LOCUS       NM_001108710            2442 bp    mRNA    linear   ROD 23-MAR-2023
DEFINITION  Rattus norvegicus cochlin (Coch), mRNA.
ACCESSION   NM_001108710 XM_001078654 XM_017594222 XM_343058
VERSION     NM_001108710.2
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 2442)
  AUTHORS   Py BF, Gonzalez SF, Long K, Kim MS, Kim YA, Zhu H, Yao J, Degauque
            N, Villet R, Ymele-Leki P, Gadjeva M, Pier GB, Carroll MC and Yuan
            J.
  TITLE     Cochlin produced by follicular dendritic cells promotes
            antibacterial innate immunity
  JOURNAL   Immunity 38 (5), 1063-1072 (2013)
   PUBMED   23684986
REFERENCE   2  (bases 1 to 2442)
  AUTHORS   Shiiba K, Shindo S, Ikezono T, Sekine K, Matsumura T, Sekiguchi S,
            Yagi T and Okubo K.
  TITLE     Cochlin expression in the rat perilymph during postnatal
            development
  JOURNAL   Acta Otolaryngol 132 (11), 1134-1139 (2012)
   PUBMED   23020749
  REMARK    GeneRIF: expression in perilymph detected from 3rd day after birth
            (DAB3), gradually increased to DAB15, then gradually decreased to
            DAB70
REFERENCE   3  (bases 1 to 2442)
  AUTHORS   Cho HJ, Park HJ, Trexler M, Venselaar H, Lee KY, Robertson NG, Baek
            JI, Kang BS, Morton CC, Vriend G, Patthy L and Kim UK.
  TITLE     A novel COCH mutation associated with autosomal dominant
            nonsyndromic hearing loss disrupts the structural stability of the
            vWFA2 domain
  JOURNAL   J Mol Med (Berl) 90 (11), 1321-1331 (2012)
   PUBMED   22610276
REFERENCE   4  (bases 1 to 2442)
  AUTHORS   Jones SM, Robertson NG, Given S, Giersch AB, Liberman MC and Morton
            CC.
  TITLE     Hearing and vestibular deficits in the Coch(-/-) null mouse model:
            comparison to the Coch(G88E/G88E) mouse and to DFNA9 hearing and
            balance disorder
  JOURNAL   Hear Res 272 (1-2), 42-48 (2011)
   PUBMED   21073934
REFERENCE   5  (bases 1 to 2442)
  AUTHORS   Goel M, Sienkiewicz AE, Picciani R, Lee RK and Bhattacharya SK.
  TITLE     Cochlin induced TREK-1 co-expression and annexin A2 secretion: role
            in trabecular meshwork cell elongation and motility
  JOURNAL   PLoS One 6 (8), e23070 (2011)
   PUBMED   21886777
REFERENCE   6  (bases 1 to 2442)
  AUTHORS   Shindo S, Ikezono T, Ishizaki M, Sekiguchi S, Mizuta K, Li L,
            Takumida M, Pawankar R and Yagi T.
  TITLE     Spatiotemporal expression of cochlin in the inner ear of rats
            during postnatal development
  JOURNAL   Neurosci Lett 444 (2), 148-152 (2008)
   PUBMED   18706483
  REMARK    GeneRIF: The expression of cochlin may be related to the maturation
            of inner ear function.
REFERENCE   7  (bases 1 to 2442)
  AUTHORS   Mizuta K, Ikezono T, Iwasaki S, Arai M, Hashimoto Y, Pawankar R,
            Watanabe T, Shindo S and Mineta H.
  TITLE     Ultrastructural co-localization of cochlin and type II collagen in
            the rat semicircular canal
  JOURNAL   Neurosci Lett 434 (1), 104-107 (2008)
   PUBMED   18304733
  REMARK    GeneRIF: Cochlin may play a role in the structural homeostasis of
            the vestibule acting in concert with the fibrillar type II collagen
            bundles.
