LOCUS       NM_001399105            2774 bp    mRNA    linear   ROD 01-JUL-2024
DEFINITION  Rattus norvegicus TAR DNA binding protein (Tardbp), transcript
            variant 1, mRNA.
ACCESSION   NM_001399105 XM_006239382
VERSION     NM_001399105.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2774)
  AUTHORS   Zhu,Y. and Sun,C.
  TITLE     Inactivation of cGAS signaling pathway mediated by TDP-43
            deficiency protects microglia from hypoxia/reoxygenation induced
            injury
  JOURNAL   Brain Res 1839, 148999 (2024)
   PUBMED   38761845
  REMARK    GeneRIF: Inactivation of cGAS signaling pathway mediated by TDP-43
            deficiency protects microglia from hypoxia/reoxygenation induced
            injury.
REFERENCE   2  (bases 1 to 2774)
  AUTHORS   Sun,R., Xi,K., Ji,S., Song,X., Xi,D., Yin,W., Shao,Y., Gu,W. and
            Jiang,J.
  TITLE     TDP-43 was Involved in Radiation-induced Neuronal Damage and May
            Not Through the BDNF/TrkB Pathway
  JOURNAL   Radiat Res 201 (3), 240-251 (2024)
   PUBMED   38235539
  REMARK    GeneRIF: TDP-43 was Involved in Radiation-induced Neuronal Damage
            and May Not Through the BDNF/TrkB Pathway.
REFERENCE   3  (bases 1 to 2774)
  AUTHORS   Ervilha Pereira,P., Schuermans,N., Meylemans,A., LeBlanc,P.,
            Versluys,L., Copley,K.E., Rubien,J.D., Altheimer,C., Peetermans,M.,
            Debackere,E., Vanakker,O., Janssens,S., Baets,J., Verhoeven,K.,
            Lammens,M., Symoens,S., De Paepe,B., Barmada,S.J., Shorter,J., De
            Bleecker,J.L., Bogaert,E. and Dermaut,B.
  TITLE     C-terminal frameshift variant of TDP-43 with pronounced
            aggregation-propensity causes rimmed vacuole myopathy but not
            ALS/FTD
  JOURNAL   Acta Neuropathol 145 (6), 793-814 (2023)
   PUBMED   37000196
  REMARK    GeneRIF: C-terminal frameshift variant of TDP-43 with pronounced
            aggregation-propensity causes rimmed vacuole myopathy but not
            ALS/FTD.
REFERENCE   4  (bases 1 to 2774)
  AUTHORS   Velebit,J., Horvat,A., Smolic,T., Prpar Mihevc,S., Rogelj,B.,
            Zorec,R. and Vardjan,N.
  TITLE     Astrocytes with TDP-43 inclusions exhibit reduced noradrenergic
            cAMP and Ca2+ signaling and dysregulated cell metabolism
  JOURNAL   Sci Rep 10 (1), 6003 (2020)
   PUBMED   32265469
  REMARK    GeneRIF: Astrocytes with TDP-43 inclusions exhibit reduced
            noradrenergic cAMP and Ca(2+) signaling and dysregulated cell
            metabolism.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2774)
  AUTHORS   LaRocca,T.J., Mariani,A., Watkins,L.R. and Link,C.D.
  TITLE     TDP-43 knockdown causes innate immune activation via protein kinase
            R in astrocytes
  JOURNAL   Neurobiol Dis 132, 104514 (2019)
   PUBMED   31229690
  REMARK    GeneRIF: Knockdown of TDP-43 in astrocytes results in accumulation
            of repetitive element transcripts and dsRNA and innate immune
            activation.
REFERENCE   6  (bases 1 to 2774)
  AUTHORS   Strong,M.J., Volkening,K., Hammond,R., Yang,W., Strong,W.,
            Leystra-Lantz,C. and Shoesmith,C.
  TITLE     TDP43 is a human low molecular weight neurofilament (hNFL)
            mRNA-binding protein
  JOURNAL   Mol Cell Neurosci 35 (2), 320-327 (2007)
   PUBMED   17481916
REFERENCE   7  (bases 1 to 2774)
  AUTHORS   Neumann,M., Sampathu,D.M., Kwong,L.K., Truax,A.C., Micsenyi,M.C.,
            Chou,T.T., Bruce,J., Schuck,T., Grossman,M., Clark,C.M.,
            McCluskey,L.F., Miller,B.L., Masliah,E., Mackenzie,I.R.,
            Feldman,H., Feiden,W., Kretzschmar,H.A., Trojanowski,J.Q. and
            Lee,V.M.
