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

    Gene ID: 12815, updated on 3-Dec-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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

    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

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

    NCBI Reference Sequences (RefSeq)

    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_001317722.2NP_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
      UniProtKB/TrEMBL
      A0A068BD44
      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