LOCUS       NM_001025444            5554 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus aprataxin (Aptx), transcript variant 2, mRNA.
ACCESSION   NM_001025444
VERSION     NM_001025444.3
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 5554)
  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 5554)
  AUTHORS   Perez,H., Abdallah,M.F., Chavira,J.I., Norris,A.S., Egeland,M.T.,
            Vo,K.L., Buechsenschuetz,C.L., Sanghez,V., Kim,J.L., Pind,M.,
            Nakamura,K., Hicks,G.G., Gatti,R.A., Madrenas,J., Iacovino,M.,
            McKinnon,P.J. and Mathews,P.J.
  TITLE     A novel, ataxic mouse model of ataxia telangiectasia caused by a
            clinically relevant nonsense mutation
  JOURNAL   Elife 10, e64695 (2021)
   PUBMED   34723800
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 5554)
  AUTHORS   Horton,J.K., Stefanick,D.F., Caglayan,M., Zhao,M.L.,
            Janoshazi,A.K., Prasad,R., Gassman,N.R. and Wilson,S.H.
  TITLE     XRCC1 phosphorylation affects aprataxin recruitment and DNA
            deadenylation activity
  JOURNAL   DNA Repair (Amst) 64, 26-33 (2018)
   PUBMED   29477978
  REMARK    GeneRIF: Interaction with phosphorylated XRCC1 is a requirement for
            significant APTX recruitment to cellular DNA damage and enzymatic
            activity in cell extracts.
REFERENCE   4  (bases 1 to 5554)
  AUTHORS   Carroll,J., Page,T.K., Chiang,S.C., Kalmar,B., Bode,D.,
            Greensmith,L., Mckinnon,P.J., Thorpe,J.R., Hafezparast,M. and
            El-Khamisy,S.F.
  TITLE     Expression of a pathogenic mutation of SOD1 sensitizes
            aprataxin-deficient cells and mice to oxidative stress and triggers
            hallmarks of premature ageing
  JOURNAL   Hum Mol Genet 24 (3), 828-840 (2015)
   PUBMED   25274775
  REMARK    GeneRIF: Study demonstrates a protective role of Aptx in vivo and
            suggests that its loss results in progressive accumulation of DNA
            breaks in the nervous system, triggering hallmarks of premature
            ageing, systemically.
REFERENCE   5  (bases 1 to 5554)
  AUTHORS   Yeo,A.J., Becherel,O.J., Luff,J.E., Cullen,J.K., Wongsurawat,T.,
            Jenjaroenpun,P., Kuznetsov,V.A., McKinnon,P.J. and Lavin,M.F.
  TITLE     R-loops in proliferating cells but not in the brain: implications
            for AOA2 and other autosomal recessive ataxias
  JOURNAL   PLoS One 9 (3), e90219 (2014)
   PUBMED   24637776
  REMARK    Erratum:[PLoS One. 2014;9(8):e105258. Jenjaroenpoon, Piroon
            [corrected to Jenjaroenpun, Piroon]]
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 5554)
  AUTHORS   Reynolds,J.J., El-Khamisy,S.F., Katyal,S., Clements,P.,
            McKinnon,P.J. and Caldecott,K.W.
  TITLE     Defective DNA ligation during short-patch single-strand break
            repair in ataxia oculomotor apraxia 1
  JOURNAL   Mol Cell Biol 29 (5), 1354-1362 (2009)
   PUBMED   19103743
  REMARK    GeneRIF: aprataxin participates in chromosomal single-strand break
            repair
REFERENCE   7  (bases 1 to 5554)
  AUTHORS   Ahel,I., Rass,U., El-Khamisy,S.F., Katyal,S., Clements,P.M.,
            McKinnon,P.J., Caldecott,K.W. and West,S.C.
