LOCUS       NM_004086               2536 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens cochlin (COCH), transcript variant 2, mRNA.
ACCESSION   NM_004086
VERSION     NM_004086.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2536)
  AUTHORS   Moyaert,J., Gilles,A., Mertens,G., Lammers,M.J.W., Gommeren,H.,
            Janssens de Varebeke,S., Fransen,E., Verhaert,N., Denys,S., van de
            Berg,R., Pennings,R., Vanderveken,O. and Van Rompaey,V.
  TITLE     Interaural and sex differences in the natural evolution of hearing
            levels in pre-symptomatic and symptomatic carriers of the
            p.Pro51Ser variant in the COCH gene
  JOURNAL   Sci Rep 14 (1), 184 (2024)
   PUBMED   38167558
  REMARK    GeneRIF: Interaural and sex differences in the natural evolution of
            hearing levels in pre-symptomatic and symptomatic carriers of the
            p.Pro51Ser variant in the COCH gene.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2536)
  AUTHORS   Gommeren,H., Moyaert,J., Bosmans,J., Mertens,G., Cras,P.,
            Engelborghs,S., Van Ombergen,A., Gilles,A., Van Dam,D. and Van
            Rompaey,V.
  TITLE     Evaluation of hearing levels and vestibular function and the impact
            on cognitive performance in (pre)-symptomatic patients with DFNA9:
            protocol for a prospective longitudinal study (Rosetta study)
  JOURNAL   BMJ Open 13 (9), e075179 (2023)
   PUBMED   37709329
  REMARK    GeneRIF: Evaluation of hearing levels and vestibular function and
            the impact on cognitive performance in (pre)-symptomatic patients
            with DFNA9: protocol for a prospective longitudinal study (Rosetta
            study).
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2536)
  AUTHORS   Lin,Y., Dai,H., Yu,G., Song,C., Liu,J. and Xu,J.
  TITLE     Inhibiting KCNMA1-AS1 promotes osteogenic differentiation of HBMSCs
            via miR-1303/cochlin axis
  JOURNAL   J Orthop Surg Res 18 (1), 73 (2023)
   PUBMED   36717952
  REMARK    GeneRIF: Inhibiting KCNMA1-AS1 promotes osteogenic differentiation
            of HBMSCs via miR-1303/cochlin axis.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2536)
  AUTHORS   Salah,M., Moyaert,J., Vanderveken,O., Schepers,S., Termote,B., Van
            Rompaey,V. and Janssens de Varebeke,S.
  TITLE     Does Vestibulo-Ocular Reflex (VOR) Gain Correlate With Radiological
            Findings in the Semi-Circular Canals in Patients Carrying the
            p.Pro51Ser (P51S) COCH Variant Causing DFNA9? Relationship Between
            the Three-Dimensional Video Head Impulse Test (vHIT) and MR/CT
            Imaging
  JOURNAL   Otol Neurotol 43 (3), e348-e354 (2022)
   PUBMED   35020687
  REMARK    GeneRIF: Does Vestibulo-Ocular Reflex (VOR) Gain Correlate With
            Radiological Findings in the Semi-Circular Canals in Patients
            Carrying the p.Pro51Ser (P51S) COCH Variant Causing DFNA9?
            Relationship Between the Three-Dimensional Video Head Impulse Test
            (vHIT) and MR/CT Imaging.
REFERENCE   5  (bases 1 to 2536)
  AUTHORS   Robijn,S.M.M., Smits,J.J., Sezer,K., Huygen,P.L.M., Beynon,A.J.,
            van Wijk,E., Kremer,H., de Vrieze,E., Lanting,C.P. and
            Pennings,R.J.E.
  TITLE     Genotype-Phenotype Correlations of Pathogenic COCH Variants in
            DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis
  JOURNAL   Biomolecules 12 (2), 220 (2022)
   PUBMED   35204720
  REMARK    GeneRIF: Genotype-Phenotype Correlations of Pathogenic COCH
            Variants in DFNA9: A HuGE Systematic Review and Audiometric
            Meta-Analysis.
            Review article
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2536)
  AUTHORS   Manolis,E.N., Yandavi,N., Nadol,J.B. Jr., Eavey,R.D., McKenna,M.,
            Rosenbaum,S., Khetarpal,U., Halpin,C., Merchant,S.N., Duyk,G.M.,
            MacRae,C., Seidman,C.E. and Seidman,J.G.
  TITLE     A gene for non-syndromic autosomal dominant progressive postlingual
            sensorineural hearing loss maps to chromosome 14q12-13
  JOURNAL   Hum Mol Genet 5 (7), 1047-1050 (1996)
   PUBMED   8817345
REFERENCE   7  (bases 1 to 2536)
  AUTHORS   Robertson,N.G., Khetarpal,U., Gutierrez-Espeleta,G.A., Bieber,F.R.
            and Morton,C.C.
  TITLE     Isolation of novel and known genes from a human fetal cochlear cDNA
            library using subtractive hybridization and differential screening
  JOURNAL   Genomics 23 (1), 42-50 (1994)
   PUBMED   7829101
REFERENCE   8  (bases 1 to 2536)
  AUTHORS   Khetarpal,U.
