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Col11a1 collagen, type XI, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12814, updated on 5-Mar-2024

Summary

Official Symbol
Col11a1provided by MGI
Official Full Name
collagen, type XI, alpha 1provided by MGI
Primary source
MGI:MGI:88446
See related
Ensembl:ENSMUSG00000027966 AllianceGenome:MGI:88446
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
cho; C530001D20Rik
Summary
This gene encodes the alpha-1 subunit of type XI collagen, one of the low abundance fibrillar collagens that is essential for normal embryonic skeletal development and the cohesive properties of cartilage. The encoded protein, in association with the alpha-1 subunit of type II collagen, forms a heterotrimeric type XI procollagen that undergoes proteolytic processing. Mice lacking the encoded protein develop severe chondrodysplasia and die at birth. [provided by RefSeq, Dec 2015]
Expression
Biased expression in limb E14.5 (RPKM 65.0), CNS E14 (RPKM 14.0) and 3 other tissues See more
Orthologs
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Genomic context

See Col11a1 in Genome Data Viewer
Location:
3 F3; 3 49.35 cM
Exon count:
69
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (113823933..114014405)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (114030479..114220756)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene mortality factor 4 like 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_08734 Neighboring gene zinc finger protein 617 pseudogene Neighboring gene STARR-seq mESC enhancer starr_08735 Neighboring gene STARR-seq mESC enhancer starr_08736 Neighboring gene STARR-seq mESC enhancer starr_08737 Neighboring gene STARR-seq mESC enhancer starr_08738 Neighboring gene STARR-seq mESC enhancer starr_08739 Neighboring gene STARR-seq mESC enhancer starr_08740 Neighboring gene STARR-seq mESC enhancer starr_08741 Neighboring gene STARR-seq mESC enhancer starr_08742 Neighboring gene predicted gene, 23750 Neighboring gene TIP41, TOR signalling pathway regulator-like pseudogene

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)
  • Spontaneous (1) 
  • Endonuclease-mediated (4) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 heparan sulfate binding ISO
Inferred from Sequence Orthology
more info
 
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables heparin binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
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 chondrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within collagen fibril organization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in detection of mechanical stimulus involved in sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within embryonic skeletal system morphogenesis 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_or_within heart morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within proteoglycan metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sensory perception of sound 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 tendon development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within tendon development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in visual perception ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen type XI trimer IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of collagen type XI 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 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 extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
collagen alpha-1(XI) chain
Names
a1(XI) collagen
pro-alpha1(XI) collagen
procollagen, type XI, 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)

  1. NM_007729.3NP_031755.2  collagen alpha-1(XI) chain preproprotein

    See identical proteins and their annotated locations for NP_031755.2

    Status: REVIEWED

    Source sequence(s)
    AC156386, AK140136, AK157734
    Consensus CDS
    CCDS17778.1
    UniProtKB/Swiss-Prot
    Q61245, Q64047, Q80WR4
    Related
    ENSMUSP00000089793.6, ENSMUST00000092155.12
    Conserved Domains (3) summary
    pfam01391
    Location:839898
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15761802
    COLFI; Fibrillar collagen C-terminal domain

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_000069.7 Reference GRCm39 C57BL/6J

    Range
    113823933..114014405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500969.2XP_006501032.1  collagen alpha-1(XI) chain isoform X1

    Conserved Domains (3) summary
    pfam01391
    Location:851910
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15851814
    COLFI; Fibrillar collagen C-terminal domain
  2. XM_006500971.2XP_006501034.1  collagen alpha-1(XI) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:766825
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15001729
    COLFI; Fibrillar collagen C-terminal domain
  3. XM_006500970.2XP_006501033.1  collagen alpha-1(XI) chain isoform X2

    Conserved Domains (3) summary
    pfam01391
    Location:800859
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15341763
    COLFI; Fibrillar collagen C-terminal domain
  4. XM_030252409.1XP_030108269.1  collagen alpha-1(XI) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:616665
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:8131042
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_375486.2 RNA Sequence