REFERENCE   8  (bases 1 to 2442)
  AUTHORS   Robertson NG, Resendes BL, Lin JS, Lee C, Aster JC, Adams JC and
            Morton CC.
  TITLE     Inner ear localization of mRNA and protein products of COCH,
            mutated in the sensorineural deafness and vestibular disorder,
            DFNA9
  JOURNAL   Hum Mol Genet 10 (22), 2493-2500 (2001)
   PUBMED   11709536
REFERENCE   9  (bases 1 to 2442)
  AUTHORS   Robertson NG, Lu L, Heller S, Merchant SN, Eavey RD, McKenna M,
            Nadol JB Jr, Miyamoto RT, Linthicum FH Jr, Lubianca Neto JF,
            Hudspeth AJ, Seidman CE, Morton CC and Seidman JG.
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC160874.1.
            
            On or before Sep 4, 2019 this sequence version replaced
            XM_017594222.1, NM_001108710.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC160874.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760393, SAMEA5760433
                                           [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
            1-2442              BC160874.1         1-2442
FEATURES             Location/Qualifiers
     source          1..2442
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10116"
                     /chromosome="6"
                     /map="6q23"
     gene            1..2442
                     /gene="Coch"
                     /note="cochlin"
                     /db_xref="GeneID:362735"
                     /db_xref="RGD:1308536"
     exon            1..20
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            21..73
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     CDS             40..1698
                     /gene="Coch"
                     /note="coagulation factor C homolog (Limulus polyphemus);
                     coagulation factor C homolog, cochlin (Limulus
                     polyphemus)"
                     /codon_start=1
                     /product="cochlin precursor"
                     /protein_id="NP_001102180.2"
                     /db_xref="GeneID:362735"
                     /db_xref="RGD:1308536"
                     /translation="MPSSWSPALCLGAWLLLLLLPRLARAEGAVPIPITCFTRGLDIR
                     KEKADVLCPGGCSLEEFSVFGNIVYASVSSICGAAVHRGVIGTSGGPVRVYSLPGREN
                     YSSVAANGIQSQTLSRWSASFAVTKGKSSTQEATGRAVSTANPPSGKRLKKTPEKKTG
                     NKDCKADIAFLIDGSFNIGQRRFNLQKNFVGKVALMLGVGTEGPHVGLVQASEHPKIE
                     FYLKNFTSAKDVLFAIKEVGFRGGNSNTGKALKHTAQKFFTADTGVRKGIPKVVVVFI
                     DGWPSDDIEEAGIVAREFGVNVFIVSVAKPIPEELGMVQDVAFVDKAVCRNNGFFSYH
                     MPNWFGTTKYVKPLVQKLCTHEQMMCSKTCYNSVNIAFLIDGSSSVGDSNFRLMLEFV
                     SNIAKTFEISDIGAKIAAVQFTYDQRTEFSFTDYNTKENVLAVLANIRYMSGGTATGD
                     AISFTVRNVFGPIRDSPNKNFLVIVTDGQSYDDVRGPAAAAHDAGITIFSVGVAWAPL
                     DDLKDMASKPKESHAFFTREFTGLEPIVSDVIRGICRDFLESQQ"
     exon            74..127
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            128..284
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            285..418
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            419..481
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            482..526
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            527..674
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            675..778
