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 156215907 103 PLYVGNLTWWTTDQQLTEALQECGVTDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVVTP 179
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 156215907 103 PLYVGNLTWWTTDQQLTEALQECGVTDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVVTP 179
Cdd:cd12643    1 ALYVGNLTWWTTDEDLTEALHSIGVNDLLEIKFFENRANGQSKGFALIVVGSEASSRKLMDKLPKKELHGQNPVVTP 77

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 156215907   104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVV 177
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG--KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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 156215907  104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFdNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEG 172
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 156215907 103 PLYVGNLTWWTTDQQLTEALQECGVTDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVVTP 179
Cdd:cd12643    1 ALYVGNLTWWTTDEDLTEALHSIGVNDLLEIKFFENRANGQSKGFALIVVGSEASSRKLMDKLPKKELHGQNPVVTP 77

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins; This subgroup corresponds to the RRM of CFIm59. 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. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 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 CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156215907 104 LYVGNLTWWTTDQQLTEALQECGVTDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVVTPATKQ 183
Cdd:cd12644    4 VYVGNFSWWTTDQDLINLIRSLGVKDVVELKFAENRANGQSKGYAEVVVASENSVHLLLELLPGKKLNGEKVDVRLATRQ 83

                 ....*..
gi 156215907 184 HLHEFEA 190
Cdd:cd12644   84 NLSQFEA 90

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 156215907   104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQNPVV 177
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG--KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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 156215907 104 LYVGNLTWWTTDQQLTEALQECGVTDLINIKFfdNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQ 173
Cdd:cd21609    2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMY--DRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGR 69

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 156215907 104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRtNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQ 173
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG--EVVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGTELGGR 67

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 156215907 104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEG 172
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHG--SIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDG 67

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 156215907 105 YVGNLTWWTTDQQLTEALQECGVtdLINIKFFDNRTNGQSKGFAMIELGSDKSIEM 160
Cdd:cd12272    3 YIGNLAWDIDEDDLRELFAECCE--ITNVRLHTDKETGEFKGYGHVEFADEESLDA 56

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 156215907 113 TTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTErLPKFDIEGQNPVVTPA 180
Cdd:cd12451   15 TIRDELREHFGECG--EVTNVRIPTDRETGELKGFAYIEFSTKEAKEKALE-LNGSDIAGGNLVVDEA 79

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 156215907  104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFdNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEG 172
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 156215907 104 LYVGNLTWWTTDQQLTEALQECGVTDLINIkfFDNRTNGQSKGFAMIELGSDKSIEM 160
Cdd:cd12550    2 VYVGNVDYGATAEELEAHFHGCGSVNRVTI--LCDKFSGHPKGFAYIEFADKESVRT 56

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 156215907 104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIELGSDKSIEMVTERLPKFDIEGQ 173
Cdd:cd12447    2 LFVGGLSWNVDDPWLKKEFEKYG--GVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGR 69

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 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
                 ....*....|....*....|....*....|....*....|....*...
gi 156215907 104 LYVGNLTWWTTDQQLTEALQECGVTdLINIKFFDNRTNGQSKGFAMIE 151
Cdd:cd12344    2 LWMGDLEPWMDEAYISSCFAKTGEE-VVSVKIIRNKQTGKSAGYCFVE 48

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 156215907 104 LYVGNLTWWTTDQQLTEALQECGvtDLINIKFFDNRTNGQSKGFAMIE 151
Cdd:cd12397    1 LFVGNLSFETTEEDLRKHFAPAG--KIRKVRMATFEDSGKCKGFAFVD 46