LOCUS       NM_028354               2055 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus tyrosyl-DNA phosphodiesterase 1 (Tdp1), transcript
            variant 2, mRNA.
ACCESSION   NM_028354 XM_001473901
VERSION     NM_028354.5
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2055)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 2055)
  AUTHORS   Khomenko,T.M., Zakharenko,A.L., Chepanova,A.A., Ilina,E.S.,
            Zakharova,O.D., Kaledin,V.I., Nikolin,V.P., Popova,N.A.,
            Korchagina,D.V., Reynisson,J., Chand,R., Ayine-Tora,D.M., Patel,J.,
            Leung,I.K.H., Volcho,K.P., Salakhutdinov,N.F. and Lavrik,O.I.
  TITLE     Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1)
            Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components
            of Complex Antitumor Therapy
  JOURNAL   Int J Mol Sci 21 (1), 126 (2019)
   PUBMED   31878088
  REMARK    GeneRIF: Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase
            I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as
            Components of Complex Antitumor Therapy.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2055)
  AUTHORS   Fam,H.K., Choi,K., Fougner,L., Lim,C.J. and Boerkoel,C.F.
  TITLE     Reactive oxygen species stress increases accumulation of
            tyrosyl-DNA phsosphodiesterase 1 within mitochondria
  JOURNAL   Sci Rep 8 (1), 4304 (2018)
   PUBMED   29523818
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2055)
  AUTHORS   Chiang,S.C., Meagher,M., Kassouf,N., Hafezparast,M., McKinnon,P.J.,
            Haywood,R. and El-Khamisy,S.F.
  TITLE     Mitochondrial protein-linked DNA breaks perturb mitochondrial gene
            transcription and trigger free radical-induced DNA damage
  JOURNAL   Sci Adv 3 (4), e1602506 (2017)
   PUBMED   28508041
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2055)
  AUTHORS   Katyal,S., Lee,Y., Nitiss,K.C., Downing,S.M., Li,Y., Shimada,M.,
            Zhao,J., Russell,H.R., Petrini,J.H., Nitiss,J.L. and McKinnon,P.J.
  TITLE     Aberrant topoisomerase-1 DNA lesions are pathogenic in
            neurodegenerative genome instability syndromes
  JOURNAL   Nat Neurosci 17 (6), 813-821 (2014)
   PUBMED   24793032
REFERENCE   6  (bases 1 to 2055)
  AUTHORS   El-Khamisy,S.F., Katyal,S., Patel,P., Ju,L., McKinnon,P.J. and
            Caldecott,K.W.
  TITLE     Synergistic decrease of DNA single-strand break repair rates in
            mouse neural cells lacking both Tdp1 and aprataxin
  JOURNAL   DNA Repair (Amst) 8 (6), 760-766 (2009)
   PUBMED   19303373
REFERENCE   7  (bases 1 to 2055)
  AUTHORS   Hawkins,A.J., Subler,M.A., Akopiants,K., Wiley,J.L., Taylor,S.M.,
            Rice,A.C., Windle,J.J., Valerie,K. and Povirk,L.F.
  TITLE     In vitro complementation of Tdp1 deficiency indicates a stabilized
            enzyme-DNA adduct from tyrosyl but not glycolate lesions as a
            consequence of the SCAN1 mutation
  JOURNAL   DNA Repair (Amst) 8 (5), 654-663 (2009)
   PUBMED   19211312
  REMARK    GeneRIF: Tdp1(-/-) fibroblasts exhibited deficiencies in processing
            3'-phosphotyrosyl single-strand breaks and 3'-phosphoglycolate
            double-strand breaks, but not 3'-phosphoglycolate single-strand
            breaks.
REFERENCE   8  (bases 1 to 2055)
  AUTHORS   Hirano,R., Interthal,H., Huang,C., Nakamura,T., Deguchi,K.,
            Choi,K., Bhattacharjee,M.B., Arimura,K., Umehara,F., Izumo,S.,
            Northrop,J.L., Salih,M.A., Inoue,K., Armstrong,D.L., Champoux,J.J.,
            Takashima,H. and Boerkoel,C.F.
  TITLE     Spinocerebellar ataxia with axonal neuropathy: consequence of a
            Tdp1 recessive neomorphic mutation?
