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

Gene ID: 561679, updated on 27-Mar-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 be an extracellular matrix structural constituent. 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 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, Apr 2022]
Orthologs
all
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Genomic context

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See col11a2 in Genome Data Viewer
Location:
chromosome: 19
Exon count:
68
Annotation release Status Assembly Chr Location
106 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. 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
  3. Characterization of the MHC class I region of the Japanese pufferfish (Fugu rubripes). Clark MS, et al. Immunogenetics, 2001. PMID 11220619
  4. Col11a1a Expression Is Required for Zebrafish Development. Hardy MJ, et al. J Dev Biol, 2020 Aug 28. PMID 32872105, Free PMC Article
  5. Prednisolone suppresses collagen-encoding gene expression causing cartilage defects in zebrafish larvae. Jiang Y, et al. Environ Toxicol Pharmacol, 2021 Oct. PMID 34332081

See all (33) 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
  
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cartilage development IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
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
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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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_005159448.4 → XP_005159505.1  collagen alpha-2(XI) chain isoform X5

    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

  2. XM_017352253.2 → XP_017207742.1  collagen alpha-2(XI) chain isoform X4

    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

  3. XM_005159450.4 → XP_005159507.1  collagen alpha-2(XI) chain isoform X6

    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_009294049.3 → XP_009292324.1  collagen alpha-2(XI) chain isoform X7

    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

  5. XM_005159443.3 → XP_005159500.1  collagen alpha-2(XI) chain isoform X1

    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

  6. XM_005159442.4 → XP_005159499.1  collagen alpha-2(XI) chain isoform X1

    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_005159445.4 → XP_005159502.1  collagen alpha-2(XI) chain isoform X3

    UniProtKB/TrEMBL
    A0A8M2B6G1
    Conserved Domains (3) summary
    pfam01391
    Location:782 → 839
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:29 → 218
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:1675 → 1902
    COLFI; Fibrillar collagen C-terminal domain

  8. XM_017352252.2 → XP_017207741.1  collagen alpha-2(XI) chain isoform X2

    UniProtKB/TrEMBL
    A0A8M6Z300
Nucleotide Protein Strain
Heading Accession and Version

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