LOCUS       NM_001008545            6513 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus TAR DNA binding protein (Tardbp), transcript variant
            2, mRNA.
ACCESSION   NM_001008545
VERSION     NM_001008545.2
KEYWORDS    RefSeq.
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 6513)
  AUTHORS   Krus,K.L., Benitez,A.M., Strickland,A., Milbrandt,J., Bloom,A.J.
            and DiAntonio,A.
  TITLE     Two cardinal features of ALS, reduced STMN2 and pathogenic TDP-43,
            synergize to accelerate motor decline in mice
  JOURNAL   Exp Neurol 384, 115068 (2025)
   PUBMED   39603486
REFERENCE   2  (bases 1 to 6513)
  AUTHORS   Torres,P., Rico-Rios,S., Ceron-Codorniu,M., Santacreu-Vilaseca,M.,
            Seoane-Miraz,D., Jad,Y., Ayala,V., Marino,G., Beltran,M.,
            Miralles,M.P., Andres-Benito,P., Fernandez-Irigoyen,J.,
            Santamaria,E., Lopez-Otin,C., Soler,R.M., Povedano,M., Ferrer,I.,
            Pamplona,R., Wood,M.J.A., Varela,M.A. and Portero-Otin,M.
  TITLE     TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic
            splicing inhibition
  JOURNAL   Acta Neuropathol 148 (1), 45 (2024)
   PUBMED   39305312
  REMARK    GeneRIF: TDP-43 regulates LC3ylation in neural tissue through ATG4B
            cryptic splicing inhibition.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 6513)
  AUTHORS   Carmen-Orozco,R.P., Tsao,W., Ye,Y., Sinha,I.R., Chang,K.,
            Trinh,V.T., Chung,W., Bowden,K., Troncoso,J.C., Blackshaw,S.,
            Hayes,L.R., Sun,S., Wong,P.C. and Ling,J.P.
  TITLE     Elevated nuclear TDP-43 induces constitutive exon skipping
  JOURNAL   Mol Neurodegener 19 (1), 45 (2024)
   PUBMED   38853250
  REMARK    GeneRIF: Elevated nuclear TDP-43 induces constitutive exon
            skipping.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 6513)
  AUTHORS   Guo,C., Wang,T., Huang,H., Wang,X., Jiang,Y. and Li,J.
  TITLE     Plasminogen degrades alpha-synuclein, Tau and TDP-43 and decreases
            dopaminergic neurodegeneration in mouse models of Parkinson's
            disease
  JOURNAL   Sci Rep 14 (1), 8581 (2024)
   PUBMED   38615036
  REMARK    GeneRIF: Plasminogen degrades alpha-synuclein, Tau and TDP-43 and
            decreases dopaminergic neurodegeneration in mouse models of
            Parkinson's disease.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 6513)
  AUTHORS   Zhang,H., Chen,C., Zhang,E.E. and Huang,X.
  TITLE     TDP-43 deficiency in suprachiasmatic nucleus perturbs rhythmicity
            of neuroactivity in prefrontal cortex
  JOURNAL   iScience 27 (4), 109522 (2024)
   PUBMED   38585660
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 6513)
  AUTHORS   Taniwaki,T., Haruna,K., Nakamura,H., Sekimoto,T., Oike,Y.,
            Imaizumi,T., Saito,F., Muta,M., Soejima,Y., Utoh,A., Nakagata,N.,
            Araki,M., Yamamura,K. and Araki,K.
  TITLE     Characterization of an exchangeable gene trap using pU-17 carrying
            a stop codon-beta geo cassette
  JOURNAL   Dev Growth Differ 47 (3), 163-172 (2005)
   PUBMED   15840001
REFERENCE   7  (bases 1 to 6513)
  AUTHORS   Wang,H.Y., Wang,I.F., Bose,J. and Shen,C.K.
  TITLE     Structural diversity and functional implications of the eukaryotic
            TDP gene family
  JOURNAL   Genomics 83 (1), 130-139 (2004)
   PUBMED   14667816
REFERENCE   8  (bases 1 to 6513)
  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
REFERENCE   9  (bases 1 to 6513)
  AUTHORS   Wang,I.F., Reddy,N.M. and Shen,C.K.