  JOURNAL   EMBO J 26 (22), 4732-4743 (2007)
   PUBMED   17948061
  REMARK    GeneRIF: This study provides a direct demonstration that Tdp1
            repairs Topo I covalent lesions in vivo and suggests that
            spinocerebellar ataxia with axonal neuropathy (SCAN1) arises from
            the recessive neomorphic mutation H493R.
REFERENCE   9  (bases 1 to 2055)
  AUTHORS   Katyal,S., el-Khamisy,S.F., Russell,H.R., Li,Y., Ju,L.,
            Caldecott,K.W. and McKinnon,P.J.
  TITLE     TDP1 facilitates chromosomal single-strand break repair in neurons
            and is neuroprotective in vivo
  JOURNAL   EMBO J 26 (22), 4720-4731 (2007)
   PUBMED   17914460
  REMARK    GeneRIF: Data indicate that TDP1 is required for neural homeostasis
            and reveal a widespread requisite for TDP1 function in response to
            acutely elevated levels of DNA topoisomerase I (Top1)-associated
            DNA strand breaks.
REFERENCE   10 (bases 1 to 2055)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC160931.2 and CT010436.19.
            
            On Mar 19, 2020 this sequence version replaced NM_028354.4.
            
            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 :: AK014855.1, SRR5189676.126702.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-35                AC160931.2         54657-54691         c
            36-604              AC160931.2         47464-48032         c
            605-648             AC160931.2         45548-45591         c
            649-704             AC160931.2         44444-44499         c
            705-801             AC160931.2         40849-40945         c
            802-836             AC160931.2         36827-36861         c
            837-929             AC160931.2         33081-33173         c
            930-1097            AC160931.2         29363-29530         c
            1098-1176           AC160931.2         28848-28926         c
            1177-1362           AC160931.2         27429-27614         c
            1363-1411           AC160931.2         26886-26934         c
            1412-1478           AC160931.2         25092-25158         c
            1479-1586           AC160931.2         23652-23759         c
            1587-1689           AC160931.2         4102-4204           c
            1690-1798           CT010436.19        8032-8140
            1799-2055           CT010436.19        17755-18011
FEATURES             Location/Qualifiers
     source          1..2055
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="12"
                     /map="12"
     gene            1..2055
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="tyrosyl-DNA phosphodiesterase 1"
                     /db_xref="GeneID:104884"
                     /db_xref="MGI:MGI:1920036"
     exon            1..35
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            36..604
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     CDS             43..1872
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     tyrosyl-DNA phodphodiesterase 1; tyr-DNA phosphodiesterase
                     1; protein expressed in male leptotene and zygotene
                     spermatocytes 501"
                     /codon_start=1
                     /product="tyrosyl-DNA phosphodiesterase 1 isoform 2"
                     /protein_id="NP_082630.2"
                     /db_xref="CCDS:CCDS26105.2"
                     /db_xref="GeneID:104884"
                     /db_xref="MGI:MGI:1920036"
                     /translation="MSQESSYGKWTISSSDESEDEKPKPDKPSASSHPQAGQGVSKEL
                     IYTCSEARKVAHKRQISPVKFNDADSVLPHKKQKSDSPEGLGWCLSSSDDDQQPDVTQ
                     QEQPKRVLPQEKKHVSSPDVTTAQKVVDRSPPASLRPQRADDEYETSGEGQDIWDMLD
                     KGNPFQFYLTRVSGIKAKYNSKALHIKDILSPLFGTLVSSAQFNYCFDVDWLIKQYPP
                     EFRKNPILLVHGDKREAKADLHAQAKPYANISLCQAKLDIAFGTHHTKMMLLLYEEGL
                     RVVIHTSNLIREDWHQKTQGIWLSPLYPRIDQGSHTAGESSTRFKADLTSYLTAYNAP
                     PLQEWIDIIQEHDLSETNVYLIGSTPGRFQGSHRDNWGHFRLRKLLQAHAPSTPKGEC
                     WPIVGQFSSIGSLGPDESKWLCSEFKDSLLALREEGRPPGKSAVPLHLIYPSVENVRT
                     SLEGYPAGGSLPYSIQTAEKQRWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKL
