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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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