DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637  33 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 112
Cdd:cd06145   1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 53292637 113 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 181
Cdd:cd06145  81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150

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
                ....*....|....*....|....*....|....*....|....*
gi 53292637 394 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFL 437
Cdd:cd12274   1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFL 45

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637  33 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 112
Cdd:cd06145   1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 53292637 113 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 181
Cdd:cd06145  81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637     32 LFGLDCE-VCLTSMGKELTRISLV-TEGG--YCLIDELVKPDLKILDYLTSFTGITKEILNPvTTKLKDVQKLLRELLPP 107
Cdd:smart00479   2 LVVIDCEtTGLDPGKDEIIEIAAVdVDGGeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637    108 DAVLVGHCLDLDLRVLKMIHP----------YVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCPNklgrDGIEDARA 175
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQRAH----RALDDARA 156

                          170
                   ....*....|...
gi 53292637    176 ALELLQYFLKYGP 188
Cdd:smart00479 157 TAKLFKKLLERLE 169

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637   296 MSTVYAGPFSKDCNVGALKKVFSSLGPVHSITL----VLETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRRlvT 371
Cdd:TIGR01645 107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMswdpATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR--P 184

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 53292637   372 ELTLECDTLVRELEQDSENQGTIYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFL 437
Cdd:TIGR01645 185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVfEAFGEIVKCQLARAPTGRGHKGYGFI 251

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 53292637    298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtgksKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 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 53292637   299 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVL---ETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIR 365
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 53292637   313 LKKVFSSLGPVHSITLVLETY----RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV--RRLVTELTlECDTLVRELEQ 386
Cdd:TIGR01622 231 LRQIFEPFGEIEFVQLQKDPEtgrsKGYGFIQFRDAEQAKEALEKMNGFELAGRPIKVglGNDFTPES-DANLAQRFQDQ 309

                          90       100
                  ....*....|....*....|....
gi 53292637   387 DSENQGTIyvaGIGETFKEHLLEQ 410
Cdd:TIGR01622 310 DGSAFSGA---GLNTPARSQLMRK 330

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637  33 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 112
Cdd:cd06145   1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 53292637 113 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 181
Cdd:cd06145  81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637  34 GLDCEVCLTSMGK-ELTRISLV-TEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQ------KLLRELL 105
Cdd:cd06137   2 ALDCEMVGLADGDsEVVRISAVdVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFgweaarAALWKFI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637 106 PPDAVLVGHCLDLDLRVLKMIHPYVIDTSLLYAG-----KQGRRFKLTFLARVILGKDIQCPNKlGRDGIEDARAALELL 180
Cdd:cd06137  82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILTREavkgpLAKRQWSLRTLCRDFLGLKIQGGGE-GHDSLEDALAAREVV 160

                .
gi 53292637 181 Q 181
Cdd:cd06137 161 L 161

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637     32 LFGLDCE-VCLTSMGKELTRISLV-TEGG--YCLIDELVKPDLKILDYLTSFTGITKEILNPvTTKLKDVQKLLRELLPP 107
Cdd:smart00479   2 LVVIDCEtTGLDPGKDEIIEIAAVdVDGGeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637    108 DAVLVGHCLDLDLRVLKMIHP----------YVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCPNklgrDGIEDARA 175
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQRAH----RALDDARA 156

                          170
                   ....*....|...
gi 53292637    176 ALELLQYFLKYGP 188
Cdd:smart00479 157 TAKLFKKLLERLE 169

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 53292637  35 LDCEVCLTSMG---KELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEIL---NPVTTKLKDVQKLLRellppD 108
Cdd:cd06149   3 IDCEMVGTGPGgreSELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLvnaTPFAVAQKEILKILK-----G 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637 109 AVLVGHCLDLDLRVLKMIHP--YVIDTS---LL---YAGKQGRRFKLTFLARVILGKDIQCpNKLGRDGIEDARAALELL 180
Cdd:cd06149  78 KVVVGHAIHNDFKALKYFHPkhMTRDTStipLLnrkAGFPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELY 156

                .
gi 53292637 181 Q 181
Cdd:cd06149 157 K 157

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
                ....*....|....*....|....*....|....*....|....*
gi 53292637 394 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFL 437
Cdd:cd12274   1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFL 45

