LOCUS       NM_001409459            2463 bp    mRNA    linear   ROD 28-AUG-2024
DEFINITION  Mus musculus cochlin (Coch), transcript variant 3, mRNA.
ACCESSION   NM_001409459 XM_017314943
VERSION     NM_001409459.1
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 2463)
  AUTHORS   Yoo,D., Park,J., Lee,C., Song,I., Lee,Y.H., Yun,T., Lee,H.,
            Heguy,A., Han,J.Y., Dasen,J.S., Kim,H. and Baek,M.
  TITLE     Little skate genome provides insights into genetic programs
            essential for limb-based locomotion
  JOURNAL   Elife 11, e78345 (2022)
   PUBMED   36288084
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2463)
  AUTHORS   Jing,W., Zhang,T., Liu,J., Huang,X., Yu,Q., Yu,H., Zhang,Q., Li,H.,
            Deng,M., Zhu,L.Q., Du,H. and Lu,Y.
  TITLE     A circuit of COCH neurons encodes social-stress-induced anxiety via
            MTF1 activation of Cacna1h
  JOURNAL   Cell Rep 37 (13), 110177 (2021)
   PUBMED   34965426
REFERENCE   3  (bases 1 to 2463)
  AUTHORS   Bae,S.H., Yoo,J.E., Hong,J.W., Park,H.R., Noh,B., Kim,H., Kang,M.,
            Hyun,Y.M., Gee,H.Y., Choi,J.Y. and Jung,J.
  TITLE     LCCL peptide cleavage after noise exposure exacerbates hearing loss
            and is associated with the monocyte infiltration in the cochlea
  JOURNAL   Hear Res 412, 108378 (2021)
   PUBMED   34735822
REFERENCE   4  (bases 1 to 2463)
  AUTHORS   Verdoodt,D., Peeleman,N., Szewczyk,K., Van Camp,G., Ponsaerts,P.
            and Van Rompaey,V.
  TITLE     Cochlin Deficiency Protects Aged Mice from Noise-Induced Hearing
            Loss
  JOURNAL   Int J Mol Sci 22 (21), 11549 (2021)
   PUBMED   34768980
  REMARK    GeneRIF: Cochlin Deficiency Protects Aged Mice from Noise-Induced
            Hearing Loss.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2463)
  AUTHORS   Verdoodt,D., Eens,S., Van Dam,D., De Deyn,P.P., Vanderveken,O.M.,
            Szewczyk,K., Saldien,V., Ponsaerts,P. and Van Rompaey,V.
  TITLE     Effect of Oral Allylnitrile Administration on Cochlear Functioning
            in Mice Following Comparison of Different Anesthetics for Hearing
            Assessment
  JOURNAL   Front Toxicol 3, 641569 (2021)
   PUBMED   35295154
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2463)
  AUTHORS   Ikezono,T., Omori,A., Ichinose,S., Pawankar,R., Watanabe,A. and
            Yagi,T.
  TITLE     Identification of the protein product of the Coch gene (hereditary
            deafness gene) as the major component of bovine inner ear protein
  JOURNAL   Biochim Biophys Acta 1535 (3), 258-265 (2001)
   PUBMED   11278165
REFERENCE   7  (bases 1 to 2463)
  AUTHORS   de Kok,Y.J., Bom,S.J., Brunt,T.M., Kemperman,M.H., van Beusekom,E.,
            van der Velde-Visser,S.D., Robertson,N.G., Morton,C.C.,
            Huygen,P.L., Verhagen,W.I., Brunner,H.G., Cremers,C.W. and
            Cremers,F.P.
  TITLE     A Pro51Ser mutation in the COCH gene is associated with late onset
            autosomal dominant progressive sensorineural hearing loss with
            vestibular defects
  JOURNAL   Hum Mol Genet 8 (2), 361-366 (1999)
   PUBMED   9931344
REFERENCE   8  (bases 1 to 2463)
  AUTHORS   Robertson,N.G., Lu,L., Heller,S., Merchant,S.N., Eavey,R.D.,
            McKenna,M., Nadol,J.B. Jr., Miyamoto,R.T., Linthicum,F.H. Jr.,
            Lubianca Neto,J.F., Hudspeth,A.J., Seidman,C.E., Morton,C.C. and
            Seidman,J.G.