                     AWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDTFKVKQKFFSSSCE
                     PTASFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS"
     exon            605..648
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            649..704
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            705..801
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            802..836
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            837..929
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            930..1097
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1098..1176
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1177..1362
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1363..1411
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1412..1478
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1479..1586
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1689
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1690..1798
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1799..2055
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1975..1980
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="hexamer: ATTAAA"
     polyA_site      2001
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="major polyA site"
     regulatory      2032..2037
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="hexamer: ATTAAA"
     polyA_site      2055
                     /gene="Tdp1"
                     /gene_synonym="2810481F14Rik; 4921509N21Rik;
                     E430034L06Rik; Gm40556; MLZ-501; SCAN1"
                     /note="major polyA site"
ORIGIN      
        1 gtctcggcgg cggcggcggc ggcctggcgg gtcagaagta taatgtccca agaaagcagc
       61 tacgggaagt ggacaatatc cagtagtgac gaaagcgagg atgagaagcc caaacctgat
      121 aagccgtcag catcctctca cccccaggct gggcagggag tgtcgaagga gctcatatac
      181 acctgctcag aggcccgcaa ggttgcacac aagagacaga tctcacctgt gaagttcaac
      241 gacgcagact cggtgctacc ccacaagaag cagaagagtg actccccgga aggtctcggc
      301 tggtgtctct ccagcagcga tgatgaccag cagccagatg tgacacagca ggaacagcct
      361 aagagagtgc tgcctcaaga gaaaaaacat gtctcctcac ccgatgtgac tactgcccag
      421 aaagttgtgg atagaagccc tcctgccagc cttaggcccc aaagggcaga cgatgagtac
      481 gagacctcag gggaaggcca ggacatctgg gacatgctgg ataaggggaa ccccttccag
      541 ttttatctca ctagagtgtc ggggattaag gcaaagtaca actccaaagc cctccacatc
      601 aaggatattt tatcccctct gtttgggaca cttgtctctt cagctcagtt taactactgc
      661 tttgacgtgg actggctcat aaagcaatat ccaccggaat tcaggaagaa cccgatcctg
      721 cttgtgcacg gtgataagag ggaagccaag gcagacttac atgcccaggc gaagccctat
      781 gcgaacattt ccctctgcca ggcaaagttg gatattgcat ttggaacaca ccacacgaaa
      841 atgatgctct tgctctatga agaaggcctc cgagttgtca tccacacctc caacctcatc
      901 cgggaagact ggcaccagaa aacccaagga atatggttga gccctttgta cccaagaatt
      961 gaccagggaa gccacacagc tggagagtca agcacccgtt tcaaagctga cctcaccagt
     1021 tatctaacgg cgtataacgc tccccctctg caggagtgga tagacatcat ccaagagcat
     1081 gacctctctg agaccaatgt ttacctcatt ggttcaaccc ctggacgctt tcaaggaagt
     1141 cacagagata actggggaca ttttaggctt agaaagcttc tgcaagcgca tgccccgtcc
     1201 acacccaagg gcgagtgctg gcctatcgtg ggtcagttct caagcatcgg ctccctgggg
     1261 cccgatgaat ccaagtggct gtgctcggag tttaaagaca gcttgctggc actgagagag
     1321 gaaggccgac ctccgggcaa gagtgcagtt cctcttcatc tgatctatcc ctctgtggaa
     1381 aatgtgcgga ccagcttaga aggataccct gctgggggct ctcttcccta tagcatccag
     1441 acggctgaaa agcagaggtg gctgcactcc tacttccaca agtggtcagc agagacatcc
     1501 ggccgaagta atgccatgcc acacattaag acgtacatga ggccctcgcc agacttcagt
     1561 aaactggctt ggttcctggt cacaagtgcg aatctgtcca aggctgcctg gggggcactg
     1621 gagaagaacg gcacccagct gatgatacgc tcctacgagc tcggggtcct cttcctcccg
     1681 tctgcgtttg gcctggacac cttcaaagtg aaacagaaat tcttctccag cagctgtgag
     1741 ccgacggcct cctttcctgt gccctatgac ctgcccccag agctgtacgg gagtaaagac
     1801 cggccttgga tttggaacat tccttatgtc aaagcacctg acacgcacgg caacatgtgg
     1861 gtgccctcct gagacgactg aacattcacc tccccttaaa gtcctgcacc cgtacaggac
     1921 tcctcgcaaa agtccttctt ggctatgtgt ctggtggtca ttgtcaacgt tcttattaaa
     1981 gaagaggtgt tattttctta attcactttt atatgtcctt aaaatcaagc tattaaattt
     2041 catagtattt aaaaa
//