  TITLE     Higher order arrangement of the eukaryotic nuclear bodies
  JOURNAL   Proc Natl Acad Sci U S A 99 (21), 13583-13588 (2002)
   PUBMED   12361981
REFERENCE   10 (bases 1 to 6513)
  AUTHORS   Araki,K., Imaizumi,T., Sekimoto,T., Yoshinobu,K., Yoshimuta,J.,
            Akizuki,M., Miura,K., Araki,M. and Yamamura,K.
  TITLE     Exchangeable gene trap using the Cre/mutated lox system
  JOURNAL   Cell Mol Biol (Noisy-le-grand) 45 (5), 737-750 (1999)
   PUBMED   10512203
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CD548243.1, AK032199.1, AY319516.1, AK146997.1, BC027105.1,
            AK045495.1, AK133207.1, CF741580.1, CK780683.1, CD353594.1,
            CF725038.1, CX202635.1, BE853411.1, BE335004.1, AK004440.1 and
            BF658781.1.
            
            On Aug 30, 2007 this sequence version replaced NM_001008545.1.
            
            Transcript Variant: This variant (2) uses alternate splice sites in
            the 3' coding region and differs in the 3' UTR compared to variant
            1. It encodes isoform 2, which has a shorter and distinct
            C-terminus compared to isoform 1.
            
            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 :: SRR17784651.520630.1,
                                           SRR7345562.4338558.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-316               CD548243.1         1-316
            317-330             AK032199.1         87-100
            331-1341            AY319516.1         1-1011
            1342-2028           AK146997.1         1962-2648
            2029-2169           BC027105.1         1764-1904
            2170-2976           AK045495.1         1201-2007
            2977-3425           AK133207.1         3694-4142
            3426-3686           CF741580.1         317-577
            3687-4284           CK780683.1         91-688
            4285-4483           CD353594.1         416-614
            4484-5096           CF725038.1         36-648
            5097-5432           CX202635.1         366-701
            5433-5947           BE853411.1         33-547
            5948-6409           BE335004.1         52-513
            6410-6505           AK004440.1         1042-1137
            6506-6513           BF658781.1         4-11                c
FEATURES             Location/Qualifiers
     source          1..6513
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 78.77 cM"
     gene            1..6513
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="TAR DNA binding protein"
                     /db_xref="GeneID:230908"
                     /db_xref="MGI:MGI:2387629"
     exon            1..316
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     exon            317..568
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     CDS             331..1245
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="isoform 2 is encoded by transcript variant 2; TAR
                     DNA-binding protein 43"
                     /codon_start=1
                     /product="TAR DNA-binding protein 43 isoform 2"
                     /protein_id="NP_001008545.1"
                     /db_xref="CCDS:CCDS38968.1"
                     /db_xref="GeneID:230908"
                     /db_xref="MGI:MGI:2387629"
