OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954396248 438 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPV 491
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 954396248 840 CSLCKGKLYAPSAYQVNGRIYHTSCVVCFNCRQD-VSESYHTVGRGIFCTNCY 891
Cdd:cd08368    1 CAGCGKPIEGRELLRALGKKWHPECFKCAECGKPlGGDSFYEKDGKPYCEKCY 53

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954396248 899 CFQCSNPILNNQSVIVHNCVYHTECLECPYCNKRIVLSEEITKNNhwKLKCESC 952
Cdd:cd08368    1 CAGCGKPIEGRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDG--KPYCEKC 52

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954396248 438 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPV 491
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 954396248   750 VESIGSRLMRNMGWKEGQGLGKSNQGITNPIESERRVQGAGLGA 793
Cdd:smart00443   3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248   129 TLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPL 71

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 954396248  130 LVVKGIPLSYNEELVRNAVVEMGvtPI-DVRIlRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIkSIRL-VRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGREL 69

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

                           10        20
                   ....*....|....*....|...
gi 954396248   225 GDWICGKCTTNNFKKRDHCFKCG 247
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACG 23

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248  123 NIEPNSTLVVKGIPLSYNEELVRNAVVEMGvtPI-DVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:TIGR01622 210 NSIPFHRLYVGNLHFNITEQDLRQIFEPFG--EIeFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEKMNGF-ELAGRPI 286

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954396248  202 -----AEVQYSINKNTYPS-ATFVTSQRGGDWICGKCTTNNFKKRDhcfkcgvrREDSDPVCGDGINEIGV 266
Cdd:TIGR01622 287 kvglgNDFTPESDANLAQRfQDQDGSAFSGAGLNTPARSQLMRKLA--------RDNEKGTGGLAIPGTDV 349

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954396248 899 CFQCSNPILNNQSVIVHNCVYHTECLECPYCNKRIVLSEEITKNNhwKLKCESC 952
Cdd:cd08368    1 CAGCGKPIEGRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDG--KPYCEKC 52

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954396248 438 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPV 491
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 954396248 440 PNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPVV 492
Cdd:cd16168    3 PDTSTYQYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLYWDGEKQTYLPAA 55

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 954396248   750 VESIGSRLMRNMGWKEGQGLGKSNQGITNPIESERRVQGAGLGA 793
Cdd:smart00443   3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 126 PNSTLVVKGIPLSYNEELVRNAVVEMGVTPI-DVRILRRRESGESRGFGFIEFMSIEEATKYMERSQG---FLEVNGRRM 201
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADLPIkDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNllpPFKIDGRVV 80

                 ....*.
gi 954396248 202 AeVQYS 207
Cdd:cd12313   81 S-VSYA 85

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 127 NSTLVVKGIPLSYNEELVRNAVVEMGVTPIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFLEVNGRRMAeVQY 206
Cdd:cd12753    1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVS-MHY 79

                 ....
gi 954396248 207 SINK 210
Cdd:cd12753   80 SDPK 83

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 954396248 442 VSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPV 491
Cdd:cd16166    5 PSGFVYDPASGYYYDASSGYYYDANTGLYYDAASGRWYSYDEETGQYVEV 54

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248   129 TLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPL 71

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 954396248 438 PAPNvsqFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSSYQTYLPVV 492
Cdd:cd16163    5 PAPT---YRSDPDSGYIYDPETGYYYDPVTGLYYDPATGEYVDPDTGTLPYDPST 56

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 127 NSTLVVKGIPLSYNEELVRNAVVEMGvtPID-VRILRRRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRMaEVQ 205
Cdd:cd12363    1 SRCLGVFGLSLYTTERDLREVFSRYG--PIEkVQVVYDQQTGRSRGFGFVYFESVEDAKEAKERLNG-QEIDGRRI-RVD 76

                 ...
gi 954396248 206 YSI 208
Cdd:cd12363   77 YSI 79

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 954396248 442 VSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQ 477
Cdd:cd16165    5 AGDWVLDSKSGYYYNAATRYYYDPKTGMYYSDETGK 40

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248 129 TLVVKGIPLSYNEELVRNAVVEMG-VTpiDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRR 200
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFGeVE--SAKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNG-KELDGRS 70

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 125 EPNSTLVVKGIPLSYNEELVRNAVVEMGvtPID-VRILRRRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRMaE 203
Cdd:cd12642    2 DPNTCLGVFGLSLYTTERDLREVFSRYG--PLAgVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANG-MELDGRRI-R 77

                 ....*..
gi 954396248 204 VQYSINK 210
Cdd:cd12642   78 VDYSITK 84

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248 129 TLVVKGIPLSYNEELVRNaVVEMGVtpiDVRILRRREsGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRM 201
Cdd:cd12404    5 TLFVKNLPYSTTQDELKE-VFEDAV---DIRIPMGRD-GRSKGIAYIEFKSEAEAEKALEEKQG-TEVDGRSI 71