  TITLE     Ubiquitinated TDP-43 in frontotemporal lobar degeneration and
            amyotrophic lateral sclerosis
  JOURNAL   Science 314 (5796), 130-133 (2006)
   PUBMED   17023659
REFERENCE   8  (bases 1 to 2774)
  AUTHORS   Shultz,M.A., Zhang,L., Gu,Y.Z., Baker,G.L., Fannuchi,M.V.,
            Padua,A.M., Gurske,W.A., Morin,D., Penn,S.G., Jovanovich,S.B.,
            Plopper,C.G. and Buckpitt,A.R.
  TITLE     Gene expression analysis in response to lung toxicants: I.
            Sequencing and microarray development
  JOURNAL   Am J Respir Cell Mol Biol 30 (3), 296-310 (2004)
   PUBMED   12947022
REFERENCE   9  (bases 1 to 2774)
  AUTHORS   Buratti,E., Dork,T., Zuccato,E., Pagani,F., Romano,M. and
            Baralle,F.E.
  TITLE     Nuclear factor TDP-43 and SR proteins promote in vitro and in vivo
            CFTR exon 9 skipping
  JOURNAL   EMBO J 20 (7), 1774-1784 (2001)
   PUBMED   11285240
REFERENCE   10 (bases 1 to 2774)
  AUTHORS   Ou,S.H., Wu,F., Harrich,D., Garcia-Martinez,L.F. and Gaynor,R.B.
  TITLE     Cloning and characterization of a novel cellular protein, TDP-43,
            that binds to human immunodeficiency virus type 1 TAR DNA sequence
            motifs
  JOURNAL   J Virol 69 (6), 3584-3596 (1995)
   PUBMED   7745706
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000005.1.
            
            On Jan 4, 2022 this sequence version replaced XM_006239382.4.
            
            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 :: SRR22399481.246352.1,
                                           SRR26643429.21897.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN16676784, SAMN16676785
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-113               JAXUCZ010000005.1  164345092-164345204 c
            114-365             JAXUCZ010000005.1  164343678-164343929 c
            366-529             JAXUCZ010000005.1  164340274-164340437 c
            530-670             JAXUCZ010000005.1  164339055-164339195 c
            671-841             JAXUCZ010000005.1  164337403-164337573 c
            842-2774            JAXUCZ010000005.1  164335062-164336994 c
FEATURES             Location/Qualifiers
     source          1..2774
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="5"
                     /map="5q36"
     gene            1..2774
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /note="TAR DNA binding protein"
                     /db_xref="GeneID:298648"
                     /db_xref="RGD:1310906"
     exon            1..113
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
     exon            114..365
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
     CDS             128..1372
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /note="isoform 1 is encoded by transcript variant 1; TAR
                     DNA-binding protein 43"
                     /codon_start=1
                     /product="TAR DNA-binding protein 43 isoform 1"
                     /protein_id="NP_001386034.1"
                     /db_xref="GeneID:298648"
                     /db_xref="RGD:1310906"
                     /translation="MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYR
                     NPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDEADASSAVKVKRAVQK
                     TSDLIVLGLPWKTTEQDLKDYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK
                     VMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTAEELQQFFCQYGEVV
                     DVFIPKPFRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRF
                     GGNPGGFGNQGGFGNSRGGGAGLGNNQGGNMGGGMNFGAFSINPAMMAAAQAALQSSW
                     GMMGMLASQQNQSGPSGNNQSQGSMQREPNQAFGSGNNSYSGSNSGAPLGWGSASNAG
                     SGSGFNGGFGSSMDSKSSGWGM"
     exon            366..529
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