                     /translation="MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYR
                     NPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQK
                     TSDLIVLGLPWKTTEQDLKDYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK
                     VMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTAEELQQFFCQYGEVV
                     DVFIPKPFRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRF
                     GGNPGGFGNQVHLISNVYGRSTSLKVVL"
     exon            569..732
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     exon            733..873
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     exon            874..1044
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     exon            1045..1189
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     exon            1190..6513
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2011..2016
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="hexamer: AATAAA"
     polyA_site      2032
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="major polyA site"
     regulatory      3404..3409
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="hexamer: AATAAA"
     polyA_site      3427
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
     regulatory      6489..6494
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="hexamer: ATTAAA"
     polyA_site      6508
                     /gene="Tardbp"
                     /gene_synonym="1190002A23Rik; TDP-43; Tdp43"
                     /note="major polyA site"
ORIGIN      
        1 ctcggaaggc cgagtggccg ttctgtcctt catctgtcag tttttcagac ccagctgttt
       61 tcattgttgc gtttctttac ttttttctat acgccgaaga gcctgctagc atccgagcct
      121 ctgggaggag agagcgcctg tggcttccct cggagagcgc ccctcctgca gggaagccag
      181 tgggagaggc cgaaggcggg cgagggcggg aggcggccct agcgccattt tgtgggcacg
      241 gagcggtagc gcggctgttg tcggattcct tcccgtctgt gcttcctcct tgtgcttcct
      301 agcagtggcc tagcggagat ttaagcaaag atgtctgaat atattcgggt aacagaagat
      361 gagaacgatg aacccattga aataccatca gaagacgatg ggacggtgtt gctgtccaca
      421 gttacagccc agtttccagg ggcatgcggc ctgcgctacc ggaatcccgt gtctcagtgt
      481 atgagaggag tccgactggt ggaaggaatt ctgcatgccc cagatgctgg ctggggcaat
      541 ctggtatatg ttgtcaacta tcccaaagat aacaaaagga aaatggatga gacagatgct
      601 tcctctgcag tgaaagtgaa aagagcagtc cagaaaacat ctgacctcat agtgttgggt
      661 ctcccctgga aaacaactga gcaggatctg aaagactatt tcagtacttt tggagaggtt
      721 cttatggttc aggtcaagaa agatcttaaa actggtcact cgaaagggtt tggctttgtt
      781 cgatttacag aatatgaaac ccaagtgaaa gtaatgtcac aacgacatat gatagatggg
      841 cgatggtgtg actgtaaact tcccaactct aagcaaagcc cagacgagcc tttgagaagc
      901 agaaaggtgt ttgttggacg ttgtacagag gacatgactg ctgaagagct tcagcagttt
      961 ttctgtcagt atggagaagt ggtagatgtc ttcattccca aaccattcag agcttttgcc
     1021 ttcgtcacct ttgcagatga taaggttgcc cagtctcttt gtggagagga tttgatcatt
     1081 aaaggaatca gcgtgcatat atccaatgct gaacctaagc ataatagcaa tagacagtta
     1141 gaaagaagtg gaagatttgg tggtaatcca ggtggctttg ggaatcaggt tcatctcatt
     1201 tcaaatgttt atggaagaag cacttcattg aaagtagtgc tgtaaatatt ctgccatagg
     1261 aatacttctg tctacatgct ttctcatcca agaattcgtc atcacgctgc acaggctgcg
