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    Coch cochlin [ Mus musculus (house mouse) ]

    Gene ID: 12810, updated on 3-Dec-2024

    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 sensory perception of sound. Located in extracellular matrix. 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, Nov 2024]
    Expression
    Biased expression in spleen adult (RPKM 141.2), ovary adult (RPKM 13.9) and 1 other tissue See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Coch in Genome Data Viewer
    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_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 40422 Neighboring gene Sec1 family domain containing 1 Neighboring gene high mobility group protein 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_32104 Neighboring gene zyg-11 homolog A pseudogene Neighboring gene striatin, calmodulin binding protein 3 Neighboring gene STARR-positive B cell enhancer ABC_E5328 Neighboring gene adaptor-related protein complex AP-4, sigma 1 Neighboring gene STARR-seq mESC enhancer starr_32110 Neighboring gene predicted gene, 22663

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables collagen binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables collagen binding ISS
    Inferred from Sequence or Structural Similarity
    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
     
    involved_in regulation of cell shape ISS
    Inferred from Sequence or Structural Similarity
    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 IEA
    Inferred from Electronic Annotation
    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

    Preferred Names
    cochlin
    Names
    coagulation factor C homolog (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.

    mRNA and Protein(s)

    1. NM_001198835.2NP_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:32114
      LCCL; LCCL domain
      cd01472
      Location:368529
      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:166330
      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_001409459.1NP_001396388.1  cochlin isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC158404
      UniProtKB/TrEMBL
      Q3U0Z1
    3. NM_001409460.1NP_001396389.1  cochlin isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      AC158404
      UniProtKB/TrEMBL
      Q3U0Z1
    4. NM_001409461.1NP_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
      UniProtKB/TrEMBL
      Q3U0Z1
    5. NM_001409462.1NP_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
      UniProtKB/TrEMBL
      Q3U0Z1
    6. NM_001409463.1NP_001396392.1  cochlin isoform 6 precursor

      Status: VALIDATED

      Source sequence(s)
      AC158404
      UniProtKB/TrEMBL
      Q3U0Z1
    7. NM_001409464.1NP_001396393.1  cochlin isoform 7 precursor

      Status: VALIDATED

      Source sequence(s)
      AC158404
      UniProtKB/TrEMBL
      Q3U0Z1
    8. NM_007728.6NP_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:32114
      LCCL; LCCL domain
      cd01472
      Location:368529
      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:166330
      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 ...

    RNA

    1. NR_176845.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC158404
    2. NR_176846.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC158404
    3. NR_176847.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC158404

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      51640156..51652558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)