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COCH cochlin [ Homo sapiens (human) ]

Gene ID: 1690, updated on 3-Jan-2019

Summary

Official Symbol
COCHprovided by HGNC
Official Full Name
cochlinprovided by HGNC
Primary source
HGNC:HGNC:2180
See related
Ensembl:ENSG00000100473 MIM:603196
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

Genomic context

See COCH in Genome Data Viewer
Location:
14q12
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (30874496..30890618)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31343741..31364285)

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 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 FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
growth plate cartilage chondrocyte morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of innate immune response IEA
Inferred from Electronic Annotation
more info
 
regulation of cell shape IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen-containing extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_008211.2 RefSeqGene

    Range
    5001..21082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001135058.1NP_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, AW629100, AY358900
    Consensus CDS
    CCDS9640.1
    UniProtKB/Swiss-Prot
    O43405
    Related
    ENSP00000496360.1, ENST00000644874.1
    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_001347720.1NP_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
    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
    O43405
    Related
    ENSP00000379862.3, ENST00000396618.8
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    30874496..30890618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021071.1XP_016876560.1  cochlin isoform X1

  2. XM_024449506.1XP_024305274.1  cochlin isoform X2

    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 ...
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