  TITLE     Mutations in a novel cochlear gene cause DFNA9, a human
            nonsyndromic deafness with vestibular dysfunction
  JOURNAL   Nat Genet 20 (3), 299-303 (1998)
   PUBMED   9806553
REFERENCE   9  (bases 1 to 2463)
  AUTHORS   Robertson,N.G., Skvorak,A.B., Yin,Y., Weremowicz,S., Johnson,K.R.,
            Kovatch,K.A., Battey,J.F., Bieber,F.R. and Morton,C.C.
  TITLE     Mapping and characterization of a novel cochlear gene in human and
            in mouse: a positional candidate gene for a deafness disorder,
            DFNA9
  JOURNAL   Genomics 46 (3), 345-354 (1997)
   PUBMED   9441737
REFERENCE   10 (bases 1 to 2463)
  AUTHORS   Crozet,F., el Amraoui,A., Blanchard,S., Lenoir,M., Ripoll,C.,
            Vago,P., Hamel,C., Fizames,C., Levi-Acobas,F., Depetris,D.,
            Mattei,M.G., Weil,D., Pujol,R. and Petit,C.
  TITLE     Cloning of the genes encoding two murine and human cochlear
            unconventional type I myosins
  JOURNAL   Genomics 40 (2), 332-341 (1997)
   PUBMED   9119401
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC158404.2.
            
            On Jul 18, 2022 this sequence version replaced XM_017314943.3.
            
            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 :: ERR3363658.4789304.1,
                                           SRR7345562.3796416.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849388, SAMN01164131
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-33                AC158404.2         121294-121326
            34-86               AC158404.2         121526-121578
            87-149              AC158404.2         121659-121721
            150-306             AC158404.2         123256-123412
            307-440             AC158404.2         124365-124498
            441-503             AC158404.2         124936-124998
            504-548             AC158404.2         125949-125993
            549-696             AC158404.2         126073-126220
            697-800             AC158404.2         129735-129838
            801-1027            AC158404.2         130568-130794
            1028-1544           AC158404.2         131117-131633
            1545-2463           AC158404.2         132778-133696
FEATURES             Location/Qualifiers
     source          1..2463
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="12"
                     /map="12 22.11 cM"
     gene            1..2463
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /note="cochlin"
                     /db_xref="GeneID:12810"
                     /db_xref="MGI:MGI:1278313"
     exon            1..33
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            34..86
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     CDS             53..1720
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 3; coagulation factor C homolog (Limulus
                     polyphemus)"
                     /codon_start=1
                     /product="cochlin isoform 1 precursor"
                     /protein_id="NP_001396388.1"
                     /db_xref="GeneID:12810"
                     /db_xref="MGI:MGI:1278313"
                     /translation="MPSSRIPALCLGAWLLLLLLPRFARAEGAGELVPIPVTCFTRGL
                     DIRKEKADVLCPGGCSLEEFSVFGNIVYASVSSICGAAVHRGVIGTSGGPVRVYSLPG
                     RENYSSVDANGIQSQMLSRWSASFAVTKGKSSTQEATGRAVSTAHPPSGKRLKKTPEK
                     KTGNKDCKADIAFLIDGSFNIGQRRFNLQKNFVGKVALMLGIGTEGPHVGLVQASEHP
                     KIEFYLKNFTSAKDVLFAIKEVGFRGGNSNTGKALKHTAQKFFTADTGVRKGIPKVVV
                     VFIDGWPSDDIEEAGIVAREFGVNVFIVSVAKPIPEELGMVQDVAFVDKAVCRNNGFF
                     SYHMPNWFGTTKYVKPLVQKLCTHEQMMCSKTCYNSVNIAFLIDGSSSVGDSNFRLML
                     EFVSNIAKTFEISDIGAKIAAVQFTYDQRTEFSFTDYNTKENVLAVLANIRYMSGGTA
                     TGDAIAFTVRNVFGPIRDSPNKNFLVIVTDGQSYDDVRGPAAAAHDAGITIFSVGVAW
                     APLDDLRDMASKPKESHAFFTREFTGLEPIVSDVIRGICRDFLESQQ"
     exon            87..149
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            150..306
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            307..440
