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    col11a1a collagen, type XI, alpha 1a [ Danio rerio (zebrafish) ]

    Gene ID: 565402, updated on 17-Sep-2024

    Summary

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    Official Symbol
    col11a1aprovided by ZNC
    Official Full Name
    collagen, type XI, alpha 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070209-167
    See related
    Ensembl:ENSDARG00000026165 AllianceGenome:ZFIN:ZDB-GENE-070209-167
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fb34e11; wu:fc11b03; zgc:158335
    Summary
    Predicted to be an extracellular matrix structural constituent. 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 cleithrum; cranial cartilage; ectoderm; hypochord; and trabecular layer. Human ortholog(s) of this gene implicated in Marshall syndrome; Stickler syndrome 2; autosomal dominant nonsyndromic deafness; and fibrochondrogenesis 1. Orthologous to human COL11A1 (collagen type XI alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See col11a1a in Genome Data Viewer
    Location:
    chromosome: 24
    Exon count:
    68
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 24 NC_007135.7 (28764019..28893251, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 24 NC_007135.6 (28684860..28814185, complement)

    Chromosome 24 - NC_007135.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC110438355 Neighboring gene trans-2,3-enoyl-CoA reductase-like 2a Neighboring gene olfactomedin 3a Neighboring gene RNA-binding region (RNP1, RRM) containing 3 Neighboring gene uncharacterized LOC103909764

    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 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. Authentication of a novel antibody to zebrafish collagen type XI alpha 1 chain (Col11a1a). Reeck JC, et al. BMC Res Notes, 2021 Sep 15. PMID 34526111, Free PMC Article
    2. Col11a1a Expression Is Required for Zebrafish Development. Hardy MJ, et al. J Dev Biol, 2020 Aug 28. PMID 32872105, Free PMC Article
    3. Prednisolone suppresses collagen-encoding gene expression causing cartilage defects in zebrafish larvae. Jiang Y, et al. Environ Toxicol Pharmacol, 2021 Oct. PMID 34332081
    4. Hexavalent chromium amplifies the developmental toxicity of graphene oxide during zebrafish embryogenesis. Chen Y, et al. Ecotoxicol Environ Saf, 2021 Jan 15. PMID 33126181
    5. A novel zinc finger protein 219-like (ZNF219L) is involved in the regulation of collagen type 2 alpha 1a (col2a1a) gene expression in zebrafish notochord. Lien HW, et al. Int J Biol Sci, 2013. PMID 24155663, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 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
    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 extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within notochord development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type XI trimer IBA
    Inferred from Biological aspect of Ancestor
    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, type XI, alpha 1a
    Names
    col11a1

    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_001083844.1 → NP_001077313.1  collagen, type XI, alpha 1a precursor

      See identical proteins and their annotated locations for NP_001077313.1

      Status: PROVISIONAL

      Source sequence(s)
      BC133083
      UniProtKB/TrEMBL
      A0A8M1NDY0, A2RUX5
      Related
      ENSDARP00000042064.6, ENSDART00000042065.9
      Conserved Domains (3) summary
      pfam01391
      Location:644 → 700
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:42 → 232
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1508 → 1734
      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_007135.7 Reference GRCz11 Primary Assembly

      Range
      28764019..28893251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005162814.2 → XP_005162871.1  collagen, type XI, alpha 1a isoform X2

      UniProtKB/TrEMBL
      A0A8M2B9R6, F1QSJ2
      Related
      ENSDARP00000002692.9, ENSDART00000003503.11
      Conserved Domains (3) summary
      pfam01391
      Location:721 → 777
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:42 → 232
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1585 → 1811
      COLFI; Fibrillar collagen C-terminal domain

    2. XM_021470209.2 → XP_021325884.1  collagen, type XI, alpha 1a isoform X6

      UniProtKB/TrEMBL
      A0A8M9PLW6
      Conserved Domains (3) summary
      pfam01391
      Location:594 → 650
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:43 → 233
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1458 → 1684
      COLFI; Fibrillar collagen C-terminal domain

    3. XM_005162815.2 → XP_005162872.1  collagen, type XI, alpha 1a isoform X3

      UniProtKB/TrEMBL
      A0A8M2B9U1
      Conserved Domains (3) summary
      pfam01391
      Location:693 → 749
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:43 → 233
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1557 → 1783
      COLFI; Fibrillar collagen C-terminal domain

    4. XM_005162818.2 → XP_005162875.1  collagen, type XI, alpha 1a isoform X5

      UniProtKB/TrEMBL
      A0A8M2B9X3
      Conserved Domains (3) summary
      pfam01391
      Location:623 → 679
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:43 → 233
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1487 → 1713
      COLFI; Fibrillar collagen C-terminal domain

    5. XM_005162813.2 → XP_005162870.1  collagen, type XI, alpha 1a isoform X1

      UniProtKB/TrEMBL
      A0A8M2BA28
      Conserved Domains (3) summary
      pfam01391
      Location:722 → 778
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:43 → 233
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1586 → 1812
      COLFI; Fibrillar collagen C-terminal domain

    6. XM_021470210.2 → XP_021325885.2  collagen, type XI, alpha 1a isoform X4

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395181.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      102740..223561 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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