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

Gene ID: 12814, updated on 28-May-2016
Official Symbol
Col11a1provided by MGI
Official Full Name
collagen, type XI, alpha 1provided by MGI
Primary source
MGI:MGI:88446
See related
Ensembl:ENSMUSG00000027966 Vega:OTTMUSG00000022509
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; 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]
Orthologs
Location:
3 F3; 3 49.35 cM
Exon count:
69
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 3 NC_000069.6 (114030479..114220327)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (113733458..113923244)

Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene mortality factor 4 like 2 pseudogene Neighboring gene zinc finger protein 617 pseudogene Neighboring gene TIP41, TOR signalling pathway regulator-like pseudogene Neighboring gene olfactomedin 3

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Spontaneous (1) 

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
cartilage condensation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
chondrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization IGI
Inferred from Genetic Interaction
more info
PubMed 
collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
detection of mechanical stimulus involved in sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
embryonic skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
proteoglycan metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
tendon development IGI
Inferred from Genetic Interaction
more info
PubMed 
tendon development IMP
Inferred from Mutant Phenotype
more info
PubMed 
ventricular cardiac muscle tissue morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen type XI trimer ISO
Inferred from Sequence Orthology
more info
 
extracellular matrix ISO
Inferred from Sequence Orthology
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
proteinaceous extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
collagen alpha-1(XI) chain
Names
a1(XI) collagen
pro-alpha1(XI) collagen
procollagen, type XI, alpha 1

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
    UniProtKB/TrEMBL
    Q3UST0
    Related
    ENSMUSP00000089793, OTTMUSP00000025652, ENSMUST00000092155, OTTMUST00000053888
    Conserved Domains (3) summary
    pfam01391
    Location:839898
    Collagen; Collagen triple helix repeat (20 copies)
    cd00110
    Location:72224
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam01410
    Location:15911802
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000069.6 Reference GRCm38.p3 C57BL/6J

    Range
    114030479..114220327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500969.1XP_006501032.1  

    Conserved Domains (3) summary
    pfam01391
    Location:851910
    Collagen; Collagen triple helix repeat (20 copies)
    cd00110
    Location:72224
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam01410
    Location:16031814
    COLFI; Fibrillar collagen C-terminal domain
  2. XM_006500971.1XP_006501034.1  

    Conserved Domains (3) summary
    pfam01391
    Location:766825
    Collagen; Collagen triple helix repeat (20 copies)
    cd00110
    Location:72224
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam01410
    Location:15181729
    COLFI; Fibrillar collagen C-terminal domain
  3. XM_006500970.1XP_006501033.1  

    Conserved Domains (3) summary
    pfam01391
    Location:800859
    Collagen; Collagen triple helix repeat (20 copies)
    cd00110
    Location:72224
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam01410
    Location:15521763
    COLFI; Fibrillar collagen C-terminal domain
  4. XM_006500972.1XP_006501035.1  

    Conserved Domains (2) summary
    pfam01391
    Location:616665
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:8311042
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_375486.1 RNA Sequence

Alternate Mm_Celera

Genomic

  1. AC_000025.1 Alternate Mm_Celera

    Range
    120412886..120608803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)