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 53292637    35 LDCE-VCLTSMGKELTRISLV-TEGGYCLIDE----LVKPDL--KILDYLTSFTGITKEILnPVTTKLKDVQKLLRELLP 106
Cdd:pfam00929   3 IDLEtTGLDPEKDEIIEIAAVvIDGGENEIGEtfhtYVKPTRlpKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637   107 PDAVLVGH-------CLDLDLRVLKMIH----PYVIDT-SLLYAGKQGRRF-KLTFLARVILGKDIQCPNklgrDGIEDA 173
Cdd:pfam00929  82 KGNLLVAHnasfdvgFLRYDDKRFLKKPmpklNPVIDTlILDKATYKELPGrSLDALAEKLGLEHIGRAH----RALDDA 157

                  ....*..
gi 53292637   174 RAALELL 180
Cdd:pfam00929 158 RATAKLF 164

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 53292637 299 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY---RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVR 367
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

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 53292637 313 LKKVFSSLGPVHSITLVLE----TYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRR 368
Cdd:cd12371  17 IKSVFEAFGKIKSCSLAPDpetgKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVGR 76

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637  65 LVKPDLKILDYLTSFTGITKEILN--PvttKLKDVQKLLRELLpPDAVLVGHCLDLDLRVL---------KMIHPYVIDT 133
Cdd:COG0847  39 LVNPERPIPPEATAIHGITDEDVAdaP---PFAEVLPELLEFL-GGAVLVAHNAAFDLGFLnaelrraglPLPPFPVLDT 114

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 53292637 134 SLLYAGK--QGRRFKLTFLARViLGKDIQcpnklGR-DGIEDARAALELLQYFLK 185
Cdd:COG0847 115 LRLARRLlpGLPSYSLDALCER-LGIPFD-----ERhRALADAEATAELFLALLR 163

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 53292637 299 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRPYFS---IQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNygfVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 53292637 297 STVYAGPFSKDCNVGALKKVFSSLGPVHSITLVL--ETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12449   1 GKLFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKdrETQRSrgFGFVTFENPDDAKDAMMAMNGKSLDGRQIRV 74

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 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 the 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 a 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 mammals, 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 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 53292637 300 YAGPFSKDCNVGALKKVFSSLGPVHSITLV--LETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12378   3 YVGDLHPDVTEAMLYEKFSPAGPVLSIRVCrdAVTRRSlgYAYVNFQQPADAERALDTLNFDVIKGKPIRI 73

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 53292637 299 VYAGPFSKDCNVGALKKVFSSLGPVHSITLVL----ETYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLdyetEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRV 72

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 53292637   312 ALKKVFSSLGPVHSITLV-LET--YRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRVRRLVTEltlecdtLVRELEQDs 388
Cdd:TIGR01628 104 ALFDTFSKFGNILSCKVAtDENgkSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK-------HEREAAPL- 175

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 53292637   389 ENQGTIYVAGIGETF-KEHLLEQSNLFPDLEAVILPKEvKSRKQKNYCF 436
Cdd:TIGR01628 176 KKFTNLYVKNLDPSVnEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAF 223

RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is 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 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 53292637 298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETY--RPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12615   1 TLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAgnDPYCFVEFHEHRHAAAALAAMNGRKIMGKEVKV 71

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 53292637 298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLE----TYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDrgsgRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINV 73

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

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 53292637 298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVL--ETYRpyfS-----IQYEVLEAAQLALETMNGSLLEGSCIRVR 367
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITdrETGR---SrgfgfVTFSTAEAAEAAIDALNGKELDGRSIVVN 74

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 53292637   297 STVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLE--TYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:TIGR01628   1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDsvTRRSlgYGYVNFQNPADAERALETMNFKRLGGKPIRI 74

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 53292637 299 VYAG--PFSKDCNvgALKKVFSSLGPVHSITLVL--ETYRP--YFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12399   1 LYVGnlPYSASEE--QLKSLFGQFGAVFDVKLPMdrETKRPrgFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72

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 53292637 298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLEtyRPYFSIQYEVLEAAQLALETMNGSLLEGSCIR 365
Cdd:cd12354   2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPD--KGYAFIRFDSHEAATHAIVSVNGTIINGQAVK 67

RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). 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. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is 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. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 53292637 298 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLE--TYRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12616   1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEhtSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV 71

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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                ....*....|....*....|....*....|....*....|....*....|....
gi 53292637 313 LKKVFSSLGPVHSITLVletyRPYFSIQYEVLEAAQLALETMNGSLLEGSCIRV 366
Cdd:cd12251  18 LRELFSEYGKVERVKKI----KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEV 67