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2024-03-29 16:13:00, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001136033            1967 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens poly-U binding splicing factor 60KDa (PUF60),
            transcript variant 3, mRNA.
ACCESSION   NM_001136033
VERSION     NM_001136033.2  GI:402794090
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1967)
  AUTHORS   Kajiwara,T., Matsushita,K., Itoga,S., Tamura,M., Tanaka,N.,
            Tomonaga,T., Matsubara,H., Shimada,H., Habara,Y., Matsuo,M. and
            Nomura,F.
  TITLE     SAP155-mediated c-myc suppressor far-upstream element-binding
            protein-interacting repressor splicing variants are activated in
            colon cancer tissues
  JOURNAL   Cancer Sci. 104 (2), 149-156 (2013)
   PUBMED   23113893
  REMARK    GeneRIF: Circulating FIR variant mRNA in the peripheral blood of
            cancer patients were significantly overexpressed compared to that
            in healthy volunteers.
REFERENCE   2  (bases 1 to 1967)
  AUTHORS   Matsushita,K., Kajiwara,T., Tamura,M., Satoh,M., Tanaka,N.,
            Tomonaga,T., Matsubara,H., Shimada,H., Yoshimoto,R., Ito,A.,
            Kubo,S., Natsume,T., Levens,D., Yoshida,M. and Nomura,F.
  TITLE     SAP155-mediated splicing of FUSE-binding protein-interacting
            repressor serves as a molecular switch for c-myc gene expression
  JOURNAL   Mol. Cancer Res. 10 (6), 787-799 (2012)
   PUBMED   22496461
  REMARK    GeneRIF: Data indicate that altered FIR and c-myc pre-mRNA
            splicing, in addition to c-Myc expression by augmented
            FIR/FIRDeltaexon2-SAP155 complex, potentially contribute to
            colorectal cancer development.
REFERENCE   3  (bases 1 to 1967)
  AUTHORS   Hsiao,H.H., Nath,A., Lin,C.Y., Folta-Stogniew,E.J., Rhoades,E. and
            Braddock,D.T.
  TITLE     Quantitative characterization of the interactions among c-myc
            transcriptional regulators FUSE, FBP, and FIR
  JOURNAL   Biochemistry 49 (22), 4620-4634 (2010)
   PUBMED   20420426
  REMARK    GeneRIF: FIR is monomeric in solution but dimerizes upon DNA
            binding; DNA-induced dimerization is mediated by FIR's RNA
            recognition motif.
REFERENCE   4  (bases 1 to 1967)
  AUTHORS   Matsushita,K., Tomonaga,T., Kajiwara,T., Shimada,H., Itoga,S.,
            Hiwasa,T., Kubo,S., Ochiai,T., Matsubara,H. and Nomura,F.
  TITLE     c-myc suppressor FBP-interacting repressor for cancer diagnosis and
            therapy
  JOURNAL   Front. Biosci. 14, 3401-3408 (2009)
   PUBMED   19273283
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1967)
  AUTHORS   Matsushita,K., Tomonaga,T., Shimada,H., Shioya,A., Higashi,M.,
            Matsubara,H., Harigaya,K., Nomura,F., Libutti,D., Levens,D. and
            Ochiai,T.
  TITLE     An essential role of alternative splicing of c-myc suppressor
            FUSE-binding protein-interacting repressor in carcinogenesis
  JOURNAL   Cancer Res. 66 (3), 1409-1417 (2006)
   PUBMED   16452196
REFERENCE   6  (bases 1 to 1967)
  AUTHORS   Poleev,A., Hartmann,A. and Stamm,S.
  TITLE     A trans-acting factor, isolated by the three-hybrid system, that
            influences alternative splicing of the amyloid precursor protein
            minigene
  JOURNAL   Eur. J. Biochem. 267 (13), 4002-4010 (2000)
   PUBMED   10866799
REFERENCE   7  (bases 1 to 1967)
  AUTHORS   Liu,J., He,L., Collins,I., Ge,H., Libutti,D., Li,J., Egly,J.M. and
            Levens,D.
  TITLE     The FBP interacting repressor targets TFIIH to inhibit activated
            transcription
  JOURNAL   Mol. Cell 5 (2), 331-341 (2000)
   PUBMED   10882074
REFERENCE   8  (bases 1 to 1967)
  AUTHORS   Bouffard,P., Barbar,E., Briere,F. and Boire,G.
  TITLE     Interaction cloning and characterization of RoBPI, a novel protein
            binding to human Ro ribonucleoproteins
  JOURNAL   RNA 6 (1), 66-78 (2000)
   PUBMED   10668799
REFERENCE   9  (bases 1 to 1967)
  AUTHORS   Page-McCaw,P.S., Amonlirdviman,K. and Sharp,P.A.