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            441..503
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            504..548
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            549..696
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            697..800
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            801..1027
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            1028..1544
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     exon            1545..2463
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1988..1993
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /note="hexamer: AATAAA"
     polyA_site      2016
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /note="major polyA site"
     regulatory      2428..2433
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
                     /note="hexamer: AATAAA"
     polyA_site      2463
                     /gene="Coch"
                     /gene_synonym="Coch-5B2; D12H14S564E"
ORIGIN      
        1 gcactcgggt gtagccgggc ggatcccacg caggtccacg gagatcctcg ccatgccctc
       61 gtccaggatc cctgctctct gcctcggtgc gtggctgctg ctgctgctgc tgccccggtt
      121 cgcgcgcgcc gagggagcgg gtgagttagt tcccattcct gtcacctgct ttaccagagg
      181 cctggatatc cgaaaagaga aagcagatgt tctctgccca ggaggctgct ctcttgagga
      241 attctctgtg tttgggaaca tagtgtatgc gtcagtgtcc agcatctgcg gcgctgctgt
      301 ccatagggga gtgattggca cctcaggggg acctgtgcgt gtctacagcc ttcctggtcg
      361 agagaactac tcctcggtag atgccaacgg catccagtct cagatgcttt cccgatggtc
      421 cgcgtccttc gctgtgacca aaggcaaaag cagtacccag gaagccacag gacgggcagt
      481 gtccacagcc cacccacctt caggtaaaag actaaagaag acaccagaga agaagactgg
      541 caacaaagac tgtaaggcag acattgcatt tctcattgat ggaagcttca atattgggca
      601 gcgccgattt aatttgcaga agaattttgt tgggaaagtg gcactaatgt tgggaattgg
      661 aacagaagga ccacacgtgg gtctcgttca agccagtgaa caccccaaaa tagaatttta
      721 cttgaaaaac tttacttcag ccaaagatgt cttgtttgcc ataaaagaag taggtttccg
      781 agggggtaac tccaacacag gaaaagcctt gaagcacact gctcagaaat tctttacagc
      841 agacactggt gtgagaaaag gaataccaaa agtggtggta gtgtttattg atggttggcc
      901 ctctgatgac attgaggaag caggcattgt ggccagagag tttggtgtca atgtatttat
      961 agtttctgtg gccaagccca ttcctgaaga actggggatg gttcaagatg ttgcatttgt
     1021 tgacaaggct gtgtgtcgga ataatggctt cttctcttat cacatgccca actggtttgg
     1081 cactacaaaa tatgtgaagc ctctggtgca gaagctctgt acgcacgaac agatgatgtg
     1141 cagcaaaacc tgctacaact cagtgaacat tgcctttctg attgacggct ccagcagtgt
     1201 tggagatagc aatttccgcc tcatgctaga atttgtttct aacatagcga agacatttga
     1261 aatctcagac attggagcca agatagctgc tgtacagttc acttatgacc agcgcaccga
     1321 gttcagtttc actgactata ataccaaaga gaacgtccta gctgtcctag cgaacatccg
     1381 ctacatgagt ggtggcacag ctactggtga tgccatcgcc tttactgtta gaaatgtatt
     1441 tggtcccata agggacagcc ccaacaaaaa cttcctggtt attgtcacag atgggcagtc
     1501 ctatgatgat gtccgaggcc ctgctgcagc tgcccatgat gcaggtatca ccatcttctc
     1561 tgttggtgtg gcttgggcac cgctggatga cctgagagat atggcctcta aacccaaaga
     1621 gtcacacgct ttctttacca gagagttcac agggttagaa ccaattgtct ctgacgtcat
     1681 cagaggcatt tgtagagact tcttagaatc ccagcaataa ccgatactct gacaactcaa
     1741 ggaatacgtg caaggggatc taatgtgcaa attatattct caatgcctat gtaactttat
     1801 agcttaccag tgtcaaaaaa tgcgtccaca gctgtttaaa gcaaatgaat attcatgtga
     1861 tgctcacaat ttagattggc cgagacttga taatcaggcc cttagaaact caggaaagaa
     1921 gagttgtcat ggattaacat tgggagttca aatatgcatt caagtggata ggtaagctac
     1981 acagctcaat aaaagaacct ggcgcttaca cacaaagcac tgttccctct ttaatcactc
     2041 tgcattgacc atgcaaggaa aacagaacag cttttaaaca cagatcaagt atacatattt
     2101 tgacccatgt ggatgttttc ttaaaaccag ccaagaacag acagctgtta ttatgtgcac
     2161 tagccataac tacacattat atggaatcat atatcaagct tcttttgtag tgtgttttca
     2221 taacttgatg gctgaaatac cacactgagt aaaggtagga ttgcctggta tttttctatt
     2281 tatatcctta attttatgtg tatagacagg catgtactcc gaggactaag aaaatgttta
     2341 agcagataac tttttttttt ttgaaaaaaa agatgtgtca agtattgtaa ccgaaaaaat
     2401 acacagctta atagcttggc tgtcagcaat aaaactgcta gtgactaagt gcctatttat
     2461 taa
//
