Coch cochlin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cochprovided by MGI
Official Full Name: cochlinprovided by MGI
Primary source: MGI:MGI:1278313
See related: Ensembl:ENSMUSG00000020953 AllianceGenome:MGI:1278313
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Coch-5B2; D12H14S564E
Summary: Predicted to enable collagen binding activity. Acts upstream of or within defense response to bacterium; positive regulation of innate immune response; and sensory perception of sound. Located in extracellular matrix and extracellular region. Is expressed in central nervous system; inner ear; olfactory epithelium; and vibrissa. Used to study autosomal dominant nonsyndromic deafness 9. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 9 and autosomal recessive nonsyndromic deafness 110. Orthologous to human COCH (cochlin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in spleen adult (RPKM 141.2), ovary adult (RPKM 13.9) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 12 B3; 12 22.11 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (51640156..51652558)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (51593283..51606619)

Chromosome 12 - NC_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cochlin Deficiency Protects Aged Mice from Noise-Induced Hearing Loss.
Title: Cochlin Deficiency Protects Aged Mice from Noise-Induced Hearing Loss.
Upon infection, the LCCL domain is cleaved from cochlin and secreted into the perilymph. This cleaved fragment sequesters infiltrating bacteria in the scala tympani and subsequently recruits resident immune cells to eliminate the bacteria.
Title: Cleaved Cochlin Sequesters Pseudomonas aeruginosa and Activates Innate Immunity in the Inner Ear.
accumulation of acellular deposits in the incudomalleal and incudostapedial joints in Coch (G88E/G88E) mice similar to those found in human DFNA9-affected temporal bones
Title: Cochlin in normal middle ear and abnormal middle ear deposits in DFNA9 and Coch (G88E/G88E) mice.
study reports that cochlin is expressed by follicular dendritic cells (FDCs) and selectively localized in the fine extracellular network of conduits in the spleen and lymph nodes; by producing cochlin, FDCs contribute to the innate immune response in defense against bacteria
Title: Cochlin produced by follicular dendritic cells promotes antibacterial innate immunity.
COCH is a part of the downstream target network of BMP4 signaling and serves as another important effector to fine-tune mouse embryonic stem cell fates.
Title: BMP induces cochlin expression to facilitate self-renewal and suppress neural differentiation of mouse embryonic stem cells.
Loss of Cochlin is associated with reduced intraocular pressure and mechanosensing.
Title: Cochlin, intraocular pressure regulation and mechanosensing.
In Coch knock-in/knockout mouse models of sensorineural hearing loss and vestibular dysfunction vestibular function is compromised before cochlear function.
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.
Up-regulation of cochlin is an important etiologic factor leading to Usher syndrome type 1F.
Title: Proteomics, bioinformatics and targeted gene expression analysis reveals up-regulation of cochlin and identifies other potential biomarkers in the mouse model for deafness in Usher syndrome type 1F.
introduced the G88E mutation by gene targeting into the mouse and have created a Coch(G88E/G88E) mouse model for the study of DFNA9 pathogenesis and cochlin function
Title: A targeted Coch missense mutation: a knock-in mouse model for DFNA9 late-onset hearing loss and vestibular dysfunction.
Cochlin was found in the trabecular meshwork of very young mice, prior to elevated intraocular pressure, suggesting that over time the protein may contribute to the events leading to increased IOP and optic nerve damage--{REVIEW}
Title: Cochlin and glaucoma: a mini-review.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Coch (e-PCR), detects polymorphism
- UniSTS:516120

AW122937 (e-PCR)
- UniSTS:180390

AF006741 (e-PCR)
- UniSTS:160207

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed

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	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cochlin

Names: coagulation factor C homolog (Limulus polyphemus)

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001198835.2 → NP_001185764.1 cochlin isoform 2 precursor

See identical proteins and their annotated locations for NP_001185764.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC158404, AF006741, AK028690

Consensus CDS

CCDS25901.1

UniProtKB/Swiss-Prot

Q3TAF5, Q62507, Q9QWK6

UniProtKB/TrEMBL

Q3U0Z1

Related

ENSMUSP00000082533.6, ENSMUST00000085412.7

Conserved Domains (3) summary

smart00603
Location:32 → 114

LCCL; LCCL domain

cd01472
Location:368 → 529

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:166 → 330

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 ...
NM_001409459.1 → NP_001396388.1 cochlin isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC158404
NM_001409460.1 → NP_001396389.1 cochlin isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC158404
NM_001409461.1 → NP_001396390.1 cochlin isoform 4 precursor

Status: VALIDATED

Description

Transcript Variant: Variants 4 and 5 encode isoforms of the same length that differ in their amino acid sequence.

Source sequence(s)

AC158404
NM_001409462.1 → NP_001396391.1 cochlin isoform 5 precursor

Status: VALIDATED

Description

Transcript Variant: Variants 4 and 5 encode isoforms of the same length that differ in their amino acid sequence.

Source sequence(s)

AC158404
NM_001409463.1 → NP_001396392.1 cochlin isoform 6 precursor

Status: VALIDATED

Source sequence(s)

AC158404
NM_001409464.1 → NP_001396393.1 cochlin isoform 7 precursor

Status: VALIDATED

Source sequence(s)

AC158404
NM_007728.6 → NP_031754.1 cochlin isoform 2 precursor

See identical proteins and their annotated locations for NP_031754.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC158404, AK028690, AK137336

Consensus CDS

CCDS25901.1

UniProtKB/Swiss-Prot

Q3TAF5, Q62507, Q9QWK6

UniProtKB/TrEMBL

Q3U0Z1

Related

ENSMUSP00000128127.3, ENSMUST00000164782.10

Conserved Domains (3) summary

smart00603
Location:32 → 114

LCCL; LCCL domain

cd01472
Location:368 → 529

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:166 → 330

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 ...