LOCUS       NM_018319               3722 bp    mRNA    linear   PRI 11-OCT-2024
DEFINITION  Homo sapiens tyrosyl-DNA phosphodiesterase 1 (TDP1), transcript
            variant 1, mRNA.
ACCESSION   NM_018319
VERSION     NM_018319.4
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 3722)
  AUTHORS   Geraud,M., Cristini,A., Salimbeni,S., Bery,N., Jouffret,V.,
            Russo,M., Ajello,A.C., Fernandez Martinez,L., Marinello,J.,
            Cordelier,P., Trouche,D., Favre,G., Nicolas,E., Capranico,G. and
            Sordet,O.
  TITLE     TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the
            repair of transcriptional DNA double-strand breaks
  JOURNAL   Cell Rep 43 (5), 114214 (2024)
   PUBMED   38761375
  REMARK    GeneRIF: TDP1 mutation causing SCAN1 neurodegenerative syndrome
            hampers the repair of transcriptional DNA double-strand breaks.
REFERENCE   2  (bases 1 to 3722)
  AUTHORS   Wei,X., Wang,Z., Hinson,C. and Yang,K.
  TITLE     Human TDP1, APE1 and TREX1 repair 3'-DNA-peptide/protein
            cross-links arising from abasic sites in vitro
  JOURNAL   Nucleic Acids Res 50 (7), 3638-3657 (2022)
   PUBMED   35349719
  REMARK    GeneRIF: Human TDP1, APE1 and TREX1 repair 3'-DNA-peptide/protein
            cross-links arising from abasic sites in vitro.
REFERENCE   3  (bases 1 to 3722)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   4  (bases 1 to 3722)
  AUTHORS   Jakobsen,A.K., Yuusufi,S., Madsen,L.B., Meldgaard,P., Knudsen,B.R.
            and Stougaard,M.
  TITLE     TDP1 and TOP1 as targets in anticancer treatment of NSCLC: Activity
            and protein level in normal and tumor tissue from 150 NSCLC
            patients correlated to clinical data
  JOURNAL   Lung Cancer 164, 23-32 (2022)
   PUBMED   34974222
  REMARK    GeneRIF: TDP1 and TOP1 as targets in anticancer treatment of NSCLC:
            Activity and protein level in normal and tumor tissue from 150
            NSCLC patients correlated to clinical data.
REFERENCE   5  (bases 1 to 3722)
  AUTHORS   Dyrkheeva,N.S., Filimonov,A.S., Luzina,O.A., Zakharenko,A.L.,
            Ilina,E.S., Malakhova,A.A., Medvedev,S.P., Reynisson,J.,
            Volcho,K.P., Zakian,S.M., Salakhutdinov,N.F. and Lavrik,O.I.
  TITLE     New Hybrid Compounds Combining Fragments of Usnic Acid and
            Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1
            Inhibition
  JOURNAL   Biomolecules 11 (7), 973 (2021)
   PUBMED   34356597
  REMARK    GeneRIF: New Hybrid Compounds Combining Fragments of Usnic Acid and
            Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1
            Inhibition.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3722)
  AUTHORS   Inamdar,K.V., Pouliot,J.J., Zhou,T., Lees-Miller,S.P.,
            Rasouli-Nia,A. and Povirk,L.F.
  TITLE     Conversion of phosphoglycolate to phosphate termini on 3' overhangs
            of DNA double strand breaks by the human tyrosyl-DNA
            phosphodiesterase hTdp1
  JOURNAL   J Biol Chem 277 (30), 27162-27168 (2002)
   PUBMED   12023295
  REMARK    GeneRIF: a role for hTdp1 in repair of free radical-mediated DNA
            double strand breaks bearing terminally blocked 3' overhangs.
REFERENCE   7  (bases 1 to 3722)
  AUTHORS   Davies,D.R., Interthal,H., Champoux,J.J. and Hol,W.G.