  TITLE     Autosomal dominant sensorineural hearing loss. Further temporal
            bone findings
  JOURNAL   Arch Otolaryngol Head Neck Surg 119 (1), 106-108 (1993)
   PUBMED   8417734
REFERENCE   9  (bases 1 to 2536)
  AUTHORS   Shearer,A.E., Hildebrand,M.S., Schaefer,A.M. and Smith,R.J.H.
  TITLE     Genetic Hearing Loss Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH,
            Gripp KW and Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301607
REFERENCE   10 (bases 1 to 2536)
  AUTHORS   Khetarpal,U., Schuknecht,H.F., Gacek,R.R. and Holmes,L.B.
  TITLE     Autosomal dominant sensorineural hearing loss. Pedigrees,
            audiologic findings, and temporal bone findings in two kindreds
  JOURNAL   Arch Otolaryngol Head Neck Surg 117 (9), 1032-1042 (1991)
   PUBMED   1910721
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF006740.1 and AL049830.3.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_004086.2.
            
            Summary: The protein encoded by this gene is highly conserved in
            human, mouse, and chicken, showing 94% and 79% amino acid identity
            of human to mouse and chicken sequences, respectively.
            Hybridization to this gene was detected in spindle-shaped cells
            located along nerve fibers between the auditory ganglion and
            sensory epithelium. These cells accompany neurites at the habenula
            perforata, the opening through which neurites extend to innervate
            hair cells. This and the pattern of expression of this gene in
            chicken inner ear paralleled the histologic findings of acidophilic
            deposits, consistent with mucopolysaccharide ground substance, in
            temporal bones from DFNA9 (autosomal dominant nonsyndromic
            sensorineural deafness 9) patients. Mutations that cause DFNA9 have
            been reported in this gene. Alternative splicing results in
            multiple transcript variants encoding the same protein. Additional
            splice variants encoding distinct isoforms have been described but
            their biological validities have not been demonstrated. [provided
            by RefSeq, Oct 2008].
            
            Transcript Variant: This variant (2) differs in the 5' UTR and uses
            an alternate in-frame splice junction in the 5' end compared to
            variant 3. The resulting isoform (b) has the same N- and C-termini
            but is shorter compared to isoform a. Variants 1 and 2 encode the
            same isoform (b).
            
            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 :: AF006740.1, SRR1660805.187027.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000396618.9/ ENSP00000379862.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2534              AF006740.1         1-2534
            2535-2536           AL049830.3         78002-78003
FEATURES             Location/Qualifiers
     source          1..2536
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q12"
     gene            1..2536
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /note="cochlin"
                     /db_xref="GeneID:1690"
                     /db_xref="HGNC:HGNC:2180"
                     /db_xref="MIM:603196"
     exon            1..33
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            34..90
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     CDS             57..1709
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; coagulation factor C homolog, cochlin (Limulus
                     polyphemus)"
                     /codon_start=1
                     /product="cochlin isoform b precursor"
                     /protein_id="NP_004077.1"
                     /db_xref="CCDS:CCDS9640.1"
                     /db_xref="GeneID:1690"
                     /db_xref="HGNC:HGNC:2180"
                     /db_xref="MIM:603196"
                     /translation="MSAAWIPALGLGVCLLLLPGPAGSEGAAPIAITCFTRGLDIRKE
                     KADVLCPGGCPLEEFSVYGNIVYASVSSICGAAVHRGVISNSGGPVRVYSLPGRENYS
                     SVDANGIQSQMLSRWSASFTVTKGKSSTQEATGQAVSTAHPPTGKRLKKTPEKKTGNK
                     DCKADIAFLIDGSFNIGQRRFNLQKNFVGKVALMLGIGTEGPHVGLVQASEHPKIEFY
                     LKNFTSAKDVLFAIKEVGFRGGNSNTGKALKHTAQKFFTVDAGVRKGIPKVVVVFIDG
                     WPSDDIEEAGIVAREFGVNVFIVSVAKPIPEELGMVQDVTFVDKAVCRNNGFFSYHMP
                     NWFGTTKYVKPLVQKLCTHEQMMCSKTCYNSVNIAFLIDGSSSVGDSNFRLMLEFVSN
                     IAKTFEISDIGAKIAAVQFTYDQRTEFSFTDYSTKENVLAVIRNIRYMSGGTATGDAI
                     SFTVRNVFGPIRESPNKNFLVIVTDGQSYDDVQGPAAAAHDAGITIFSVGVAWAPLDD
