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 1720423266 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 560
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720423266 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 560
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720423266 586 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkDWKLKGRNA 656
Cdd:cd12274     1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 227 LDCE-VCLTSMGKELTRISLV-TEGGYCLIDE----LVKPDL--KILDYLTSFTGITKEILnPVTTKLKDVQKLLRELLP 298
Cdd:pfam00929   3 IDLEtTGLDPEKDEIIEIAAVvIDGGENEIGEtfhtYVKPTRlpKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 299 PDAVLVGH-------CLDLDLRVLKMIH----PYVIDT-SLLYAGKQGRRF-KLTFLARVILGKDIQCPNklgrDGIEDA 365
Cdd:pfam00929  82 KGNLLVAHnasfdvgFLRYDDKRFLKKPmpklNPVIDTlILDKATYKELPGrSLDALAEKLGLEHIGRAH----RALDDA 157

                  ....*..
gi 1720423266 366 RAALELL 372
Cdd:pfam00929 158 RATAKLF 164

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720423266  585 TIYVAGIGETFKEHLLEQ--SNlFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGKdwKLKGR 654
Cdd:smart00360   1 TLFVGNLPPDTTEEELRElfSK-FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGR 69

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 1720423266 491 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVL---ETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIR 557
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRdetGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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 1720423266 505 LKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV--RRLVTELTlECDTLVRELEQ 578
Cdd:TIGR01622 231 LRQIFEPFGEIEFVQLQKDPEtgrsKGYGFIQFRDAEQAKEALEKMNGFELAGRPIKVglGNDFTPES-DANLAQRFQDQ 309

                          90       100
                  ....*....|....*....|....
gi 1720423266 579 DSENQGTIyvaGIGETFKEHLLEQ 602
Cdd:TIGR01622 310 DGSAFSGA---GLNTPARSQLMRK 330

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 227 LDCE-VCLTSMGKE--LTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTkLKDVQKLLRELLpPDAVL 303
Cdd:cd06144     3 LDCEmVGVGPDGSEsaLARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELL-KGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720423266 304 VGHCLDLDLRVLKMIHPYVI--DTS----LLYAGKqGRRFKLTFLARVILGKDIQCpnkLGRDGIEDARAALEL 371
Cdd:cd06144    81 VGHALKNDLKVLKLDHPKKLirDTSkykpLRKTAK-GKSPSLKKLAKQLLGLDIQE---GEHSSVEDARAAMRL 150

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720423266 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 560
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720423266 586 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkDWKLKGRNA 656
Cdd:cd12274     1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 227 LDCEVCLTSMG---KELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEIL---NPVTTKLKDVQKLLRellppD 300
Cdd:cd06149     3 IDCEMVGTGPGgreSELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLvnaTPFAVAQKEILKILK-----G 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 301 AVLVGHCLDLDLRVLKMIHP--YVIDTS---LL---YAGKQGRRFKLTFLARVILGKDIQCpNKLGRDGIEDARAALELL 372
Cdd:cd06149    78 KVVVGHAIHNDFKALKYFHPkhMTRDTStipLLnrkAGFPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELY 156

                  .
gi 1720423266 373 Q 373
Cdd:cd06149   157 K 157

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720423266 489 STVYAGPFSKDCNVGALKKVFSSLGPVHSITL----VLETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 560
Cdd:cd12370     1 CRVYVGSIYFELGEDTIRQAFAPFGPIKSIDMswdpVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKVGR 76

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 1720423266 491 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY---RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVR 559
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720423266  490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtgksKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720423266  585 TIYVAGIGETFKEHLLEQ--SNlFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGKdwKLKGR 654
Cdd:smart00360   1 TLFVGNLPPDTTEEELRElfSK-FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGR 69

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 505 LKKVFSSLGPVHSITLVLE----TYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 560
Cdd:cd12371    17 IKSVFEAFGKIKSCSLAPDpetgKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVGR 76

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720423266 505 LKKVFSSLGPVHSITLVLET----YRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVrRLVTE 564
Cdd:cd12284    15 LRGIFEPFGKIEFVQLQKDPetgrSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKV-GHVTE 77

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720423266 491 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRPYFS---IQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:cd12614     1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNygfVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720423266 505 LKKVFSSLGPVHSITLVL--ETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:cd12398    17 LKEIFSEVGPVVSFRLVTdrETGKPkgYGFCEFRDAETALSAVRNLNGYELNGRPLRV 74

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720423266 488 MSTVYAGPFSKDCNVGALKKVFSSLGPVHSITLVL--ETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRVR 559
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITdrETGRSrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVN 76

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 489 STVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLE--TYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV----RR 560
Cdd:TIGR01628   1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDsvTRRSlgYGYVNFQNPADAERALETMNFKRLGGKPIRImwsqRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720423266 561 LVTELTLECDTLVRELEQDSENqgtiyvAGIGETFKEhlleqsnlFPDLEAVILPKEVKSrKQKNYCFLKFKTVNSAQVA 640
Cdd:TIGR01628  81 PSLRRSGVGNIFVKNLDKSVDN------KALFDTFSK--------FGNILSCKVATDENG-KSRGYGFVHFEKEESAKAA 145

                  ....*.
gi 1720423266 641 LEILKG 646
Cdd:TIGR01628 146 IQKVNG 151

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 1720423266 488 MSTVYAGPFSKDCNVGALKKVFSSLGPVHSITLVL--ETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:cd12671     6 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYdrETGKPkgYGFCEYQDQETALSAMRNLNGYELNGRALRV 80

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They 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.

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gi 1720423266 492 YAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYR--PYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:cd12352     2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHGGndPYCFVEFYEHNHAAAALQAMNGRKILGKEVKV 70

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.

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gi 1720423266 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLE-TYRPYFS-IQYEVLEAAQLALETMNGSLLEGSCIRV 558
Cdd:cd12454     5 SIFVGQLDPKTTDSELFRRFSKYGKIVDCKLIKRpEPVNAFAfLRFESEEAAEAAVEEENHSEFLNKQIRV 75

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 1720423266 505 LKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV--RRLVTELTlECDTLVRELEQ 578
Cdd:TIGR01622 231 LRQIFEPFGEIEFVQLQKDPEtgrsKGYGFIQFRDAEQAKEALEKMNGFELAGRPIKVglGNDFTPES-DANLAQRFQDQ 309

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gi 1720423266 579 DSENQGTIyvaGIGETFKEHLLEQ 602
Cdd:TIGR01622 310 DGSAFSGA---GLNTPARSQLMRK 330

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.

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gi 1720423266 491 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVR 559
Cdd:cd21609     2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDRYtgrsRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVN 74

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.

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gi 1720423266 586 IYVAGIG-ETFKEHLLEQSNLFPDLEAVILPKEVKSRKQKNYCFLKFK 632
Cdd:cd12583     2 IFVGGLSpDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFK 49

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

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gi 1720423266 586 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkdWKLKGRN 655
Cdd:cd12370     3 VYVGSIYFELGEDTIRQAfAPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG--VMLGGRN 71

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.

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gi 1720423266 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLEtyRPYFSIQYEVLEAAQLALETMNGSLLEGSCIR 557
Cdd:cd12354     2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPD--KGYAFIRFDSHEAATHAIVSVNGTIINGQAVK 67