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    col11a2 collagen, type XI, alpha 2 [ Danio rerio (zebrafish) ]

    Gene ID: 561679, updated on 14-Nov-2024

    Summary

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    Official Symbol
    col11a2provided by ZNC
    Official Full Name
    collagen, type XI, alpha 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000208-23
    See related
    Ensembl:ENSDARG00000012422 AllianceGenome:ZFIN:ZDB-GENE-000208-23
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    col11a1
    Summary
    Predicted to enable heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within cartilage morphogenesis. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including immature eye; notochord; pectoral fin bud; skeletal element; and trabecular layer. Human ortholog(s) of this gene implicated in cleft palate; nonsyndromic deafness (multiple); and osteochondrodysplasia (multiple). Orthologous to human COL11A2 (collagen type XI alpha 2 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See col11a2 in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (7179742..7225228, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (7260817..7306303, complement)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene bromodomain containing 2a Neighboring gene hydroxysteroid (17-beta) dehydrogenase 8 Neighboring gene retinoid x receptor, beta a Neighboring gene succinate dehydrogenase complex, subunit A, flavoprotein (Fp)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The mechanical impact of col11a2 loss on joints; col11a2 mutant zebrafish show changes to joint development and function, which leads to early-onset osteoarthritis. Lawrence EA, et al. Philos Trans R Soc Lond B Biol Sci, 2018 Sep 24. PMID 30249781, Free PMC Article
    2. COL11A2 as a candidate gene for vertebral malformations and congenital scoliosis. Rebello D, et al. Hum Mol Genet, 2023 Sep 16. PMID 37462524, Free PMC Article
    3. Characterization of the MHC class I region of the Japanese pufferfish (Fugu rubripes). Clark MS, et al. Immunogenetics, 2001. PMID 11220619
    4. Acute multi-sgRNA knockdown of KEOPS complex genes reproduces the microcephaly phenotype of the stable knockout zebrafish model. Jobst-Schwan T, et al. PLoS One, 2018. PMID 29346415, Free PMC Article
    5. Col11a1a Expression Is Required for Zebrafish Development. Hardy MJ, et al. J Dev Biol, 2020 Aug 28. PMID 32872105, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cartilage morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-2(XI) chain
    Names
    collagen XI alpha 1

    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_001079992.2 → NP_001073461.2  collagen alpha-2(XI) chain isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      FP017221, FP085392
      UniProtKB/TrEMBL
      A0A8M1NB54, F6NLZ6
      Related
      ENSDARP00000095569.4, ENSDART00000104799.5
      Conserved Domains (3) summary
      pfam01391
      Location:573 → 630
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1466 → 1693
      COLFI; Fibrillar collagen C-terminal domain

    2. NM_001328265.1 → NP_001315194.1  collagen alpha-2(XI) chain isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      FP017221, FP085392
      UniProtKB/TrEMBL
      A0A8M1P8Y1, I3ISS1
      Related
      ENSDARP00000125963.1, ENSDART00000151138.3
      Conserved Domains (3) summary
      pfam01391
      Location:681 → 738
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1574 → 1801
      COLFI; Fibrillar collagen C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      7179742..7225228 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005159443.4 → XP_005159500.1  collagen alpha-2(XI) chain isoform X2

      See identical proteins and their annotated locations for XP_005159500.1

      UniProtKB/TrEMBL
      A0A8M2B5Z5
      Conserved Domains (3) summary
      pfam01391
      Location:899 → 956
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1792 → 2019
      COLFI; Fibrillar collagen C-terminal domain

    2. XM_068215158.1 → XP_068071259.1  collagen alpha-2(XI) chain isoform X1

    3. XM_005159450.5 → XP_005159507.1  collagen alpha-2(XI) chain isoform X7

      UniProtKB/TrEMBL
      A0A8M2B659, F1R5X4
      Related
      ENSDARP00000119303.2, ENSDART00000133179.4
      Conserved Domains (3) summary
      pfam01391
      Location:599 → 656
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1492 → 1719
      COLFI; Fibrillar collagen C-terminal domain

    4. XM_005159448.5 → XP_005159505.1  collagen alpha-2(XI) chain isoform X6

      UniProtKB/TrEMBL
      A0A8M2B6B8
      Conserved Domains (3) summary
      pfam01391
      Location:642 → 699
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1535 → 1762
      COLFI; Fibrillar collagen C-terminal domain

    5. XM_009294049.4 → XP_009292324.1  collagen alpha-2(XI) chain isoform X8

      UniProtKB/TrEMBL
      A0A8M1NB54, F6NLZ6
      Conserved Domains (3) summary
      pfam01391
      Location:573 → 630
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1466 → 1693
      COLFI; Fibrillar collagen C-terminal domain

    6. XM_005159442.5 → XP_005159499.1  collagen alpha-2(XI) chain isoform X2

      See identical proteins and their annotated locations for XP_005159499.1

      UniProtKB/TrEMBL
      A0A8M2B5Z5
      Conserved Domains (3) summary
      pfam01391
      Location:899 → 956
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1792 → 2019
      COLFI; Fibrillar collagen C-terminal domain

    7. XM_017352253.3 → XP_017207742.1  collagen alpha-2(XI) chain isoform X5

      UniProtKB/TrEMBL
      A0A8M1P8Y1, I3ISS1
      Conserved Domains (3) summary
      pfam01391
      Location:681 → 738
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:29 → 218
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1574 → 1801
      COLFI; Fibrillar collagen C-terminal domain

    8. XM_068215160.1 → XP_068071261.1  collagen alpha-2(XI) chain isoform X4

    9. XM_068215159.1 → XP_068071260.1  collagen alpha-2(XI) chain isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version

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