHnASKKTSNNLwPNRRTLFLVNVPPDATERDLILLFKP-YGTVEKVV 77
Cdd:cd12293     2 EINGFLVLPVtvpspsASPEKTTHYLYIRKH-ASKNPAETL-PASRTLFLVNLPVDSTERHLRKLFGLgGGRIESVL 76

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.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1860672248  47 RTLFLVNVPPDATERDLILLFKPYGTVEKVVF 78
Cdd:cd12394     1 RTVFVGNLPVTVKKKALKKLFKEFGKIESVRF 32

RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p 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. In contrast, 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
                  ....*....|....*....|....*....|..
gi 1860672248  47 RTLFLVNVPPDATERDLILLFKPYGTVEKVVF 78
Cdd:cd12294     1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVEL 32

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.

                          10        20
                  ....*....|....*....|....*....
gi 1860672248  48 TLFLVNVPPDATERDLILLFKPYGTVEKV 76
Cdd:cd12377     1 CIFVYNLAPDADESLLWQLFGPFGAVQNV 29

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
                  ....*....|....*....|....*....|....*.
gi 1860672248  49 LFLVNVPPDATERDLILLFKPYGTVE--KVVFDLDG 82
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKsiRLVRDETG 36

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.

                          10        20
                  ....*....|....*....|....*
gi 1860672248  49 LFLVNVPPDATERDLILLFKPYGTV 73
Cdd:cd12343     2 IFVGNLPDAATSEELRALFEKYGKV 26

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 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
                  ....*....|....*....|....*....|....*
gi 1860672248  47 RTLFLVNVPPDATERDLILLFKPYGTVE--KVVFD 79
Cdd:cd12676     2 RTLFVRNLPFDATEDELYSHFSQFGPLKyaRVVKD 36

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.

                          10        20
                  ....*....|....*....|....
gi 1860672248  47 RTLFLVNVPPDATERDLILLFKPY 70
Cdd:cd12420     1 RTLFVSGLPLDVKERELYNLFRPL 24

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.

                          10        20        30
                  ....*....|....*....|....*....|
gi 1860672248  47 RTLFLVNVPPDATERDLILLFKPYGTVEKV 76
Cdd:cd12275     2 RSLFVINVPRDVTESTLRRLFEVYGDVRGV 31