  TITLE     The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1
  JOURNAL   Structure 10 (2), 237-248 (2002)
   PUBMED   11839309
  REMARK    GeneRIF: 1.69 A crystal structure of human tyrosyl-DNA
            phosphodiesterase
REFERENCE   8  (bases 1 to 3722)
  AUTHORS   Interthal,H., Pouliot,J.J. and Champoux,J.J.
  TITLE     The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the
            phospholipase D superfamily
  JOURNAL   Proc Natl Acad Sci U S A 98 (21), 12009-12014 (2001)
   PUBMED   11572945
  REMARK    GeneRIF: Protein assay of expressed FLJ11090 shows that it encodes
            human tyrosyl-DNA phodphodiesterase (TDP1).
REFERENCE   9  (bases 1 to 3722)
  AUTHORS   Pouliot,J.J., Yao,K.C., Robertson,C.A. and Nash,H.A.
  TITLE     Yeast gene for a Tyr-DNA phosphodiesterase that repairs
            topoisomerase I complexes
  JOURNAL   Science 286 (5439), 552-555 (1999)
   PUBMED   10521354
  REMARK    GeneRIF: Sequences nearly identical to FLJ11090 are highly
            homologous to the yeast TDP1 gene.  Tdp1 protein cleaves the
            linkage between a phosphotyrosyl group and the 3'-end of DNA, and
            has been shown to be involved in the repair of TOP1-induced DNA
            damage.
REFERENCE   10 (bases 1 to 3722)
  AUTHORS   Salih,M.A.M., Takashima,H. and Boerkoel,C.F.
  TITLE     Spinocerebellar Ataxia with Axonal Neuropathy Type 1
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301284
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BU849335.1, BC015474.1,
            AL137128.4, AK023514.1 and BM661793.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_018319.3.
            
            Summary: The protein encoded by this gene is involved in repairing
            stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis
            of the phosphodiester bond between the tyrosine residue of
            topoisomerase I and the 3-prime phosphate of DNA. This protein may
            also remove glycolate from single-stranded DNA containing 3-prime
            phosphoglycolate, suggesting a role in repair of free-radical
            mediated DNA double-strand breaks. This gene is a member of the
            phospholipase D family and contains two PLD phosphodiesterase
            domains. Mutations in this gene are associated with the disease
            spinocerebellar ataxia with axonal neuropathy (SCAN1). [provided by
            RefSeq, Aug 2016].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (a). Variants 1 and 2 encode the same isoform.
            
            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 :: SRR1803612.110052.1,
                                           SRR1803613.119885.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000335725.9/ ENSP00000337353.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                BU849335.1         29-52
            25-2299             BC015474.1         1-2275
            2300-3405           AL137128.4         174024-175129
            3406-3697           AK023514.1         1794-2085
            3698-3722           BM661793.1         17-41               c
FEATURES             Location/Qualifiers
     source          1..3722
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q32.11"
     gene            1..3722
                     /gene="TDP1"
                     /note="tyrosyl-DNA phosphodiesterase 1"
                     /db_xref="GeneID:55775"
                     /db_xref="HGNC:HGNC:18884"
                     /db_xref="MIM:607198"
     exon            1..44
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            45..267
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            268..833
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     CDS             275..2101