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            779..1005
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            1006..1522
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
     exon            1523..2419
                     /gene="Coch"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gccgggcgga tcccacgcag gtccacgcag acccccgcca tgccctcgtc ctggagccct
       61 gctctctgcc tcggtgcgtg gctgctgctg ctgctgctgc ctcggctcgc gcgcgcggag
      121 ggagccgtgc ccatccccat cacctgcttt accagaggcc tggatatccg gaaagaaaaa
      181 gcggatgttc tctgcccagg aggctgctct ctggaggaat tttctgtgtt tgggaacata
      241 gtgtatgcct cggtgtccag catctgcggg gctgctgtcc acaggggagt gattggcacc
      301 tcagggggcc cagtgcgtgt ctatagcctt cctggtagag agaactattc ctcggtggct
      361 gccaatggca ttcagtctca gaccctttcc agatggtctg cttccttcgc tgtgaccaaa
      421 ggcaaaagca gtacccagga agccacggga cgggcagtgt ccacagccaa tccgccctca
      481 ggtaaaagac tgaagaaaac accggagaag aagactggca ataaagactg caaggcagac
      541 attgcatttc tcatcgatgg aagctttaat atagggcagc gccgatttaa tttgcagaag
      601 aattttgttg ggaaggtggc actaatgttg ggagttggaa ccgaaggacc acacgtgggc
      661 ctcgttcaag ccagtgaaca ccccaaaata gaattttact tgaaaaactt tacttcggcc
      721 aaagatgtct tgtttgccat aaaagaagta ggtttccgag ggggtaactc caacacagga
      781 aaagctttga agcacactgc tcagaaattc tttacagcag acactggtgt gagaaaagga
      841 ataccaaaag tggtggtggt gtttattgat ggttggcctt ctgatgacat tgaggaagca
      901 ggcattgtgg ccagagagtt tggtgtcaat gtatttatag tttccgtggc caagcccatc
      961 cctgaagaac tggggatggt tcaagatgtt gcatttgttg acaaggctgt gtgcaggaat
     1021 aatggcttct tctcttatca catgcccaac tggtttggca ctacaaaata tgtaaagcct
     1081 ctggtgcaga agctctgtac tcatgaacag atgatgtgca gcaaaacctg ttacaactca
     1141 gtcaatattg cctttctgat tgatggctcc agcagcgttg gagatagcaa tttccgcctc
     1201 atgcttgaat ttgtttctaa catagcgaag acatttgaaa tctcagacat tggagccaag
     1261 atagcagctg tacagttcac ttatgatcag cgcacagaat tcagtttcac tgactataac
     1321 accaaagaga acgtcctagc tgtcctagcg aatatacgct acatgagtgg tgggacagct
     1381 acgggtgatg ccatttcctt tactgttaga aatgtatttg gtcccataag ggacagcccc
     1441 aacaaaaact tcctggttat tgtcacagat ggacagtcct acgatgatgt ccgaggtcca
     1501 gctgcagctg cccatgatgc aggtatcacc atcttctctg ttggtgtggc ttgggcacct
     1561 ctggatgacc tgaaagacat ggcctctaaa cccaaagagt cccacgcctt ctttaccaga
     1621 gagtttacag gattggaacc gattgtctct gatgtcatta gaggcatctg tagagatttc
     1681 ttagaatccc agcaataacc gatactctga caacgcaagg aatacgtaca agggatctaa
     1741 tgttcaaatt gtgttctcaa tgcctatata acttttagct taccagtgtc aaaaagtatg
     1801 tcaacagctg tttaaaggaa atgtacattc atttgaagct cacaatttag attggcttga
     1861 taatcaggtc cttagaaact caggaaagag gagatgtcat ggcttaaagt tgggaggtca
     1921 aatatgcata caagtgcata ggtaagctac ttagcttaat aaaagaacct gacgcttaga
     1981 cacaacgcac tgttccttct ttaatcactc tgcattgacc atgcaaggaa acaagacagc
     2041 ttttaaacac agatcaagtc taagtatttt gccccacgtt gatgttttct taaaatcagc
     2101 caaggacagc tgttattctg tgtactagtc ataactacac attttatata ctcatgtatc
     2161 tagcttcttt tgtagtgttt tcataactta atggctgaaa tattacattg agtaaatgta
     2221 ggattgcggt atttttctat ttatatcctt aactttatgt gtacagacag gcatatactc
     2281 caaggactaa gaaaatgttt aagcaggtaa cgtttctttt ttttttttgg aaaaaaaaat
     2341 gtttcaagta ttgtaacagg aaaaatactt ggtataatag cttggctatg tcagcaataa
     2401 aatgactagt gactgagtaa aaaaaaaaaa aaaaaaaaaa aa
//