     1321 tctttgacgg tgggtgttcc atttttatcc gctactcttt atttcatgga gtcgtatcaa
     1381 cgctatgaac gcaaggctgt gatatggaac cagaaggctg tttgaacttt tgaaaccttg
     1441 tgtgggattg atggtggtgc cgaggcatga aaggctagta tgagcgagaa aaggagagcg
     1501 cgtgcagaga cttggtggtg gaaaatggat attttttaac ttggagagat gtgtcactca
     1561 atcctgtggc tttggtgaga gagtgtgcag agagcaatga tagcaaataa cgtacgaatg
     1621 ttttacatca aaggacatcc acatcagttg gaagactttg agttttgttc ttaggaaacc
     1681 cactttagtt gaatgtgtta agtgaaatac ttgtacttcc ctccccctct gtcaactgct
     1741 gtgaatgctg tatggtgtgt gttctcctct gttactgatc tggaagtgtg ggaacgtgaa
     1801 ctgaagctga tgggctgcga acatggactg agcttgtggt gtgctttgca ggagaacttg
     1861 gaagcagagt tcaccagtga gctcaggtgt ctcaaagaag ggtggaagtt ctcatgtctg
     1921 ttagctattc ataagaatgc tgtttgctgc agttctgtgt cctgtgcttg gatgcttttt
     1981 tataagagtt gtcattgttg gaaattctta aataaaactg atttaaataa tatgtgtctt
     2041 tgttttgcag ccctgaatgc aaagaattca tagcagttaa ttcccctttt tgaccctttt
     2101 gagatggaac tttcataaag tttcttggca gtagtttatt ttgcttcaaa taaacttatt
     2161 tgaaaagttg tctcaagtca aatggattca tcacctgtca tgcattgaca cctgataccc
     2221 agacttaatt gctatttgtt cttgcattgt ccaaagtgaa agtttttctt tggtttgttt
     2281 ttaatttagt ttttcttaag tctgggtgac cgcacctaaa atggtaagca gttaccctct
     2341 ggcttgttct gagtgcctct gtgcatttga ttttctattt acatgctgta taaatctcca
     2401 ctggggaatc atgccttcta aaaatatttg ggagagggca aaagagttga tttctaatgc
     2461 tttgtagcag agcatatcaa tgggaaagaa ggttaagcac ctttctgttt gggatttgaa
     2521 aagtggaatt aattgcaata gggatgaagt agaagaaacc aagaaaccat gtgcctgaaa
     2581 tacattaaga agcctgattg atagctttaa gaactagtag ggtgggttgt cttacctgtg
     2641 gcagtcttaa gtgaggtagg cttttgccct cctgaatgtg ggggttatgt agtgatgaat
     2701 atgctcacaa aatcagatta gactgtcaat gcattgttaa tgtaaaagca ataatacatt
     2761 gattattgta cttttcctgt aactactgag accggaggcg ctccttttct aactggaaga
     2821 atgggacagt ttttgtgttg gtagtttttc ctaatgccct tacctaaata gattatgata
     2881 aataggtttg tcattttgca agttgcgtgt tttaaaattt tatatccgtt agagacttgt
     2941 tatgaacaca ttgtttcatt atacagtatc ctctgtaaaa ggatcgtgag ttattgtaag
     3001 tttttttctc tgcatctaac cctgcatgat ttccaaaccc tgtgcatctg aattttgcat
     3061 tttagcactg tttgcactgt tactcagcag cagtaacatg gtaacattaa aatggttttc
     3121 ggggacctcc aaagacggcc aggagtcctg gggtaagtta cttgtcaatg gcatggtttt
     3181 gatccctttt ttacacttgt taaagactta ctggtcatag aagtctttca gtgttgatca
     3241 gccttttaac atgtttatgg atgacatagc tgtagttagt tacttgccgt aaatgaggtt
     3301 ttagaaataa actacttggc aaagatttgg ttttgaaagt ctggtcatca aaacgcgttc
     3361 attccttaga aataatgaag aacaactctt tgaaccacag ttgaataaaa ggttttcttg
     3421 ccaccaacag tttagtgtct ggagtcttac tggaagaaaa aaaaattcta tatcatgaca
     3481 atgctagaaa agttaaggtg acttatgtgg gaagatgcaa tatagcattt tcatccttta
     3541 aaatttgagt ctccaggtgg gtgtggtggc ccatgctttt aatcccagaa ttggtgtaaa
     3601 tgagttgtag gccagctatt tccccatctt gaggcaccct gtcttgcctt gttggaagag
     3661 ccagttaaaa tcaaacatga cctttaaggt cagcatctta gcagaagagc agtttatttc
     3721 aggataactt actgtttttg atacataagc aaatgactgt accttgtaca gttacggttg
     3781 acttccctga gcccaacgct cacctaagaa aagtgggctg ggtatagtga aacacctgtt
     3841 aaggtttttg gaatgatttg ctaaattgcc cttgtaaagg gtaaaatgct gtttcgtgtt
     3901 ctttttatct gacaatttgg tgaatctggt agaacatgcc tatatcccaa tattctggaa