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 140 NEELVRNAVVEMGVTPIDVRILRRRESGESRGFGFIEFMSIEEATKYMersqgfLEVNGR 199
Cdd:cd12610   12 DENFIKRAFATMGETVLSVKIIRNRVTGGPAGYCFVEFADEATAERCL------HKLNGK 65

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 954396248 129 TLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRM 201
Cdd:cd12447    1 TLFVGGLSWNVDDPWLKKEFEKYG-GVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSG-KEIDGRQI 71

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 954396248 129 TLVVKGIPLSYNEELVRNAVVEMG-VTpiDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGeVT--SVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGA-ELMGRTL 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248  130 LVVKGIPLSYNEELVRNAVVEMGvtPI-DVRIlRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIkSIRL-VRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGREL 69

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954396248 128 STLVVKGIPLSYNEELVRNAVVEMGVtPIDVRILRRREsGESRGFGFIEFMSIEEAT---KYMERS 190
Cdd:cd12565    1 SRIIVKNLPKYVTEKRLKEHFSKKGE-ITDVKVMRTKD-GKSRRFGFIGFKSEEEAQkavKYFNKT 64

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954396248 129 TLVVKGIPLSYNEELVRNAVVEM-----GVTpiDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGflEVNGR 199
Cdd:cd12451    1 TIFVKGFDASLGEDTIRDELREHfgecgEVT--NVRIPTDRETGELKGFAYIEFSTKEAKEKALELNGS--DIAGG 72

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 132 VKGIPLSYNEELVRNAVVEMGVTpIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:cd12671   11 VGNIPYEATEEQLKDIFSEVGPV-VSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGY-ELNGRAL 78

The first LIM domain of Cysteine Rich Protein 1 (CRP1); The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 954396248 840 CSLCKGKLYAPSAYQVNGRIYHTSCVVCFNCRQDVSESYHTV-GRGIFCTNCY 891
Cdd:cd09479    3 CGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVhGEEIYCKSCY 55

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954396248 135 IPLSYNEELVRNAVVEMGVTpIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRR 200
Cdd:cd12398    8 IPYDATEEQLKEIFSEVGPV-VSFRLVTDRETGKPKGYGFCEFRDAETALSAVRNLNGY-ELNGRP 71

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. 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. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954396248 127 NSTLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRRrESGESRGFGFIEFMSIEEATKYMErsqgflEVNGR 199
Cdd:cd12381    1 GVNLYVKNLDDTIDDEKLREEFSPFG-TITSAKVMTD-EGGRSKGFGFVCFSSPEEATKAVT------EMNGR 65

glycine-rich RNA-binding protein 4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248 127 NSTLVVKGIPLSYNEELVRNAVVEMGVTpIDVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRMaEVQY 206
Cdd:PLN03134  34 STKLFIGGLSWGTDDASLRDAFAHFGDV-VDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDG-KELNGRHI-RVNP 110

                         90
                 ....*....|....*....
gi 954396248 207 SINKNTYPSATFVTSQRGG 225
Cdd:PLN03134 111 ANDRPSAPRAYGGGGGYSG 129

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 954396248 128 STLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRRREsGESRGFGFIEFMSIEEATKYMERSQG 192
Cdd:cd12320    1 TKLIVKNVPFEATRKEIRELFSPFG-QLKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEALKS 63

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or 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 also contains four RRMs.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954396248 130 LVVKGIPLSYNEE----LVRNAVVEM----GVTPIDVRILRRRES------GESRGFGFIEF 177
Cdd:cd12416    3 LCVRNLPKSVDDKklkkLFLKAVKERakkkGVKIKEVKVMRDKKRlnsdgkGRSKGYGFVEF 64

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954396248  123 NIEPNSTLVVKGIPLSYNEELVRNAVVEMGvtPI-DVRILRRRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 201
Cdd:TIGR01622 210 NSIPFHRLYVGNLHFNITEQDLRQIFEPFG--EIeFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEKMNGF-ELAGRPI 286

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954396248  202 -----AEVQYSINKNTYPS-ATFVTSQRGGDWICGKCTTNNFKKRDhcfkcgvrREDSDPVCGDGINEIGV 266
Cdd:TIGR01622 287 kvglgNDFTPESDANLAQRfQDQDGSAFSGAGLNTPARSQLMRKLA--------RDNEKGTGGLAIPGTDV 349

RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 954396248 129 TLVVKGIPLSYNEELVRNAVVemgvTPIDVRILRRRESGESRGFGFIEFMSIEEA 183
Cdd:cd12406    2 TLFVKGLSEDTTEETLKEAFE----GAISARIATDRDTGSSKGFGFVDFSSEEDA 52

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 954396248 130 LVVKGIPLSYNEELVRNAVVEMGVTpIDVRILRRRESGESRGFGFIEFMSIEEATKYM 187
Cdd:cd12321    2 LIVLGLPWKTTEQDLKEYFSTFGEV-LMVQVKKDPKTGRSKGFGFVRFASYETQVKVL 58