  TITLE     The neurodegenerative disease protein aprataxin resolves abortive
            DNA ligation intermediates
  JOURNAL   Nature 443 (7112), 713-716 (2006)
   PUBMED   16964241
  REMARK    GeneRIF: neurological disorders associated with APTX mutations may
            be caused by the gradual accumulation of unrepaired DNA strand
            breaks resulting from abortive DNA ligation events
REFERENCE   8  (bases 1 to 5554)
  AUTHORS   Bailey,P.J., Klos,J.M., Andersson,E., Karlen,M., Kallstrom,M.,
            Ponjavic,J., Muhr,J., Lenhard,B., Sandelin,A. and Ericson,J.
  TITLE     A global genomic transcriptional code associated with CNS-expressed
            genes
  JOURNAL   Exp Cell Res 312 (16), 3108-3119 (2006)
   PUBMED   16919269
REFERENCE   9  (bases 1 to 5554)
  AUTHORS   Moreira,M.C., Barbot,C., Tachi,N., Kozuka,N., Uchida,E., Gibson,T.,
            Mendonca,P., Costa,M., Barros,J., Yanagisawa,T., Watanabe,M.,
            Ikeda,Y., Aoki,M., Nagata,T., Coutinho,P., Sequeiros,J. and
            Koenig,M.
  TITLE     The gene mutated in ataxia-ocular apraxia 1 encodes the new
            HIT/Zn-finger protein aprataxin
  JOURNAL   Nat Genet 29 (2), 189-193 (2001)
   PUBMED   11586300
REFERENCE   10 (bases 1 to 5554)
  AUTHORS   Date,H., Onodera,O., Tanaka,H., Iwabuchi,K., Uekawa,K.,
            Igarashi,S., Koike,R., Hiroi,T., Yuasa,T., Awaya,Y., Sakai,T.,
            Takahashi,T., Nagatomo,H., Sekijima,Y., Kawachi,I., Takiyama,Y.,
            Nishizawa,M., Fukuhara,N., Saito,K., Sugano,S. and Tsuji,S.
  TITLE     Early-onset ataxia with ocular motor apraxia and hypoalbuminemia is
            caused by mutations in a new HIT superfamily gene
  JOURNAL   Nat Genet 29 (2), 184-188 (2001)
   PUBMED   11586299
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL833775.7, AK010516.1, AK005286.1 and AL929313.13.
            
            On Sep 26, 2013 this sequence version replaced NM_001025444.2.
            
            Transcript Variant: This variant (2) differs in the 5' UTR and the
            5' coding region and intiates translation at a downstream start
            codon, compared to variant 1. It encodes isoform b, which has a
            shorter N-terminus, compared to isoform a.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR9219380.55693.1,
                                           SRR10223971.4614.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164135 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-14                AL833775.7         15041-15054         c
            15-49               AK010516.1         2-36
            50-1161             AK005286.1         2-1113
            1162-5554           AL929313.13        96164-100556        c
FEATURES             Location/Qualifiers
     source          1..5554
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 20.46 cM"
     gene            1..5554
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="aprataxin"
                     /db_xref="GeneID:66408"
                     /db_xref="MGI:MGI:1913658"
     exon            1..58
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            59..195