     3961 tggacttggt gttaatttaa tagctgatct aatgtgaagg tcacacacct gctttccgct
     4021 taccttccaa aaggtattct ggaaccactc agaagttact cagaaagtaa gagcactttc
     4081 tgagctcatt aagaccaaat ctacacacta gacacaacaa gccctttgtt ggccagaaat
     4141 ggaaacagcc agtataaaat aagtagattg tagggaatca aatacaactt gttttttctg
     4201 tgttgggggt tggccaagca ctgttaaaca caaatcaaag ctgatattgg caagtgtttg
     4261 gacctgtaac aatctcacct gctctgattt tggggtaggc tgtcattctt aggtttgtta
     4321 ctaagcttcc caggtacttg gcgatatgag gaacaatgat tggacgatgc aaattagaaa
     4381 ttacttatta tgttctcaat ccagggaata tagttgatga cttttgtgta gaccccatac
     4441 tggtctgccg ccccacaatt aatggaaccc caggaaacta ttcctcccac aaaccatcgc
     4501 tgtgtctcat tatctagaaa cactaatgcc cccccactgt cacctctgca gctgtccttg
     4561 ccaccagtct ctaagccagc acagagcatg ttagcgctta ctcttactcc tggatagagc
     4621 ttttcataca cggcggtaca tttttggtgg tcagcaattg gtatgtccac aaacattagg
     4681 tttctagcaa gaagcccctt ctgggttaac ccccagccag ccacagttcc agtgaagtct
     4741 gttctcatta aggatgcagc ttcttttcgc ggtaggcaaa caggcatgat gcttccgttg
     4801 attgtgactt tgttcttgag tttaatcaat gctatatcat tgtcaaaacc agcaccgtga
     4861 gtgtagcctt catgtataaa gatttcctcg ggccaggctt gagtgtaatg aggtgagagc
     4921 cttttgagga tgcccattcg gatgttcagg gaggacgctg ccattctttt ctcatataca
     4981 gcatgagcgg ctgttaggac ccaattgtca tgtataagtg cacctgctgc tgctgtagtt
     5041 tgacccagca acaagacttg ccaaggaaag tcaccaggct ttgcaggctg ccctccaact
     5101 atgcgtcctc ctatagtgtg tgtggacagc ccacaaactg agggataaaa aacaagtatt
     5161 taatgcccta caaattgata ggcatcctcc ctgttgagtg aggctattta agtttttgtt
     5221 tagcctgctc acctccttgt aaagatcagt aagagatctc agagattgtt ttgctgaaag
     5281 agaacagcat gagggagtct ggacaggact tgtgtgcagg aggacatgac actacttaga
     5341 ggccaaagac aaccccctca ccacaccctg agctgcttgt ttttctcttt ttgggctctc
     5401 tgggaattct gggaaagcag gaactatgat ttacaaagtt tctgttgtct ttaaatgtaa
     5461 gactctaaat tacaatgttg cagcaatagc caaagtgctt ctggttcaaa aattggtaat
     5521 tttggtctgg tggagccctc caaacacttt taccgttctt tgcaaactga gggctcagga
     5581 atgcaacaca tgttctttat tgtggttgtg cactttgatt aaaacttgga agccgcatgt
     5641 cagccaaata caaggctaga aaactaattt aaaccagcta acacgggggt aatgagtgta
     5701 ttattacctt tcaattaaaa aaaaagcact ctcaactgtt gttggagcca attctggtaa
     5761 agaaatttaa gtactattaa aaggcaaatt gcattaatgt ttaaaaatct tgatgtcgtt
     5821 gaaaacaatt gcttagggaa ataatgaagt tattagcttt ggggtttaat agcattttta
     5881 cagagaagaa aagtaacaag agttcttggt tataaatgta taaacggttt gagataattt
     5941 aagaaatcat ttaatttttt atgcttgcct agttataagg tcaaaaacaa tcaagtgcat
     6001 gatgcaccta gcttccgtgt ggaaggggaa atgtgagcac actgttggga aacactaagc
     6061 tccagcctca gccaagtgct gagctttctg cctccccagc cagaccctgc ctattgtctg
     6121 ccagctactc tgtcagctat gaatctcttt tataaatggc gtccattacc aggctcacaa
     6181 accgggggga gtttttctcc tttggagctc gtccagaatc catcagcctc acacacatat
     6241 ttacctgcaa gtcattggaa aagcaaaaat gtttagctgt agttgtcatt tgcttgaata
     6301 accccttgaa aaatgttgat tcttgagcat ctgtggtggg gagaggtgtg tgaataacca
     6361 ttttacatga tttcataaat aggtgtctgc attaccatgt ttgcttgcaa agtggaaacc
     6421 ttttagatgt gtaacttgaa tatgtatcaa gatctcaagt gcttaatgat aaggttttga
     6481 cttgttaaat taaaccattt ggaatatatt gtg
//
