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

Gene ID: 12815, updated on 3-Apr-2024

Summary

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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
human all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Col11a2 deletion reveals the molecular basis for tectorial membrane mechanical anisotropy. Masaki K, et al. Biophys J, 2009 Jun 3. PMID 19486694, Free PMC Article
  2. A novel retinoic acid-response element requires an enhancer element mediator for transcriptional activation. Harris LR, et al. Biochem J, 2004 Oct 1. PMID 15206905, Free PMC Article
  3. Chondrocyte-specific enhancer elements in the Col11a2 gene resemble the Col2a1 tissue-specific enhancer. Bridgewater LC, et al. J Biol Chem, 1998 Jun 12. PMID 9614107
  4. Insulation of the ubiquitous Rxrb promoter from the cartilage-specific adjacent gene, Col11a2. Murai J, et al. J Biol Chem, 2008 Oct 10. PMID 18682388
  5. Genetic modifiers of vision and hearing. Haider NB, et al. Hum Mol Genet, 2002 May 15. PMID 12015279

See all (58) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The expression patterns suggest essential roles for Col11a1 and Col11a2 in the basilar or tectorial membranes.
    Title: Col11a1 and Col11a2 mRNA expression in the developing mouse cochlea: implications for the correlation of hearing loss phenotype with mutant type XI collagen genotype.
  2. The present study has revealed a novel retinoic acid-response element in Col11a2 that does not interact directly with the promoter, but instead requires the D/E enhancer to mediate transcriptional activation.
    Title: A novel retinoic acid-response element requires an enhancer element mediator for transcriptional activation.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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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_001317722.2 → NP_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:1270 → 1328
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1519 → 1714
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains

  2. NM_001401301.1 → NP_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_009926.3 → NP_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:1205 → 1263
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1454 → 1649
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    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_006523559.5 → XP_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:1375 → 1433
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1624 → 1819
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:230 → 518
    PHA03247; large tegument protein UL36; Provisional

  2. XM_006523562.5 → XP_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:1315 → 1373
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1564 → 1759
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains
    PRK12323
    Location:288 → 456
    PRK12323; DNA polymerase III subunit gamma/tau
    pfam09770
    Location:230 → 367
    PAT1; Topoisomerase II-associated protein PAT1

  3. XM_006523560.5 → XP_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:1354 → 1412
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1603 → 1798
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:294 → 654
    PHA03247; large tegument protein UL36; Provisional
    pfam09770
    Location:230 → 367
    PAT1; Topoisomerase II-associated protein PAT1

  4. XM_006523563.5 → XP_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:1294 → 1352
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1543 → 1738
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03247
    Location:230 → 594
    PHA03247; large tegument protein UL36; Provisional

  5. XM_006523568.5 → XP_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:1231 → 1289
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1480 → 1675
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains

  6. XM_006523569.5 → XP_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:1210 → 1268
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1459 → 1654
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains

  7. XM_006523561.5 → XP_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:1349 → 1407
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1598 → 1793
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains
    PHA03378
    Location:236 → 342
    PHA03378; EBNA-3B; Provisional
    PRK12323
    Location:258 → 446
    PRK12323; DNA polymerase III subunit gamma/tau

  8. XM_006523567.5 → XP_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:1244 → 1302
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1493 → 1688
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains

  9. XM_006523570.5 → XP_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:1184 → 1242
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1433 → 1628
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32 → 213
    TSPN; Thrombospondin N-terminal -like domains

  10. XM_006523571.2 → XP_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:897 → 955
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:1146 → 1341
    COLFI; Fibrillar collagens C-terminal domain

RNA

  1. XR_385275.5 RNA Sequence

  2. XR_385276.5 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q64739.3 GenPept UniProtKB/Swiss-Prot:Q64739

Gene LinkOut

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