                     LKDMASKPKESHAFFTREFTGLEPIVSDVIRGICRDFLESQQ"
     exon            91..138
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            139..295
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            296..429
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            430..492
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            493..537
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            538..685
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            686..789
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            790..1016
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            1017..1533
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     exon            1534..2536
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2029..2034
                     /regulatory_class="polyA_signal_sequence"
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /note="hexamer: AATAAA"
     polyA_site      2057
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /note="major polyA site"
     regulatory      2510..2515
                     /regulatory_class="polyA_signal_sequence"
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
                     /note="hexamer: AATAAA"
     polyA_site      2536
                     /gene="COCH"
                     /gene_synonym="COCH-5B2; COCH5B2; DFNA9; DFNB110"
ORIGIN      
        1 gcactcgggc gcagccgggt ggatctcgag caggtgtgag cagcctatca gtcaccatgt
       61 ccgcagcctg gatcccggct ctcggcctcg gtgtgtgtct gctgctgctg ccggggcccg
      121 cgggcagcga gggagccgct cccattgcta tcacatgttt taccagaggc ttggacatca
      181 ggaaagagaa agcagatgtc ctctgcccag ggggctgccc tcttgaggaa ttctctgtgt
      241 atgggaacat agtatatgct tctgtatcga gcatatgtgg ggctgctgtc cacaggggag
      301 taatcagcaa ctcaggggga cctgtacgag tctatagcct acctggtcga gaaaactatt
      361 cctcagtaga tgccaatggc atccagtctc aaatgctttc tagatggtct gcttctttca
      421 cagtaactaa aggcaaaagt agtacacagg aggccacagg acaagcagtg tccacagcac
      481 atccaccaac aggtaaacga ctaaagaaaa cacccgagaa gaaaactggc aataaagatt
      541 gtaaagcaga cattgcattt ctgattgatg gaagctttaa tattgggcag cgccgattta
      601 atttacagaa gaattttgtt ggaaaagtgg ctctaatgtt gggaattgga acagaaggac
      661 cacatgtggg ccttgttcaa gccagtgaac atcccaaaat agaattttac ttgaaaaact
      721 ttacatcagc caaagatgtt ttgtttgcca taaaggaagt aggtttcaga gggggtaatt
      781 ccaatacagg aaaagccttg aagcatactg ctcagaaatt cttcacggta gatgctggag
      841 taagaaaagg gatccccaaa gtggtggtgg tatttattga tggttggcct tctgatgaca
      901 tcgaggaagc aggcattgtg gccagagagt ttggtgtcaa tgtatttata gtttctgtgg
      961 ccaagcctat ccctgaagaa ctggggatgg ttcaggatgt cacatttgtt gacaaggctg
     1021 tctgtcggaa taatggcttc ttctcttacc acatgcccaa ctggtttggc accacaaaat
     1081 acgtaaagcc tctggtacag aagctgtgca ctcatgaaca aatgatgtgc agcaagacct
     1141 gttataactc agtgaacatt gcctttctaa ttgatggctc cagcagtgtt ggagatagca
     1201 atttccgcct catgcttgaa tttgtttcca acatagccaa gacttttgaa atctcggaca
     1261 ttggtgccaa gatagctgct gtacagttta cttatgatca gcgcacggag ttcagtttca
     1321 ctgactatag caccaaagag aatgtcctag ctgtcatcag aaacatccgc tatatgagtg
     1381 gtggaacagc tactggtgat gccatttcct tcactgttag aaatgtgttt ggccctataa
     1441 gggagagccc caacaagaac ttcctagtaa ttgtcacaga tgggcagtcc tatgatgatg
     1501 tccaaggccc tgcagctgct gcacatgatg caggaatcac tatcttctct gttggtgtgg
     1561 cttgggcacc tctggatgac ctgaaagata tggcttctaa accgaaggag tctcatgctt
     1621 tcttcacaag agagttcaca ggattagaac caattgtttc tgatgtcatc agaggcattt
     1681 gtagagattt cttagaatcc cagcaataat ggtaacattt tgacaactga aagaaaaagt
     1741 acaaggggat ccagtgtgta aattgtattc tcataatact gaaatgcttt agcatactag
     1801 aatcagatac aaaactatta agtatgtcaa cagccattta ggcaaataag cactccttta
     1861 aagccgctgc cttctggtta caatttacag tgtactttgt taaaaacact gctgaggctt
     1921 cataatcatg gctcttagaa actcaggaaa gaggagataa tgtggattaa aaccttaaga
     1981 gttctaacca tgcctactaa atgtacagat atgcaaattc catagctcaa taaaagaatc
     2041 tgatacttag accaaaagca acattcgttc tctaaccatt ctgtattgat tatataagca
     2101 aaatgaaaag agaaacttaa atgaacacag ctctttaaca tggttcaggt acacatattt
     2161 tgacccaagt ggatattttc ttaaaaccaa tcaataatag ctagctatta ctgcagacta
     2221 taaaatctgg atatagaaag gagacctgta tcaaactgct tttgtagtgt gttttcataa
     2281 caacttatga ctaaaaatat cacactgaat aagagagcag gattgccagg tatttttcta
     2341 tttctctcct taattttata tgtatataga tatatttggc ttatattcta agtcacctaa
     2401 gtacttaaaa gttaagttgg taaagtattt actgactgct tataaacatt taaagacaaa
     2461 gacatttcaa ataactgcag aaaaaatatt gtagtttgaa tatttaagca ataaaactgc
     2521 tagtgagtta ttgtaa
//