                     /gene="TDP1"
                     /EC_number="3.1.4.-"
                     /note="isoform a is encoded by transcript variant 1;
                     tyr-DNA phosphodiesterase 1"
                     /codon_start=1
                     /product="tyrosyl-DNA phosphodiesterase 1 isoform a"
                     /protein_id="NP_060789.2"
                     /db_xref="CCDS:CCDS9888.1"
                     /db_xref="GeneID:55775"
                     /db_xref="HGNC:HGNC:18884"
                     /db_xref="MIM:607198"
                     /translation="MSQEGDYGRWTISSSDESEEEKPKPDKPSTSSLLCARQGAANEP
                     RYTCSEAQKAAHKRKISPVKFSNTDSVLPPKRQKSGSQEDLGWCLSSSDDELQPEMPQ
                     KQAEKVVIKKEKDISAPNDGTAQRTENHGAPACHRLKEEEDEYETSGEGQDIWDMLDK
                     GNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPE
                     FRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLR
                     VVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPS
                     LKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW
                     PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTS
                     LEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIA
                     WFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEP
                     MATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS"
     exon            834..877
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            878..933
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            934..1030
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1031..1065
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1066..1158
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1159..1326
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1327..1405
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1406..1591
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1592..1640
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1641..1707
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1708..1815
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1816..1918
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            1919..2027
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     exon            2028..3722
                     /gene="TDP1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2279..2284
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TDP1"
                     /note="hexamer: AATAAA"
     polyA_site      2303
                     /gene="TDP1"
                     /note="major polyA site"
     regulatory      3700..3705
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TDP1"
                     /note="hexamer: AATAAA"
     polyA_site      3722
                     /gene="TDP1"
                     /note="major polyA site"
ORIGIN      
        1 gaaggggcgg gatccgaggc aagcgttggt tctgtgcgcc tcagagttgg agcacacagc
       61 tgtattaaaa aggcaaatcg aaggccgggc gcggtgactc acgcctgtca tcctagcact
      121 ttgggaggcc gaggcggctg aatcacttga ggttaggagt ttgagatcag cccgggcaac
      181 atggtgaaac cccgtctcta caaaaataga aaaattagcc gagcgtgatg gtggatgcct
      241 gtaatcctag ctcctcggga ggctaaggag tataatgtct caggaaggcg attatgggag
      301 gtggaccata tctagtagtg atgaaagtga ggaagaaaag ccaaaaccag acaagccatc
      361 tacctcttct cttctctgtg ccaggcaagg agcagcaaat gagcccaggt acacctgttc
      421 cgaggcccag aaagctgcac acaagaggaa aatatcacct gtgaaattca gcaatacaga
      481 ttcagtttta cctcccaaaa ggcagaaaag cggttcccag gaggacctcg gctggtgtct
      541 gtccagcagt gatgatgagc tgcaaccaga aatgccgcag aagcaggctg agaaagtggt
      601 gatcaaaaag gagaaagaca tctctgctcc caatgacggc actgcccaaa gaactgaaaa
      661 tcatggcgct cccgcctgcc acaggctcaa agaggaggaa gacgagtatg agacatcagg
