RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins; This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 63055061  82 ALYIGNLTWWTTDEDLTDAIRSIGINDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPIVTP 158
Cdd:cd12643   1 ALYVGNLTWWTTDEDLTEALHSIGVNDLLEIKFFENRANGQSKGFALIVVGSEASSRKLMDKLPKKELHGQNPVVTP 77

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins; This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 63055061  82 ALYIGNLTWWTTDEDLTDAIRSIGINDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPIVTP 158
Cdd:cd12643   1 ALYVGNLTWWTTDEDLTEALHSIGVNDLLEIKFFENRANGQSKGFALIVVGSEASSRKLMDKLPKKELHGQNPVVTP 77

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

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQN 153
Cdd:COG0724   4 IYVGNLPYSVTEEDLRELFSEYG--EVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRT 72

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 63055061    83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFeNRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHG 151
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins; This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 63055061  82 ALYIGNLTWWTTDEDLTDAIRSIGINDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPIVTP 158
Cdd:cd12643   1 ALYVGNLTWWTTDEDLTEALHSIGVNDLLEIKFFENRANGQSKGFALIVVGSEASSRKLMDKLPKKELHGQNPVVTP 77

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGINDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPIVTP 158
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGVVDVKEIKFFEHKANGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPCVVTP 76

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPIVTP 158
Cdd:cd21608   2 LYVGNLSWDTTEDDLRDLFSEFG--EVESAKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNE 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 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRaNGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQ 152
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFG--EVVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGTELGGR 67

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 63055061    83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFeNRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHG 151
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGINDVLEIKFfeNRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQ 152
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMY--DRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGR 69

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMdllsKRELHGQNPIVTP 158
Cdd:cd12577   1 MFIGGLNWDTTEEGLRDYFSQFG--TVVDCTIMKDSATGRSRGFGFLTFEDPSSVNEVM----KKEHVLDGKIIDP 70

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDL 143
Cdd:cd12758   2 MFIGGLSWDTSKKDLTEYLSRFG--EVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQ 152
Cdd:cd12447   2 LFVGGLSWNVDDPWLKKEFEKYG--GVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGR 69

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRANGQSKGFALV 129
Cdd:cd12400   3 LFVGNLPYDTTAEDLKEHFKKAG--EPPSVRLLTDKKTGKSKGCAFV 47

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGinDVLEIKFFENRAnGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQN 153
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFG--KVKDVKIIKDRA-GVSKGYGFVTFETQEDAEKIQKWGANLVFKGKK 72

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM1 of SECp43, 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63055061  83 LYIGNLTWWTTDEDLTDAIRSIGiNDVLEIKFFENRANGQSKGFALVCVGSDSSSRKLMDLLSKRELHGQNPI 155
Cdd:cd12610   2 LWMGDLEPYMDENFIKRAFATMG-ETVLSVKIIRNRVTGGPAGYCFVEFADEATAERCLHKLNGKPIPGSNPP 73