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col2a1 collagen, type II, alpha 1 [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 394828, updated on 5-Jul-2025
Official Symbol
col2a1provided by Xenbase
Official Full Name
collagen, type II, alpha 1provided by Xenbase
Primary source
Xenbase:XB-GENE-6258353
See related
Ensembl:ENSXETG00000010655 AllianceGenome:Xenbase:XB-GENE-6258353
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Xenopus tropicalis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
Also known as
col11a3; xcol2a1; col2a1-a; col2a1-b
Summary
Predicted to enable metal ion binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Is expressed in appendage; cardiovascular system; and musculoskeletal system. Human ortholog(s) of this gene implicated in Stickler syndrome (multiple); bone disease (multiple); cleft palate; eye disease (multiple); and multiple epiphyseal dysplasia with myopia and deafness. Orthologous to human COL2A1 (collagen type II alpha 1 chain). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs
human mouse all
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See col2a1 in Genome Data Viewer
Location:
chromosome: 2
Exon count:
54
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 2 NC_030678.2 (143714087..143762160)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 2 NC_030678.1 (140468231..140516271)

Chromosome 2 - NC_030678.2Genomic Context describing neighboring genes Neighboring gene E3 ubiquitin-protein ligase TRIM39 Neighboring gene general transcription factor IIH subunit 4 Neighboring gene transmembrane protein 106C Neighboring gene vitamin D receptor

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Klein SL, et al. Dev Dyn, 2002 Dec. PMID 12454917
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Homology

Gene Ontology Provided by Xenbase

Function Evidence Code Pubs
enables extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
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
  
Preferred Names
collagen alpha-1(II) chain
Names
X-col II
alpha-1 type II collagen

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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_203889.1 → NP_989220.1  collagen alpha-1(II) chain precursor

    See identical proteins and their annotated locations for NP_989220.1

    Status: PROVISIONAL

    Source sequence(s)
    BC063191
    UniProtKB/Swiss-Prot
    Q6P4Z2
    Related
    ENSXETP00000043834.4, ENSXETT00000043834.4
    Conserved Domains (5) summary
    pfam01391
    Location:497 → 556
    Collagen; Collagen triple helix repeat (20 copies)
    smart00214
    Location:38 → 93
    VWC; von Willebrand factor (vWF) type C domain
    PRK07764
    Location:816 → 1057
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam09606
    Location:393 → 785
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam01410
    Location:1256 → 1491
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Xenopus tropicalis Annotation Release 104 details...Open this link in a new tab

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

Reference UCB_Xtro_10.0 Primary Assembly

Genomic

  1. NC_030678.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    143714087..143762160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_012956661.3 → XP_012812115.1  collagen alpha-1(II) chain isoform X1

    UniProtKB/TrEMBL
    A0A8J0SEY3
    Conserved Domains (3) summary
    pfam01391
    Location:497 → 556
    Collagen; Collagen triple helix repeat (20 copies)
    smart00214
    Location:38 → 93
    VWC; von Willebrand factor (vWF) type C domain
    pfam01410
    Location:1205 → 1437
    COLFI; Fibrillar collagen C-terminal domain

  2. XM_012956663.3 → XP_012812117.1  collagen alpha-1(II) chain isoform X2

    UniProtKB/TrEMBL
    F7B315
    Related
    ENSXETP00000023334.3, ENSXETT00000023334.4
    Conserved Domains (2) summary
    pfam01391
    Location:427 → 486
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:1189 → 1421
    COLFI; Fibrillar collagen C-terminal domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P4Z2.1 GenPept UniProtKB/Swiss-Prot:Q6P4Z2

Gene LinkOut

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