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Col2a1 collagen, type II, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12824, updated on 21-Sep-2021

Summary

Official Symbol
Col2a1provided by MGI
Official Full Name
collagen, type II, alpha 1provided by MGI
Primary source
MGI:MGI:88452
See related
Ensembl:ENSMUSG00000022483
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
L; Co; Del; Dmm; Lpk; Col2; Del1; Col2a; Rgsc4; Rgsc8; Col2a-1; M100413; Rgsc413; Rgsc856
Summary
This gene encodes the alpha-1 subunit of the fibril-forming type II collagen, the major component of cartilage and the vitreous humor of the eye. The encoded preproprotein forms homotrimeric, triple helical procollagen that undergoes proteolytic processing during fibirl formation. Mice harboring certain mutations in this gene exhibit severe chondrodysplasia characterized by short limbs and trunch, craniofacial deformities and cleft palate. A complete lack of the encoded protein in mice results in postnatal lethality. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Dec 2015]
Expression
Biased expression in limb E14.5 (RPKM 504.7), CNS E14 (RPKM 67.6) and 1 other tissue See more
Orthologs
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Genomic context

See Col2a1 in Genome Data Viewer
Location:
15 F1; 15 53.97 cM
Exon count:
54
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (97873483..97902722, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (97975602..98004724, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (97806033..97835155, complement)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene vitamin D (1,25-dihydroxyvitamin D3) receptor Neighboring gene predicted gene, 52171 Neighboring gene transmembrane protein 106C Neighboring gene predicted gene, 46536 Neighboring gene predicted gene, 41395 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene predicted gene, 25668

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)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC90638

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables MHC class II protein binding ISO
Inferred from Sequence Orthology
more info
 
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables platelet-derived growth factor binding ISO
Inferred from Sequence Orthology
more info
 
enables proteoglycan binding ISO
Inferred from Sequence Orthology
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within anterior head development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within bone development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cartilage condensation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to BMP stimulus IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within central nervous system development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within chondrocyte differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within chondrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in collagen fibril organization ISO
Inferred from Sequence Orthology
more info
 
involved_in embryonic skeletal joint morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within endochondral ossification IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within heart morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within limb bud formation IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within limb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in notochord development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within notochord development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within ossification IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within otic vesicle development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within proteoglycan metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within roof of mouth development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
involved_in skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in skeletal system development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within tissue homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in visual perception ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen type II trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen type II trimer IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen type II trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
part_of collagen type II trimer ISO
Inferred from Sequence Orthology
more info
 
located_in collagen-containing extracellular matrix HDA PubMed 
located_in collagen-containing extracellular matrix ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
collagen alpha-1(II) chain
Names
alpha-1 type II collagen
chondrocalcin
procollagen, type II, alpha 1

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_001113515.2NP_001106987.2  collagen alpha-1(II) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_001106987.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    AC113444, BC082331
    Consensus CDS
    CCDS49716.1
    UniProtKB/Swiss-Prot
    P28481
    Related
    ENSMUSP00000085693.6, ENSMUST00000088355.12
    Conserved Domains (2) summary
    pfam01391
    Location:733792
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:11861418
    COLFI; Fibrillar collagen C-terminal domain
  2. NM_031163.3NP_112440.2  collagen alpha-1(II) chain isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_112440.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC113444, BC082331
    Consensus CDS
    CCDS37189.2
    UniProtKB/Swiss-Prot
    P28481
    Related
    ENSMUSP00000023123.9, ENSMUST00000023123.15
    Conserved Domains (3) summary
    pfam01391
    Location:801860
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00093
    Location:3488
    VWC; von Willebrand factor type C domain
    pfam01410
    Location:12541486
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    97873483..97902722 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036159114.1XP_036015007.1  collagen alpha-1(II) chain isoform X1

    Conserved Domains (3) summary
    PRK07764
    Location:670877
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam01391
    Location:622678
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:10691304
    COLFI; Fibrillar collagen C-terminal domain
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