     exon            530..670
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
     exon            671..841
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
     exon            842..2774
                     /gene="Tardbp"
                     /gene_synonym="Tdp-43"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gggcgggagg cggccctagc gccattttgt gggcacgaag cggtagctcg gctgttgttg
       61 ggttcctttc cgtcttcgat ccttcgttgt gcttcctagc agcggcccag tggagattta
      121 agcaaagatg tctgaatata ttcgggtaac agaagatgag aatgatgagc ccattgaaat
      181 accatcagaa gacgatggga cagtgttgct gtccacagtt acagcccagt ttccaggggc
      241 gtgtggcctg cgctaccgga atccagtgtc tcagtgtatg agaggtgtcc gactggtgga
      301 aggaattctg catgccccag atgctggctg gggcaatctg gtctatgttg tcaactatcc
      361 caaagataac aaaaggaaaa tggatgaggc ggatgcttcc tctgcagtga aagtgaaaag
      421 agcagtccag aagacatctg acctcatagt gttgggtctc ccctggaaaa caacagagca
      481 ggacctaaaa gactacttca gtacttttgg agaggttctt atggttcagg tcaagaaaga
      541 tcttaaaact ggtcactcaa aagggtttgg ctttgttcga tttacggaat atgaaactca
      601 agtgaaagta atgtcacagc gacatatgat agatgggcga tggtgtgact gtaaacttcc
      661 aaattctaag caaagcccag acgagccttt gagaagcaga aaggtgtttg ttggacgttg
      721 tacagaggac atgactgctg aagagcttca gcagttcttc tgtcagtatg gagaagtggt
      781 agatgtcttc attcccaaac cattcagagc ttttgccttt gttacctttg cagatgataa
      841 ggttgcccag tctctttgtg gagaggactt gatcattaaa ggaatcagcg tgcatatatc
      901 caatgctgaa cctaagcata atagcaatag acagttagaa agaagtggaa gatttggtgg
      961 taatccaggt ggctttggga atcagggtgg gtttggtaac agtagagggg gtggagctgg
     1021 cttgggaaat aaccagggtg gtaatatggg tggagggatg aattttggtg cttttagcat
     1081 taatccagcg atgatggctg cagctcaggc agcgttacag agcagttggg gtatgatggg
     1141 catgttagcc agccagcaga accagtcagg cccatctggg aataaccaaa gccagggcag
     1201 catgcagagg gaaccaaatc aggcttttgg ttctggaaat aactcttaca gtggttctaa
     1261 ttctggtgcc ccccttggtt gggggtcagc atcaaatgca ggatcaggca gtggttttaa
     1321 tggaggcttt ggctcaagca tggattctaa atcctctggc tggggaatgt aggtgggtgg
     1381 gggtggttag taggttggtt ggtaggttag gtaggtttag aatggtggga ttcaaatttt
     1441 tctaaactca tggtaagtat attgtaaaat acatatgtac taaaattttc agattggttt
     1501 gttcagtgtg gagtatattc agcagtattt ttgacatttt tctttagaaa aaagagggaa
     1561 aaactaaatg aattttataa gttttgttat ataaagggtt aaaatactga gtgggtgaaa
     1621 gtgaactgct gtttgcctaa ttggtaaacc aacactacaa ttgatctcag aaggtttctc
     1681 tgtaatattc tatcattgga attgttaatg aattctttgc atgttcagag tagaaaccat
     1741 tggttagaac tacattcttt tctccttatt ttaatttgaa tcccacccta tgaatttctt
     1801 ccttaggaaa atctccattt gggagatcat gatgtcatgg tgtttggttc ttttggtttt
     1861 gtttttaaca cttgtcttcc ttcatatacg aaagtacaat atgaagcctt catttaatct
     1921 ctgcagttca tctcatttca aatgtttatg gaagaagcac ttcattgaaa gtagtgctgt
     1981 aaatattctg ccataggaat acttctgtct acatgctttc tcatccaaga attcgtcatc
     2041 acgctgcaca ggctgcgtct ttgacggtgg gtgttccatt tttatccgct actctttatt
     2101 tcatggaatc gtatcaacgc tatgaacgca aggctgtgat atggaaccag aaggctgttt
     2161 gaacttttga aaccttgtgt gggattgatg gtggtgccga ggcatgaaag gctagtatga
     2221 gcgagaaaag gagagagcgc gtgcagagac ttggtggtgg aaaatggata ttttttaact
     2281 tggagagatg tgtccctcaa tcctgtggct ttggtgcgag agtgtgcaga gagcaatgat
     2341 agcagataac taacgtacga gtgtttctgc atcagaggac atccacgtct gttggaagac
     2401 tttgagtttt gttcttagga aacccacagt agctgaatgt gttaagtgaa atacttgtac
     2461 ttccctcccc tctgtcaact gctgtgaatg ctgtatggtg tgtgttctcc tctgttactg
     2521 atctggaagt gtgggaacgt gaactgaagc tgatgggctg cgaacatgga ctgagcttgt
     2581 ggtgtgcttt gcaggagaac ttggaagcag agttcaccag tgagctcagg tgtctcaaag
     2641 aagggtggaa gttctcatgt ctgttagcta ttcataagaa tgctgtttgc tgcagttctg
     2701 tgtcctgtgc ttggatgctt tttataagag ttgtcattgt tggaaattct taaataaaac
     2761 tgatttaaat aata
//