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     CDS             66..1073
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /EC_number="3.6.1.72"
                     /EC_number="3.6.1.71"
                     /note="isoform b is encoded by transcript variant 2;
                     forkhead-associated domain histidine triad-like protein"
                     /codon_start=1
                     /product="aprataxin isoform b"
                     /protein_id="NP_001020615.1"
                     /db_xref="CCDS:CCDS38712.1"
                     /db_xref="GeneID:66408"
                     /db_xref="MGI:MGI:1913658"
                     /translation="MRVCWLVRQDSRHQRIKLPHLEAVVIGRSPETKITDKKCSRQQV
                     QLKAECNKGYVKVQQMGVNPTSIDSGVIGKDQEKKLLPGQVLHMVNGLYPYIVEFEEV
                     AESPNLTQRKRKRSDCDSEEMEAESGTGLAPGSSPSQCSVSPKKDKNGATKKESLGHW
                     SQGLKMSMKDPKMQVYKDDQVVVIKDKYPKARHHWLVLPWASISSLKVVTSEHLELLK
                     HMHAVGEKVIADFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFN
                     TEYFLESQAVIKMVQEAGRVTVKDGTCELLKLPLRCHECQQLLPSIPQLKEHLRKHWG
                     G"
     exon            196..242
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            243..527
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            528..587
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            588..814
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            815..918
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     exon            919..5554
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1142..1147
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="hexamer: ACTAAA"
     polyA_site      1165
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="major polyA site"
     regulatory      1369..1374
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="hexamer: AATATA"
     polyA_site      1390
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
     regulatory      5221..5226
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="hexamer: AATAAA"
     polyA_site      5250
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
     regulatory      5534..5539
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
                     /note="hexamer: AATAAA"
     polyA_site      5554
                     /gene="Aptx"
                     /gene_synonym="2410016G21Rik; FHA-HIT"
ORIGIN      
        1 accggaagcg gcgaggcgca gtagagcagc gtgaagtttg tgggtgtcca cagtcgagag
       61 ctaagatgcg agtgtgctgg ttggtgagac aggacagcag gcaccagcga atcaaacttc
      121 cccatttgga agctgttgtg attggtcgaa gcccagagac caagatcaca gataagaaat
      181 gttcccgaca gcaagtacag ttgaaagcag agtgtaacaa gggatatgtc aaagtacagc
      241 agatgggggt caaccccacc agcattgact cgggcgtcat cgggaaggac caagagaaga
      301 agctgctgcc tggtcaggtt ctccacatgg tgaatggact ttatccatac atcgtagagt
      361 ttgaggaagt ggcagagagc cctaacctaa cacagaggaa gagaaagagg tcagactgtg
      421 atagtgagga gatggaagct gagtctggga cagggctggc acctgggagc agccccagcc
      481 agtgctctgt gtcccctaag aaggacaaga atggagccac caaaaaggaa tcactgggcc
      541 actggagtca aggcttgaag atgtctatga aagaccccaa aatgcaggtt tacaaagacg
