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    COCH cochlin [ Homo sapiens (human) ]

    Gene ID: 1690, updated on 3-Apr-2024

    Summary

    Official Symbol
    COCHprovided by HGNC
    Official Full Name
    cochlinprovided by HGNC
    Primary source
    HGNC:HGNC:2180
    See related
    Ensembl:ENSG00000100473 MIM:603196; AllianceGenome:HGNC:2180
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DFNA9; COCH5B2; DFNB110; COCH-5B2
    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]
    Expression
    Biased expression in pancreas (RPKM 45.5), prostate (RPKM 16.0) and 1 other tissue See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COCH in Genome Data Viewer
    Location:
    14q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (30874559..30895615)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (25072046..25093101)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31343765..31359824)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ribosomal protein L12 pseudogene 5 Neighboring gene ribosomal protein L27 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5649 Neighboring gene uncharacterized LOC100506071 Neighboring gene striatin 3 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 17 Neighboring gene microRNA 624

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    cochlin
    Names
    coagulation factor C homolog, cochlin (Limulus polyphemus)

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008211.3 RefSeqGene

      Range
      5002..21061
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135058.2NP_001128530.1  cochlin isoform b precursor

      See identical proteins and their annotated locations for NP_001128530.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) 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).
      Source sequence(s)
      AF006740, AL049830, AY358900
      Consensus CDS
      CCDS9640.1
      UniProtKB/Swiss-Prot
      A8K9K9, D3DS84, O43405, Q96IU6
      UniProtKB/TrEMBL
      A0A2R8Y3T0
      Related
      ENSP00000496360.1, ENST00000644874.2
      Conserved Domains (3) summary
      smart00603
      Location:30112
      LCCL; LCCL domain
      cd01472
      Location:366527
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      cd01482
      Location:164328
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    2. NM_001347720.2NP_001334649.1  cochlin isoform a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AL049830
      Consensus CDS
      CCDS86382.1
      UniProtKB/TrEMBL
      A0A2R8Y3T0, A0A2U3TZE7
      Related
      ENSP00000216361.5, ENST00000216361.9
    3. NM_004086.3NP_004077.1  cochlin isoform b precursor

      See identical proteins and their annotated locations for NP_004077.1

      Status: REVIEWED

      Description
      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).
      Source sequence(s)
      AF006740, AL049830
      Consensus CDS
      CCDS9640.1
      UniProtKB/Swiss-Prot
      A8K9K9, D3DS84, O43405, Q96IU6
      UniProtKB/TrEMBL
      A0A2R8Y3T0
      Related
      ENSP00000379862.3, ENST00000396618.9
      Conserved Domains (3) summary
      smart00603
      Location:30112
      LCCL; LCCL domain
      cd01472
      Location:366527
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      cd01482
      Location:164328
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      30874559..30895615
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431063.1XP_047287019.1  cochlin isoform X2

      UniProtKB/TrEMBL
      A0A2U3TZE7
    2. XM_047431062.1XP_047287018.1  cochlin isoform X1

    3. XM_047431064.1XP_047287020.1  cochlin isoform X4

      UniProtKB/Swiss-Prot
      A8K9K9, D3DS84, O43405, Q96IU6
      Related
      ENSP00000494838.1, ENST00000643575.1
    4. XM_017021071.2XP_016876560.1  cochlin isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y3T0, A0A2U3TZE7
    5. XM_024449506.1XP_024305274.1  cochlin isoform X3

      UniProtKB/TrEMBL
      A0A2R8Y3T0
      Related
      ENSP00000493569.1, ENST00000555117.2
      Conserved Domains (3) summary
      smart00603
      Location:30112
      LCCL; LCCL domain
      cd01472
      Location:385546
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      cl00057
      Location:164347
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      25072046..25093101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375540.1XP_054231515.1  cochlin isoform X2

    2. XM_054375538.1XP_054231513.1  cochlin isoform X1

    3. XM_054375542.1XP_054231517.1  cochlin isoform X4

    4. XM_054375539.1XP_054231514.1  cochlin isoform X2

    5. XM_054375541.1XP_054231516.1  cochlin isoform X3