  TITLE     PUF60: a novel U2AF65-related splicing activity
  JOURNAL   RNA 5 (12), 1548-1560 (1999)
   PUBMED   10606266
REFERENCE   10 (bases 1 to 1967)
  AUTHORS   Bouffard,P., Briere,F., Wellinger,R.J. and Boire,G.
  TITLE     Identification of ribonucleoprotein (RNP)-specific protein
            interactions using a yeast RNP interaction trap assay (RITA)
  JOURNAL   BioTechniques 27 (4), 790-796 (1999)
   PUBMED   10524322
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC105049.5, BG771821.1,
            BC011265.1 and AW249619.1.
            On Sep 1, 2012 this sequence version replaced gi:209862866.
            
            Summary: This gene encodes a nucleic acid-binding protein that
            plays a role in a variety of nuclear processes, including pre-mRNA
            splicing and transcriptional regulation. The encoded protein forms
            a complex with the far upstream DNA element (FUSE) and FUSE-binding
            protein at the myelocytomatosis oncogene (MYC) promoter. This
            complex represses MYC transcription through the core-TFIIH basal
            transcription factor. Alternatively spliced transcript variants
            encoding multiple isoforms have been observed for this gene.
            [provided by RefSeq, Aug 2012].
            
            Transcript Variant: This variant (3) differs in the 5' UTR, lacks a
            portion of the 5' coding region, and initiates translation at an
            alternate in-frame downstream start site, compared to variant 1.
            The encoded isoform (c) has a shorter N-terminus, compared to
            isoform a.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC011265.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025081, ERS025082 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-11                AC105049.5         29175-29185
            12-83               BG771821.1         11-82
            84-1919             BC011265.1         1-1836
            1920-1967           AW249619.1         1-48                c
FEATURES             Location/Qualifiers
     source          1..1967
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="8"
                     /map="8q24.3"
     gene            1..1967
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="poly-U binding splicing factor 60KDa"
                     /db_xref="GeneID:22827"
                     /db_xref="HGNC:17042"
                     /db_xref="MIM:604819"
     exon            1..126
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    124..126
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="upstream in-frame stop codon"
     exon            127..213
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     variation       183
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:11540342"
     exon            214..309
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     CDS             232..1782
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="isoform c is encoded by transcript variant 3; FBP
                     interacting repressor; pyrimidine tract binding splicing
                     factor; Ro ribonucleoprotein-binding protein 1;
                     FUSE-binding protein-interacting repressor;
                     poly(U)-binding-splicing factor PUF60; Siah binding
                     protein 1"
                     /codon_start=1
                     /product="poly(U)-binding-splicing factor PUF60 isoform c"
                     /protein_id="NP_001129505.1"
                     /db_xref="GI:209862867"
                     /db_xref="CCDS:CCDS47935.1"
                     /db_xref="GeneID:22827"
                     /db_xref="HGNC:17042"
                     /db_xref="MIM:604819"
                     /translation="
MENGQSTAAKLGLPPLTPEQQEALQKAKKYAMEQSIKSVLVKQTIAHQQQQLTNLQMAAVTMGFGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLGTPGLVSPALTLAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPSVGVVNPILASPPTLGLLEPKKEKEEEELFPESERPEMLSEQEHMSISGSSARHMVMQKLLRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLSA
"
     misc_feature    <286..>561
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="P-loop containing Nucleoside Triphosphate
                     Hydrolases; Region: P-loop_NTPase; cl09099"
                     /db_xref="CDD:214148"
     misc_feature    490..714
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM (RNA recognition motif), 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...; Region: RRM; cd00590"
                     /db_xref="CDD:100104"
     misc_feature    order(496..498,616..618,622..624)
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RNA/DNA binding site [nucleotide binding]; other
                     site"
                     /db_xref="CDD:100104"
     misc_feature    706..714
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM dimerization site [polypeptide binding]; other
                     site"
                     /db_xref="CDD:100104"
     misc_feature    781..1005
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM (RNA recognition motif), 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...; Region: RRM; cd00590"
                     /db_xref="CDD:100104"
     misc_feature    order(787..789,907..909,913..915)
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RNA/DNA binding site [nucleotide binding]; other
                     site"
                     /db_xref="CDD:100104"
     misc_feature    997..1005
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM dimerization site [polypeptide binding]; other