      601 accaggtggt ggtgattaag gataaatacc ccaaggcccg tcaccactgg ctggtcttac
      661 cgtgggcctc catttccagt ctgaaggttg tgaccagtga acaccttgaa cttctcaaac
      721 atatgcacgc tgtgggggag aaggtgatag cagattttgc tggatccagc aaactgcgct
      781 tccgattggg ctaccatgcc attcccagca tgagccacgt acatcttcat gtgatcagcc
      841 aggattttga ttctccttgc cttaaaaaca aaaagcattg gaattctttt aatacagaat
      901 actttctgga atcacaagct gtgatcaaga tggttcagga agccggcaga gtgactgtta
      961 aagatggcac ttgtgagctc ttgaagctgc ctctccgttg ccatgagtgt cagcagctgc
     1021 tgccttccat cccgcagctg aaagagcacc tcaggaagca ctggggcggg tgacactcgt
     1081 ctcggcgacc aagggcagtg ctagcatctg tccgcattgc ctatgctccg ttcaatcctg
     1141 aactaaagcg tacacttctt cgaaacaaag cttatttatt cttgagcagc cacacattgg
     1201 gtgcactctg gtgcaggaac tgggaattcg ggttttgtgg gtgtattctc tggtaatgga
     1261 ggctgagaca tgcctggtca cccttcccag gaccatgaca ggcctgacta atgagagggc
     1321 aaagccggct tgagactcaa atgcacgatg tagaagcaga ggattggtaa tatattttgt
     1381 tcctaccctc gttcctggat tgtgtagtat ctgttcatca aggtagctga ggttctgagg
     1441 ggcctggttc tgcctttagt ctgctctatg agattcctct tcccccatga ggaggctttc
     1501 aatctactgc accaggctga gtgtctagtt gaaaatatgt ggcagtcatc tacacagaga
     1561 gataatttgt gtatgactgt gtcagggaag aggaagtggt aatactgggc acagtaatgt
     1621 taacagtaca gtctgtgctg agggcagcct ggggtggtgt gaactgtaca gtctgtgctg
     1681 agggcagcct ggggcggtgt gaactataca gtctgtgctg agggcagcct ggggcggtgt
     1741 gagctgtaca gtctgtgctg agggcagcct ggggcggtgt gaactgtaca gtctgtgctg
     1801 agggcagcct ggggcggtgt gaactgtaca gtctgtgctg agggcagcct ggggcggtgt
     1861 gaactgtaca gtctgtgctg agggcagcct ggggcggtgt gaactgtaca gtctgtgctg
     1921 agggcagcct gggggcggtg tgaactgtat agtctgtgct gagggcagcc tggggcggtg
     1981 tgaactgtat agtctgtgct gagggcagac tggggcggtg tgagctgtac agtctgtgct
     2041 gagggcagcc tggggtggtg tgagctatat agtctgtgct gagggcagcc tggagtggtg
     2101 tgaactgtac agtctgtgct gagggcagcc tggggtggtg tgagctgtca gttgactgta
     2161 cagtctgcat ggagagcagc ctgggcaatg tgtattttta gcttcaggca gattttactg
     2221 aggcttccac tactgctctt gagaattaca gagcatttat ctaaacttca gataaagttt
     2281 ccccaatgca tctgggaaaa acagatgttg caaaatagtt catttaattt ctacctaata
     2341 ctatatagtt tagcacatca atattaaact gagtatttgg ttatacagta ctaggagtgt
     2401 gtgtatcaga cagtgtaaga atgtcaggta taatggggaa cattctgaga gtgagatgac
     2461 catgcttaca ttcttcattc tgccccaaat agattttgta aggccgggct aagtgcctgc
     2521 tgttattcct gaggacccga gttttgttcc cagcacccac agcaggtggc tcacagacac
     2581 ctatagctcc aggggatcct acaccctctt ttgagcgccg tgggcatgca ttccagtaca
     2641 caaacctgaa tacagacata catattcata cataattaaa atttttaaaa aattagatct
     2701 cttagaggaa aaaaatataa attatgacat gcaggaacca ggtgttgagg tattaagtat
     2761 attcatccca tagctctcct ctccccagtg ggctttcatc actaggggga gaagactgtc
     2821 tggcctctgc attacttgac agacgtgtca ttgcacaatt agttgaagcc ttccttcaga
     2881 agcagaggga gggatgatgg gagactgcag agtagaagaa agccagccac atctaaagcc
     2941 aggcacagtg gcaaagtctc ctgcaatccc caaatgtagg aggtggtgga gcaaggaggg
     3001 ccgggagttc cgggttatcc ttgtctgtat ggtgaactgg aagtctggac tacatgaggc
