LOCUS       NM_078480               1868 bp    mRNA    linear   PRI 20-FEB-2025
DEFINITION  Homo sapiens poly(U) binding splicing factor 60 (PUF60), transcript
            variant 1, mRNA.
ACCESSION   NM_078480
VERSION     NM_078480.3
KEYWORDS    RefSeq; MANE Select.
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 1868)
  AUTHORS   Khoroshkin,M., Buyan,A., Dodel,M., Navickas,A., Yu,J., Trejo,F.,
            Doty,A., Baratam,R., Zhou,S., Lee,S.B., Joshi,T., Garcia,K.,
            Choi,B., Miglani,S., Subramanyam,V., Modi,H., Carpenter,C.,
            Markett,D., Corces,M.R., Mardakheh,F.K., Kulakovskiy,I.V. and
            Goodarzi,H.
  TITLE     Systematic identification of post-transcriptional regulatory
            modules
  JOURNAL   Nat Commun 15 (1), 7872 (2024)
   PUBMED   39251607
  REMARK    Erratum:[Nat Commun. 2024 Oct 28;15(1):9277. doi:
            10.1038/s41467-024-52903-4.. PMID: 39468017]
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1868)
  AUTHORS   Baum,E., Huang,W., Vincent-Delorme,C., Brunelle,P., Antebi,A. and
            Dafsari,H.S.
  TITLE     Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related
            Disorders
  JOURNAL   Int J Mol Sci 25 (4), 2053 (2024)
   PUBMED   38396730
  REMARK    GeneRIF: Novel Genetic and Phenotypic Expansion in Ameliorated
            PUF60-Related Disorders.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1868)
  AUTHORS   Grimes,H., Ansari,M., Ashraf,T., Cueto-Gonzalez,A.M., Calder,A.,
            Day,M., Fernandez Alvarez,P., Foster,A., Lahiri,N., Repetto,G.M.,
            Scurr,I., Varghese,V. and Low,K.J.
  TITLE     PUF60-related developmental disorder: A case series and phenotypic
            analysis of 10 additional patients with monoallelic PUF60 variants
  JOURNAL   Am J Med Genet A 191 (10), 2610-2622 (2023)
   PUBMED   37303278
  REMARK    GeneRIF: PUF60-related developmental disorder: A case series and
            phenotypic analysis of 10 additional patients with monoallelic
            PUF60 variants.
REFERENCE   4  (bases 1 to 1868)
  AUTHORS   Xu,N., Ren,Y., Bao,Y., Shen,X., Kang,J., Wang,N., Wang,Z., Han,X.,
            Li,Z., Zuo,J., Wei,G.H., Wang,Z., Zong,W.X., Liu,W., Xie,G. and
            Wang,Y.
  TITLE     PUF60 promotes cell cycle and lung cancer progression by regulating
            alternative splicing of CDC25C
  JOURNAL   Cell Rep 42 (9), 113041 (2023)
   PUBMED   37682709
  REMARK    GeneRIF: PUF60 promotes cell cycle and lung cancer progression by
            regulating alternative splicing of CDC25C.
REFERENCE   5  (bases 1 to 1868)
  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 1868)
  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 1868)
  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 1868)
  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 1868)
  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 1868)
  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 AF114818.1, AF217197.2 and
            AW249619.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_078480.2.
