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col2a1a collagen, type II, alpha 1a [ Oryzias latipes (Japanese medaka) ]

Gene ID: 100529192, updated on 8-Mar-2024

Summary

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Gene symbol
col2a1a
Gene description
collagen, type II, alpha 1a
See related
EnsemblRapid:ENSORLG00000012738
Gene type
protein coding
RefSeq status
MODEL
Organism
Oryzias latipes
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Ovalentaria; Atherinomorphae; Beloniformes; Adrianichthyidae; Oryziinae; Oryzias
Also known as
col2a1b
Orthologs
zebrafish all
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Genomic context

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See col2a1a in Genome Data Viewer
Location:
chromosome: 7
Exon count:
54
Annotation release Status Assembly Chr Location
103 current ASM223467v1 (GCF_002234675.1) 7 NC_019865.2 (19314881..19336215)
102 previous assembly ASM31367v1 (GCF_000313675.1) 7 NC_019865.1 (19558349..19579315)

Chromosome 7 - NC_019865.2Genomic Context describing neighboring genes Neighboring gene acid-sensing ion channel 1 Neighboring gene glutaminase kidney isoform, mitochondrial Neighboring gene SPRY domain containing 4 Neighboring gene achalasia, adrenocortical insufficiency, alacrimia Neighboring gene mitogen-activated protein kinase kinase kinase 12

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Molecular cloning and expression of the col2a1a and col2a1b genes in the medaka, Oryzias latipes. Matsumoto T, et al. Gene Expr Patterns, 2012 Jan-Feb. PMID 22123453
  2. sec24d encoding a component of COPII is essential for vertebra formation, revealed by the analysis of the medaka mutant, vbi. Ohisa S, et al. Dev Biol, 2010 Jun 1. PMID 20346938
  3. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables protein binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type II trimer IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
collagen alpha-1(II) chain
Names
Type II collagen B

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Oryzias latipes Annotation Release 103 details...Open this link in a new tab

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

Reference ASM223467v1 Primary Assembly

Genomic

  1. NC_019865.2 Reference ASM223467v1 Primary Assembly

    Range
    19314881..19336215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_023957127.1 → XP_023812895.1  collagen alpha-1(II) chain isoform X1

    UniProtKB/TrEMBL
    H2MBQ6
    Related
    ENSORLP00000015981.3, ENSORLT00000015982.3
    Conserved Domains (5) summary
    pfam01391
    Location:839 → 897
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00093
    Location:36 → 91
    VWC; von Willebrand factor type C domain
    pfam01410
    Location:1256 → 1488
    COLFI; Fibrillar collagen C-terminal domain
    cl26386
    Location:814 → 1012
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
    cl28310
    Location:581 → 788
    Rho; Transcription termination factor Rho [Transcription]

  2. XM_023957128.1 → XP_023812896.1  collagen alpha-1(II) chain isoform X2

    UniProtKB/TrEMBL
    A0A3B3ICN5
    Related
    ENSORLP00000041829.1, ENSORLT00000035728.2
    Conserved Domains (4) summary
    pfam01391
    Location:770 → 828
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:1187 → 1419
    COLFI; Fibrillar collagen C-terminal domain
    cl26386
    Location:745 → 943
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
    cl28310
    Location:512 → 719
    Rho; Transcription termination factor Rho [Transcription]
Nucleotide Protein
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