     3061 ctgtgtcaaa taagcaaata aaacatttaa aagggggaaa taaagttata tctgaggtgc
     3121 caaagaatat tattttgccc gtttgacctt ggcccttcat agccaggaag gacaatgtta
     3181 tcaaagcagt ggttatgatt caaatctgga ctaactccac aggctcatgt ttcagagtgg
     3241 caggtccttt ccatgcagtg tgtgctagat gctgtggagc ctttaggaag tgaggcctgg
     3301 ctggcagaca tagtctccag gatcaggctt ttgaaggcta tacctgttcc tggttggcct
     3361 cctgtgaata ggccacccat ctctgctact gtgggctgac acacactgtg tgtgtgtagg
     3421 caagaggaca atttccagat gtcagttgtc tccaccatgt gggtcctggg gattgaactc
     3481 atgtcattgg gcttggctat aagtgtcttt acccactgag ttccagtaag tcagaagtac
     3541 tctttttaaa aagtaataac ttaattctca agtaaacaca cacacacaca cacacacaca
     3601 cacacacaca cacacaccca cccaccacaa ccttacctca tcccaagcta tcctagaact
     3661 caacatgtag actaggttgg ctttgaactt gcagagatct gccagtctgt ggatccaggc
     3721 tgctgggatg caagtacacc acaaaaagaa aacacaaaac aaaacaaatg cacaaggatt
     3781 aggtagacat tgtctgtatt taattacgat tcagtgtctt ctgagaatga aatattgtca
     3841 tggaatacca ttcccttctg cagtaatgtt cagatctgcc tctttagaat gctctttcct
     3901 tttggatgtt gataatggtg cattggctgg ttttgtgtgt caatttgaca caagctaaga
     3961 gtcatcagag aagaaggatg ttcagttgag aaaatgagat ccaactgtaa ggcattttca
     4021 taattagtga ccaatgggga gagcaccatt ggaggtggtg ccatccctgg actagtggtc
     4081 ctaggtccta tgagaaggca gctgagcaag ccaggggaag caagccattg ggtggcaccc
     4141 cgctcgtggt ctctgcatca gtttctgctt ctaggttcct tccctgtttg agtttctgtc
     4201 ctgacttcct ttggtgatga acatactggc tgtgggattg ccagtttgtc actcaggctt
     4261 tatggtgaca ccaggacatt caaaatttgg aggtatataa tggagcatta tttaagccat
     4321 aaataagaag gaaattgtgt ccttttcgag aagacagata cccgggacat catcctgtgg
     4381 aatgcagtca gccagactca gaacaattac ctcatattgg tggtctcaaa gttcttggct
     4441 cccctgactc caggcccgtt ggaggcagag tatggcagag attgacgcat gcacaaagcc
     4501 accttagcac accagacaaa ggcagagaca acacttacct attctgagat tggtcttact
     4561 atgtagccaa gactgacctg gaactcatgt agctcagctt ggtcttgaat tcaagaccca
     4621 actgcctttg ccttgaaagt tctgggtata ttgctatcgt gcccagctag gaagtgttct
     4681 cagaacactg atttcagagc atgagacccc ttcatgtgtg ggtcaccgtg agtcaactaa
     4741 cccttctgtg gctggaccct gcaggtaagg ggtggagcac agggcagagg aggggcttct
     4801 ggcactcagt tctaaggagc cagtggacca gctggattct tatctgccgc tgacatttcc
     4861 acaccacaga ctctctagtt tgtggcagct gggaacttac ttttgttttc aagaacccag
     4921 cgataggtca gattctcaaa tacagccgat tgtggtggtc atgagtgaga agagactcaa
     4981 gatgttagga ggagaccaca gtatgtagac ctgactgaac ttgcccctga caagctgaca
     5041 gcccattgca tcatctttac atgaatgaga aaaaggtacc tgttgcacgt ggaaaccttt
     5101 aacccaaatc ccctgaggcc ggagccgcta tgagacacaa ctacatgaca gtgtaggctg
     5161 gggaccctgt ttcccatggg gtcctctgtc accttcacaa tggaattctg actacctgaa
     5221 aataaaggac acaagatttt gttgagtgaa taaagtagtg tcatgctttt tgctagcaaa
     5281 cagtaaagag acttctctca cactggactg taatgaggga ggtagtgtgc tgtatggtca
     5341 accagttttt catctgatag cctcttgatg ccatcctgaa tgggcaaagg ctctcttaca
     5401 ggtaggaatg aggggtgtgt ggagaagaca gtatgttttc tacctaatgt tttagctttt
     5461 cagtccacaa aatgggattc tcctgtgaga gcgtttcagt tttctcactt tggccaccag
     5521 gtggcagcat gtgaataaag aatttttaat cctc
//