            
            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 (1) encodes the 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 :: AF190744.1, AF114818.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000526683.6/ ENSP00000434359.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-380               AF114818.1         53-432
            381-1835            AF217197.2         328-1782
            1836-1868           AW249619.1         10-42               c
FEATURES             Location/Qualifiers
     source          1..1868
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="8"
                     /map="8q24.3"
     gene            1..1868
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /note="poly(U) binding splicing factor 60"
                     /db_xref="GeneID:22827"
                     /db_xref="HGNC:HGNC:17042"
                     /db_xref="MIM:604819"
     exon            1..36
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     CDS             13..1692
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /note="isoform a is encoded by transcript variant 1; FBP
                     interacting repressor; pyrimidine tract binding splicing
                     factor; Ro ribonucleoprotein-binding protein 1;
                     FUSE-binding protein-interacting repressor; poly(U)
                     binding splicing factor 60KDa; Siah binding protein 1"
                     /codon_start=1
                     /product="poly(U)-binding-splicing factor PUF60 isoform a"
                     /protein_id="NP_510965.1"
                     /db_xref="CCDS:CCDS47934.1"
                     /db_xref="GeneID:22827"
                     /db_xref="HGNC:HGNC:17042"
                     /db_xref="MIM:604819"
                     /translation="MATATIALQVNGQQGGGSEPAAAAAVVAAGDKWKPPQGTDSIKM
                     ENGQSTAAKLGLPPLTPEQQEALQKAKKYAMEQSIKSVLVKQTIAHQQQQLTNLQMAA
                     VTMGFGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM
                     SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL
                     AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEK
                     AQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPGGLPPAAAVAAAAATAKIT
                     AQEAVAGAAVLGTLGTPGLVSPALTLAQPLGTLPQAVMAAQAPGVITGVTPARPPIPV
                     TIPSVGVVNPILASPPTLGLLEPKKEKEEEELFPESERPEMLSEQEHMSISGSSARHM
                     VMQKLLRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEED
                     AEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLSA"
     exon            37..123
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            124..219
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            220..309
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            310..360
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            361..522
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            523..615
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            616..829
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            830..1020
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            1021..1156
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            1157..1392
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     exon            1393..1868
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1806..1811
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /note="hexamer: GATAAA"
     polyA_site      1835
                     /gene="PUF60"
                     /gene_synonym="FIR; RoBPI; SIAHBP1; VRJS"
                     /note="major polyA site"
ORIGIN      
        1 gacggacgca agatggcgac ggcgaccata gctctccagg tcaatggcca gcaaggaggg
       61 gggtccgagc cggcggcggc ggcggcagtg gtggcagcgg gagacaaatg gaaacctcca
      121 cagggcacag actccatcaa gatggagaac gggcagagca cagccgccaa gctggggctg
      181 cctcccctga cgcccgagca gcaggaggcc cttcagaagg ccaagaagta cgccatggag
      241 cagagcatca agagtgtgct ggtgaagcag accatcgcgc accagcagca gcagctcacc
      301 aacctgcaga tggcagcagt gacaatgggc tttggagatc ctctctcacc tttgcaatcg
      361 atggcggctc agcggcagcg ggcgctggcc atcatgtgcc gcgtctacgt gggctctatc
      421 tactatgagc tgggggagga caccatccgc caggcctttg ccccctttgg ccccatcaag
      481 agcatcgaca tgtcctggga ctccgtcacc atgaagcaca agggctttgc cttcgtggag
      541 tatgaggtcc ccgaagctgc acagctggcc ttggagcaga tgaactcggt gatgctgggg
      601 ggcaggaaca tcaaggtggg cagacccagc aacatagggc aggcccagcc catcatagac
      661 cagttggctg aggaggcacg ggccttcaac cgcatctacg tggcctctgt gcaccaggac
      721 ctctcagacg atgacatcaa gagcgtgttt gaggcctttg gcaagatcaa gtcctgcaca
      781 ctggcccggg accccacaac tggcaagcac aagggctacg gcttcattga gtacgagaag
      841 gcccagtcgt cccaagatgc tgtgtcttcc atgaacctct ttgacctggg tggccagtac
      901 ttgcgggtgg gcaaggctgt cacaccgccc atgcccctac tcacaccagc cacgcctgga
      961 ggcctcccac ctgccgctgc tgtggcagct gctgcagcca ctgccaagat cacagctcag
     1021 gaagcagtgg ccggagcagc ggtgctgggt accctgggca cacctggact ggtgtcccca
     1081 gcactgaccc tggcccagcc cctgggcact ttgccccagg ctgtcatggc tgcccaggca
     1141 cctggagtca tcacaggtgt gaccccagcc cgtcctccta tcccggtcac catcccctcg
     1201 gtgggagtgg tgaaccccat cctggccagc cctccaacgc tgggtctcct ggagcccaag
     1261 aaggagaagg aagaagagga gctgtttccc gagtcagagc ggccagagat gctgagcgag
     1321 caggagcaca tgagcatctc gggcagtagc gcccgacaca tggtgatgca gaagctgctc
     1381 cgcaagcagg agtctacagt gatggttctg cgcaacatgg tggaccccaa ggacatcgat
     1441 gatgacctgg aaggggaggt gacagaggag tgtggcaagt tcggggccgt gaaccgcgtc
     1501 atcatctacc aagagaaaca aggcgaggag gaggatgcag aaatcattgt caagatcttt
     1561 gtggagtttt ccatagcctc tgagactcat aaggccatcc aggccctcaa tggccgctgg
     1621 tttgctggcc gcaaggtggt ggctgaagtg tacgaccagg agcgttttga taacagtgac
     1681 ctctctgcgt gacagtggtc cctctccccg gacttgcact tgttccttgt ttcctctggg
     1741 ttttatagtg atacagtggt gtccccgggg ccaggcgcgc tctgcccagc ccagcctaca
     1801 gtgcggataa aggtgcggat gctgctggcc ctgaacgtcc gtgtgtctgc cgtcggtcct
     1861 gtcaccga
//
