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

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 AllianceGenome:MGI:88452
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: Dmm; Lpk; Col2; Del1; Col2a; 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: human all
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Genomic context

Location:: 15 F1; 15 53.97 cM

Exon count:: 54

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (97873483..97902525, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (97975602..98004724, complement)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Conditional deletion of HDAC4 from collagen type 2alpha1-expressing cells increases angiogenesis in vivo.
Title: Conditional deletion of HDAC4 from collagen type 2α1-expressing cells increases angiogenesis in vivo.
Skeletal deterioration in COL2A1-related spondyloepiphyseal dysplasia occurs prior to osteoarthritis.
Title: Skeletal deterioration in COL2A1-related spondyloepiphyseal dysplasia occurs prior to osteoarthritis.
TARM1 contributes to development of arthritis by activating dendritic cells through recognition of collagens.
Title: TARM1 contributes to development of arthritis by activating dendritic cells through recognition of collagens.
Data suggest that collagen II matrikines stimulate angiogenesis in skeletal growth and development, revealing novel strategies for stimulating angiogenesis in other contexts such as fracture healing and surgical applications.
Title: Disrupted type II collagenolysis impairs angiogenesis, delays endochondral ossification and initiates aberrant ossification in mouse limbs.
Col2a1 positive cells were found to be specifically distributed in the superficial and inner zones of the anterior horn, as well as the inner zone of the posterior horn in mice, indicating that Col2a1-CreER(T2) mice can be a used for studying gene function in menisci
Title: Postnatal deletion of Alk5 gene in meniscal cartilage accelerates age-dependent meniscal degeneration in mice.
blocking the expression of the R992C collagen II mutant at the early prenatal stages leads to long-term positive effects.
Title: Epiphyseal growth plate architecture is unaffected by early postnatal activation of the expression of R992C collagen II mutant.
this study's findings indicate that endothelial Del-1 not influence atherosclerosis development in ApoE(-/-) mice
Title: Endothelial cell-specific overexpression of developmental endothelial locus-1 does not influence atherosclerosis development in ApoE(-/-) mice.
Overexpression of Dlx2 enhances early chondrocyte differentiation by increasing accumulation of Col2alpha1, type II collagen and aggrecan, but interferes later stages of chondrocyte differentiation through inhibiting MMP13 expression.
Title: Dlx2 overexpression enhanced accumulation of type II collagen and aggrecan by inhibiting MMP13 expression in mice chondrocytes.
Detection of transcripts of Collagen type2 A1 (Col2a1) revealed that both e trabecular cartilageand the anterior part of the hypophyseal cartilage developing anterior to the persistent epithelial stalk of the anterior lobe of the pituitary gland were suppressed in the Foxc1(ch/ch) .
Title: Transcription factor Foxc1 is involved in anterior part of cranial base formation.
found bone destruction and bone loss phenotype in vertebral bone in beta-catenin(Col2CreER) KO mice
Title: Specific Deletion of β-Catenin in Col2-Expressing Cells Leads to Defects in Epiphyseal Bone.

Submit: New GeneRIF Correction See all GeneRIFs (54)

Variation

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Alleles

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

Chemically induced (ENU) (6) 1 citation
Endonuclease-mediated (7) 1 citation
Radiation induced (1) 1 citation
Spontaneous (2) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:464658 (e-PCR)
- UniSTS:464658

Col2a1 (e-PCR), detects polymorphism
- UniSTS:464658

Col2a1 (e-PCR), detects polymorphism
- UniSTS:508440

Col2a1 (e-PCR), detects polymorphism
- UniSTS:507422

Col2a1 (e-PCR), detects polymorphism
- UniSTS:507423

NoName (e-PCR)
- UniSTS:548133

NoName (e-PCR)
- UniSTS:548134

NoName (e-PCR)
- UniSTS:548135

NoName (e-PCR)
- UniSTS:548136

PMC156609P2 (e-PCR)
- UniSTS:271414

Col2a1 (e-PCR), detects polymorphism
- UniSTS:141369

Col2a1 (e-PCR), detects polymorphism
- UniSTS:265066

Col2a1 (e-PCR), detects polymorphism
- UniSTS:259692

GDB:577659 (e-PCR)
- UniSTS:157813

D15Mit41 (e-PCR), detects polymorphism
- UniSTS:127659

D15Mit43 (e-PCR), detects polymorphism
- UniSTS:127661

COL2A1 (e-PCR)
- UniSTS:503994

RH128349 (e-PCR)
- UniSTS:211657

GDB:177260 (e-PCR)
- UniSTS:154850

COL2A1 (e-PCR)
- UniSTS:258280

Col2a1 (e-PCR), detects polymorphism
- UniSTS:478963

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables MHC class II protein binding	IEA Inferred from Electronic Annotation more info
enables MHC class II protein binding	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
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 protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	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
involved_in central nervous system development	IEP Inferred from Expression Pattern more info	PubMed
involved_in 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
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	IEA Inferred from Electronic Annotation 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
acts_upstream_of extrinsic apoptotic signaling pathway in absence of ligand	IMP Inferred from Mutant Phenotype 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
involved_in 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	IEP Inferred from Expression Pattern more info	PubMed
involved_in ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in 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	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type II trimer	IBA Inferred from Biological aspect of Ancestor more info
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
part_of collagen type XI trimer	NAS Non-traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
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 collagen-containing extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
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

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Preferred Names: collagen alpha-1(II) chain

Names: alpha-1 type II collagen; chondrocalcin; procollagen, type II, alpha 1

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_001113515.3 → NP_001106987.2 collagen alpha-1(II) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_001106987.2

Status: VALIDATED

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, AC134554

Consensus CDS

CCDS49716.1

UniProtKB/Swiss-Prot

P28481

Related

ENSMUSP00000085693.6, ENSMUST00000088355.12

Conserved Domains (2) summary

pfam01391
Location:733 → 792

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1186 → 1418

COLFI; Fibrillar collagen C-terminal domain
NM_031163.4 → NP_112440.2 collagen alpha-1(II) chain isoform 1 preproprotein

See identical proteins and their annotated locations for NP_112440.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC113444, AC134554

Consensus CDS

CCDS37189.2

UniProtKB/Swiss-Prot

P28481, Q61428, Q62031, Q62032, Q62033, Q641K3, Q6LDB1, Q6LDI8, Q6LDI9, Q80VY3, Q80X38, Q8CEF7, Q8K0N6

Related

ENSMUSP00000023123.9, ENSMUST00000023123.15

Conserved Domains (3) summary

pfam01391
Location:801 → 860

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:34 → 88

VWC; von Willebrand factor type C domain

pfam01410
Location:1254 → 1486

COLFI; Fibrillar collagen C-terminal domain