RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720380963  749 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 824
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720380963  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

zinc finger;

                            10        20
                    ....*....|....*....|.
gi 1720380963   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720380963  749 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 824
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720380963  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

RNA recognition motif;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720380963  1120 DREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA--AIHGARFKGQDLKL 1173
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrDKETGKskgfAFVEFESEEDAEKAleALNGKELDGRPLKV 73

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720380963  937 DNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS-------------------EDKAEIMKTLE 996
Cdd:COG5185    272 ENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiqNLTAEIEQGQE 350

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1720380963  997 ILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 1050
Cdd:COG5185    351 SLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404

Nup53/35/40-type RNA recognition motif;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1720380963 1108 PRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA 1159
Cdd:pfam14605    1 STWIVVSGYPAELAYLVRRHFADFGEIVKHYFPPETNSMYLKYASRKDAEQA 52

zinc finger;

                            10        20
                    ....*....|....*....|.
gi 1720380963   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                           10        20
                   ....*....|....*....|..
gi 1720380963  496 RCRDYDEKGFCMRGDMCPFDHG 517
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720380963  749 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 824
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720380963 1104 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1175
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720380963  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

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 1720380963  752 LELRKVPPELNNiSKLNEHFSRFGTLVNLQVAYNGDPEG---ALIQFATYEEAKKAISS-TEAVLNNRFIKV 819
Cdd:cd00590      1 LFVGNLPPDTTE-EDLRELFSKFGEVVSVRIVRDRDGKSkgfAFVEFESPEDAEKALEAlNGTELGGRPLKV 71

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720380963 1122 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGAR---FKGQDLKLAWNK 1177
Cdd:cd12224     16 KDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAAERTFNkliIKGRRLKVKWGR 74

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1720380963  750 TKLELRKVPPELNNISKLNEHFSRFGTLVNLQVayNGDPEGALIQFATYEEAKKA 804
Cdd:cd12443      1 TAIVCKNIPEELNDKEILRRHFSKFGKVARVFC--NPRKNLAIVHFKDHESAALA 53

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720380963 1120 DREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA-----AIHGARFkgqdLKLAW 1175
Cdd:cd12257     15 NITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAyrspeAVFNNRF----IKVFW 71

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720380963  937 DNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS-------------------EDKAEIMKTLE 996
Cdd:COG5185    272 ENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiqNLTAEIEQGQE 350

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1720380963  997 ILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 1050
Cdd:COG5185    351 SLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404

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 1720380963  757 VPPELNNiSKLNEHFSRFGTLVNLQVAY--NGDPEG-ALIQFATYEEAKKAISST-EAVLNNRFIK 818
Cdd:pfam00076    6 LPPDTTE-EDLKDLFSKFGPIKSIRLVRdeTGRSKGfAFVEFEDEEDAEKAIEALnGKELGGRELK 70

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720380963  756 KVPPELNNISKLNEHFSRFGTLVNLQVAY-NGDPEG-ALIQFATYEEAKKA 804
Cdd:cd12390      9 RLPKDFRDGSELRKLFSQVGKPTFCQLAMgNGVPRGfAFVEFASAEDAEEA 59

zinc finger;

                            10        20
                    ....*....|....*....|.
gi 1720380963   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26

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 1720380963 1120 DREDLLPHFAQYGEIEDCQI-----DDASLHAIITFKTRAEAEAA--AIHGARFKGQDLK 1172
Cdd:pfam00076   11 TEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAieALNGKELGGRELK 70

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720380963 1120 DREDLLPHFAQYGEIEDCQI----DDASLH-AIITFKTRAEAEAA--AIHGAR 1165
Cdd:cd12635     14 SEDDVRRLFEPFGSIEECTIlrgpDGNSKGcAFVKFSSHAEAQAAinALHGSQ 66

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 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 1720380963  765 SKLNEHFSRFGTLVNLQVAYNGDPEG---ALIQFATYEEAKKAISSTEAV-LNNRFIKVYW 821
Cdd:cd12414     14 DDLKKLFSKFGKVLEVTIPKKPDGKLrgfAFVQFTNVADAAKAIKGMNGKkIKGRPVAVDW 74

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720380963 1117 TESDREDLLPHFAQYGEIEDCQI-----DD----ASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAWNKPI 1179
Cdd:cd12223     11 PSVTEEVLLREFGRFGPLASVKImwprtEEerrrNRNCGFVAFMSRADAERAmrELNGKDVMGYELKLGWGKAV 84

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720380963 1122 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAW 1175
Cdd:cd12354     15 ALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAivSVNGTIINGQAVKCSW 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                           10        20
                   ....*....|....*....|..
gi 1720380963  496 RCRDYDEKGFCMRGDMCPFDHG 517
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26