                     site"
                     /db_xref="CDD:100104"
     misc_feature    1516..1737
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM (RNA recognition motif), 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...; Region: RRM; cd00590"
                     /db_xref="CDD:100104"
     misc_feature    order(1642..1644,1648..1650)
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RNA/DNA binding site [nucleotide binding]; other
                     site"
                     /db_xref="CDD:100104"
     misc_feature    1732..1737
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /note="RRM dimerization site [polypeptide binding]; other
                     site"
                     /db_xref="CDD:100104"
     exon            310..399
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     exon            400..450
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     variation       441
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:11540341"
     exon            451..612
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     variation       537
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:11540345"
     exon            613..705
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     exon            706..919
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     exon            920..1110
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     variation       1017
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:11540343"
     exon            1111..1246
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     exon            1247..1482
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     exon            1483..1958
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /inference="alignment:Splign:1.39.8"
     STS             1580..1830
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /standard_name="WI-19511"
                     /db_xref="UniSTS:31309"
     STS             1771..1914
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
                     /standard_name="RH70666"
                     /db_xref="UniSTS:37443"
     polyA_site      1925
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
     polyA_site      1958
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1"
ORIGIN      
gcggccggctcgcggcctcagcttccggcctgcggaccccagcttccggcggggcggggcgggggcctgggcgcggcgtgtggcccttgcgggcgagcctggcggggttgcgttcctgtccgctagcaggtcaatggccagcaaggaggggggtccgagccggcggcggcggcggcagtggtggcagcgggagacaaatggaaacctccacagggcacagactccatcaagatggagaacgggcagagcacagccgccaagctggggctgcctcccctgacgcccgagcagcaggaggcccttcagaaggccaagaagtacgccatggagcagagcatcaagagtgtgctggtgaagcagaccatcgcgcaccagcagcagcagctcaccaacctgcagatggcagcagtgacaatgggctttggagatcctctctcacctttgcaatcgatggcggctcagcggcagcgggcgctggccatcatgtgccgcgtctacgtgggctctatctactatgagctgggggaggacaccatccgccaggcctttgccccctttggccccatcaagagcatcgacatgtcctgggactccgtcaccatgaagcacaagggctttgccttcgtggagtatgaggtccccgaagctgcacagctggccttggagcagatgaactcggtgatgctggggggcaggaacatcaaggtgggcagacccagcaacatagggcaggcccagcccatcatagaccagttggctgaggaggcacgggccttcaaccgcatctacgtggcctctgtgcaccaggacctctcagacgatgacatcaagagcgtgtttgaggcctttggcaagatcaagtcctgcacactggcccgggaccccacaactggcaagcacaagggctacggcttcattgagtacgagaaggcccagtcgtcccaagatgctgtgtcttccatgaacctctttgacctgggtggccagtacttgcgggtgggcaaggctgtcacaccgcccatgcccctactcacaccagccacgcctggaggcctcccacctgccgctgctgtggcagctgctgcagccactgccaagatcacagctcaggaagcagtggccggagcagcggtgctgggtaccctgggcacacctggactggtgtccccagcactgaccctggcccagcccctgggcactttgccccaggctgtcatggctgcccaggcacctggagtcatcacaggtgtgaccccagcccgtcctcctatcccggtcaccatcccctcggtgggagtggtgaaccccatcctggccagccctccaacgctgggtctcctggagcccaagaaggagaaggaagaagaggagctgtttcccgagtcagagcggccagagatgctgagcgagcaggagcacatgagcatctcgggcagtagcgcccgacacatggtgatgcagaagctgctccgcaagcaggagtctacagtgatggttctgcgcaacatggtggaccccaaggacatcgatgatgacctggaaggggaggtgacagaggagtgtggcaagttcggggccgtgaaccgcgtcatcatctaccaagagaaacaaggcgaggaggaggatgcagaaatcattgtcaagatctttgtggagttttccatagcctctgagactcataaggccatccaggccctcaatggccgctggtttgctggccgcaaggtggtggctgaagtgtacgaccaggagcgttttgataacagtgacctctctgcgtgacagtggtccctctccccggacttgcacttgttccttgtttcctctgggttttatagtgatacagtggtgtccccggggccaggcgcgctctgcccagcccagcctacagtgcggataaaggtgcggatgctgctggccctgaacgtccgtgtgtctgccgtcggtcctgtcaccgaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:22827 -> Molecular function: GO:0000166 [nucleotide binding] evidence: IEA
            GeneID:22827 -> Molecular function: GO:0003677 [DNA binding] evidence: IEA
            GeneID:22827 -> Molecular function: GO:0003723 [RNA binding] evidence: IEA
            GeneID:22827 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:22827 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:22827 -> Biological process: GO:0006355 [regulation of transcription, DNA-dependent] evidence: IEA
            GeneID:22827 -> Biological process: GO:0006397 [mRNA processing] evidence: IEA
            GeneID:22827 -> Biological process: GO:0006915 [apoptotic process] evidence: IEA
            GeneID:22827 -> Biological process: GO:0008380 [RNA splicing] evidence: IEA
            GeneID:22827 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
            GeneID:22827 -> Cellular component: GO:0005730 [nucleolus] evidence: IDA
            GeneID:22827 -> Cellular component: GO:0019907 [cyclin-dependent protein kinase activating kinase holoenzyme complex] evidence: IDA
            GeneID:22827 -> Cellular component: GO:0030529 [ribonucleoprotein complex] evidence: IEA

by @meso_cacase at DBCLS
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