Coch cochlin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cochprovided by RGD
Official Full Name: cochlinprovided by RGD
Primary source: RGD:1308536
See related: EnsemblRapid:ENSRNOG00000005286 AllianceGenome:RGD:1308536
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable collagen binding activity. Predicted to be involved in regulation of cell shape. Predicted to act upstream of or within sensory perception of sound. Predicted to be located in extracellular matrix. Predicted to be active in collagen-containing extracellular matrix. 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, Nov 2024]
Expression: Biased expression in Spleen (RPKM 257.3), Brain (RPKM 24.1) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 6q23

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (74766485..74780504)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (69031139..69045124)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (72359702..72373710)

Chromosome 6 - NC_086024.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

expression in perilymph detected from 3rd day after birth (DAB3), gradually increased to DAB15, then gradually decreased to DAB70
Title: Cochlin expression in the rat perilymph during postnatal development.
Cochlin may play a role in the structural homeostasis of the vestibule acting in concert with the fibrillar type II collagen bundles.
Title: Ultrastructural co-localization of cochlin and type II collagen in the rat semicircular canal.
The expression of cochlin may be related to the maturation of inner ear function.
Title: Spatiotemporal expression of cochlin in the inner ear of rats during postnatal development.

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General gene information

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Markers

RH128933 (e-PCR)
- UniSTS:212241

RH143184 (e-PCR)
- UniSTS:232431

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables collagen binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cochlin

Names: coagulation factor C homolog (Limulus polyphemus); coagulation factor C homolog, cochlin (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_001108710.2 → NP_001102180.2 cochlin precursor

Status: VALIDATED

Source sequence(s)

BC160874

UniProtKB/TrEMBL

A0A8I5ZPB6, A0A9K3Y6Q1, B1H259, F7FPJ4

Related

ENSRNOP00000112568.1, ENSRNOT00000129330.1

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 ...