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Col11a2 collagen, type XI, alpha 2 [ Mus musculus (house mouse) ]

Gene ID: 12815, updated on 30-Apr-2024

Summary

Official Symbol
Col11a2provided by MGI
Official Full Name
collagen, type XI, alpha 2provided by MGI
Primary source
MGI:MGI:88447
See related
Ensembl:ENSMUSG00000024330 AllianceGenome:MGI:88447
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
Summary
This gene encodes the alpha-2 subunit of type XI collagen, one of the low abundance fibrillar collagens found in cartilage. The encoded protein, in association with other collagen subunits, forms a heterotrimeric type XI procollagen that may undergo proteolytic processing similar to the alpha-1 subunit. Mice lacking the encoded protein exhibit a mild phenotype similar to nonocular Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED) as well as a nonsyndromic form of deafness called DFNA13. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Biased expression in limb E14.5 (RPKM 60.6) and CNS E14 (RPKM 9.3) See more
Orthologs
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Genomic context

See Col11a2 in Genome Data Viewer
Location:
17 B1; 17 17.98 cM
Exon count:
68
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (34257462..34285659)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (34038919..34066684)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5594 Neighboring gene STARR-positive B cell enhancer ABC_E5595 Neighboring gene solute carrier family 39 (zinc transporter), member 7 Neighboring gene retinoid X receptor beta Neighboring gene STARR-positive B cell enhancer ABC_E11636 Neighboring gene STARR-positive B cell enhancer ABC_E5596 Neighboring gene histocompatibility 2, P region beta locus Neighboring gene cDNA sequence BC051537 Neighboring gene histocompatibility 2, P region alpha locus

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

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent IC
Inferred by Curator
more info
PubMed 
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 heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cartilage development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cartilage development ISO
Inferred from Sequence Orthology
more info
 
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
 
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 roof of mouth development ISO
Inferred from Sequence Orthology
more info
 
involved_in sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within 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 
involved_in soft palate development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within tissue homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
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 NAS
Non-traceable Author Statement
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
 

General protein information

Preferred Names
collagen alpha-2(XI) chain
Names
procollagen, type XI, alpha 2

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_001317722.2NP_001304651.1  collagen alpha-2(XI) chain isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS89075.1
    UniProtKB/TrEMBL
    A0A068BD44
    Related
    ENSMUSP00000157723.2, ENSMUST00000237490.2
    Conserved Domains (3) summary
    pfam01391
    Location:12701328
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15191714
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  2. NM_001401301.1NP_001388230.1  collagen alpha-2(XI) chain isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    CR974462
    UniProtKB/Swiss-Prot
    Q61432, Q64739, Q9Z1W0
    Related
    ENSMUSP00000122082.3, ENSMUST00000131134.9
  3. NM_009926.3NP_034056.1  collagen alpha-2(XI) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_034056.1

    Status: VALIDATED

    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS28640.1
    UniProtKB/TrEMBL
    A0A068BD44, I7HJS8
    Related
    ENSMUSP00000084772.5, ENSMUST00000087497.11
    Conserved Domains (3) summary
    pfam01391
    Location:12051263
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14541649
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains

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_000083.7 Reference GRCm39 C57BL/6J

    Range
    34257462..34285659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523559.5XP_006523622.1  collagen alpha-2(XI) chain isoform X1

    See identical proteins and their annotated locations for XP_006523622.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (4) summary
    pfam01391
    Location:13751433
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:16241819
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:230518
    PHA03247; large tegument protein UL36; Provisional
  2. XM_006523562.5XP_006523625.1  collagen alpha-2(XI) chain isoform X4

    See identical proteins and their annotated locations for XP_006523625.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (5) summary
    pfam01391
    Location:13151373
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15641759
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    PRK12323
    Location:288456
    PRK12323; DNA polymerase III subunit gamma/tau
    pfam09770
    Location:230367
    PAT1; Topoisomerase II-associated protein PAT1
  3. XM_006523560.5XP_006523623.1  collagen alpha-2(XI) chain isoform X2

    See identical proteins and their annotated locations for XP_006523623.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (5) summary
    pfam01391
    Location:13541412
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:16031798
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:294654
    PHA03247; large tegument protein UL36; Provisional
    pfam09770
    Location:230367
    PAT1; Topoisomerase II-associated protein PAT1
  4. XM_006523563.5XP_006523626.1  collagen alpha-2(XI) chain isoform X5

    See identical proteins and their annotated locations for XP_006523626.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (4) summary
    pfam01391
    Location:12941352
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15431738
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:230594
    PHA03247; large tegument protein UL36; Provisional
  5. XM_006523568.5XP_006523631.1  collagen alpha-2(XI) chain isoform X8

    See identical proteins and their annotated locations for XP_006523631.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (3) summary
    pfam01391
    Location:12311289
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14801675
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  6. XM_006523569.5XP_006523632.1  collagen alpha-2(XI) chain isoform X9

    See identical proteins and their annotated locations for XP_006523632.1

    UniProtKB/TrEMBL
    A0A068BD44
    Related
    ENSMUSP00000109890.2, ENSMUST00000114252.9
    Conserved Domains (3) summary
    pfam01391
    Location:12101268
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14591654
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  7. XM_006523561.5XP_006523624.1  collagen alpha-2(XI) chain isoform X3

    See identical proteins and their annotated locations for XP_006523624.1

    UniProtKB/TrEMBL
    A0A068BD44
    Conserved Domains (5) summary
    pfam01391
    Location:13491407
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15981793
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03378
    Location:236342
    PHA03378; EBNA-3B; Provisional
    PRK12323
    Location:258446
    PRK12323; DNA polymerase III subunit gamma/tau
  8. XM_006523567.5XP_006523630.1  collagen alpha-2(XI) chain isoform X7

    See identical proteins and their annotated locations for XP_006523630.1

    UniProtKB/TrEMBL
    A0A068BD44
    Related
    ENSMUSP00000109893.2, ENSMUST00000114255.9
    Conserved Domains (3) summary
    pfam01391
    Location:12441302
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14931688
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  9. XM_006523570.5XP_006523633.1  collagen alpha-2(XI) chain isoform X10

    See identical proteins and their annotated locations for XP_006523633.1

    UniProtKB/TrEMBL
    A0A068BD44
    Related
    ENSMUSP00000157425.2, ENSMUST00000237989.2
    Conserved Domains (3) summary
    pfam01391
    Location:11841242
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14331628
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  10. XM_006523571.2XP_006523634.1  collagen alpha-2(XI) chain isoform X11

    See identical proteins and their annotated locations for XP_006523634.1

    Conserved Domains (2) summary
    pfam01391
    Location:897955
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:11461341
    COLFI; Fibrillar collagens C-terminal domain

RNA

  1. XR_385275.5 RNA Sequence

  2. XR_385276.5 RNA Sequence