      721 ggagggccag gacatttggg acatgctgga taaagggaac cccttccagt tttacctcac
      781 tagagtctct ggagttaagc caaagtataa ctctggagcc ctccacatca aggatatttt
      841 atctccttta tttgggacgc ttgtttcttc agctcagttt aactactgct ttgacgtgga
      901 ctggctcgta aaacagtatc caccagagtt caggaagaag ccaatcctgc ttgtgcatgg
      961 tgataagcga gaggctaagg ctcacctcca tgcccaggcc aagccttacg agaacatctc
     1021 tctctgccag gcaaagttgg atattgcgtt tggaacacac cacacgaaaa tgatgctgct
     1081 gctctatgaa gaaggcctcc gggttgtcat acacacctcc aacctcatcc atgctgactg
     1141 gcaccagaaa actcaaggaa tatggttgag ccccttatac ccacgaattg ctgatggaac
     1201 ccacaaatct ggagagtcgc caacacattt taaagctgat ctcatcagtt acttgatggc
     1261 ttataatgcc ccttctctca aggagtggat agatgtcatt cacaagcacg atctctctga
     1321 aacaaatgtt tatcttattg gttcaacccc aggacgcttt caaggaagtc aaaaagataa
     1381 ttggggacat tttagactta agaagcttct gaaagaccat gcctcatcca tgcctaacgc
     1441 agagtcctgg cctgtcgtag gtcagttttc aagcgttggc tccttgggag ccgatgaatc
     1501 aaagtggtta tgttctgagt ttaaagagag catgctgaca ctggggaagg aaagcaagac
     1561 tccaggaaaa agctctgttc ctctttactt gatctatcct tctgtggaaa atgtgcggac
     1621 cagtttagaa ggatatcctg ctgggggctc tcttccctat agcatccaga cagctgaaaa
     1681 acagaattgg ctgcattcct attttcacaa atggtcagct gagacttctg gccgcagcaa
     1741 tgccatgcca catattaaga catatatgag gccttctcca gacttcagta aaattgcttg
     1801 gttccttgtc acaagcgcaa atctgtccaa ggctgcctgg ggagcattgg agaagaatgg
     1861 cacccagctg atgatccgct cctacgagct cggggtcctt ttcctccctt cagcatttgg
     1921 tctagacagt ttcaaagtga aacagaagtt cttcgctggc agccaggagc caatggccac
     1981 ctttcctgtg ccatatgatt tgcctccaga actgtatgga agtaaagatc ggccatggat
     2041 atggaacatt ccttatgtca aagcaccgga tacgcatggg aacatgtggg tgccctcctg
     2101 agaatcttga ggcactgtga aatttaagtg taagacattg agccacaaac atggaatctc
     2161 ttctttgtac tggatgtcca cttcccttaa agtcttattt gcacccttac aaaatctttc
     2221 caaaggtcac tcttatgaat ggatgttggt tatactttta atggacatta acattcctaa
     2281 taaagtatta gtttcttaat tcacttttat atgttttgga aagaaaatta gtgaacttct
     2341 ctatgttaaa aatacgtact gcttgagtat cccctgtctg aaatgcttgg gaccagaagt
     2401 gtttcagctt ttggattttt ttgaattttg gaatatttgc atagcataat gagatatctt
     2461 gggaatggga cccaaatcta aacacaaaat tcatttatgt ttcatataca ccttatatac
     2521 aataacctaa aggtgatttt atatgatatt ttgagtaatt ttatgcatga aacaaagttt
     2581 tgacaggctt ttgaccgtga ttcatcacat gagttcaggc atggaaattt tcatttggag
     2641 catcatgtca gcactcaaaa agttctggat cttggagcag ttcagatttt cagattaggg
     2701 atgctcaaat ctatatagat ataaaattat cctcacagta acatagaatc tcttggtgct
     2761 gtcagctgtt gggaattgaa gattgacttt gtgcttccac cctccatcca gaaaggcacc
     2821 cttcattcca ccagaacttt acccaggaag aacacgatca tttccttttt caccgatgcc
     2881 ctctctcagc tttctgagta cgtctcttgg ggtcgctgga ggtgatccta ggatctgtct
     2941 ctgagaccaa tgtgctgttt cagccccctg cagctaagaa ttgtattgac tgtcctcaca
     3001 gcggcttttc atagctttca gcttcagctt tacgaggctt ctcctctctc cctggcaccc
     3061 tgctggctgc ctcactgctt acagacaggt cccaccaaac ccaaacacct gcctagggta
     3121 aatgggtctc tcttctatcc ccagaaactt tcagaggaag cagctcatag aaacatacaa
     3181 aagcacacaa gtattttggg aaaaaatcct aaaaggtgac ttaatttgat gccttaaatt
     3241 cacaagtgag gaagctaagg cctagaaggt taaggatgtc cccagggtca cacagtgagc
     3301 ggggctcaga gcttgagtgt ctttgtgctt tgtgtacatt gtgttctccc tagggtgctt
     3361 tagaccctgt ttgttttctt ctgcatgagg ctgatttcca gtttgtcatc aacctcttta
     3421 tcttataatt taggatagag ttgaacgtta gtcttgaaag attttctaaa gtagtctttc
     3481 aaactgttcc tcagaggcct aggattttcc aaaagtacct taggaacctt gtaggctgca
     3541 gtgggggtgt ggcgatagag caggaggcag ggagacaggg ctgcagggcc tcccaccttc
     3601 caacagacag gctctgctgt atctgttgta catactggga ttctgtaaag gacattatct
     3661 ggggtgttgt atgtattttt gtgtgttctg ctttttttaa ataaacttga aaagctactg
     3721 aa
//
