U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 12815, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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. 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
    3. 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
    4. Genetic modifiers of vision and hearing. Haider NB, et al. Hum Mol Genet, 2002 May 15. PMID 12015279
    5. 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

    See all (60) 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

    Go to the top of the page Help

    Alleles

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

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 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 osteoblast differentiation IEA
    Inferred from Electronic Annotation
    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 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

    Go to the top of the page Help
    Preferred Names
    collagen alpha-2(XI) chain
    Names
    procollagen, type XI, alpha 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous