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col3a1 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 100124865, updated on 7-Apr-2025

Summary

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Official Symbol
col3a1provided by Xenbase
Official Full Name
collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)provided by Xenbase
Primary source
Xenbase:XB-GENE-5864292
See related
Ensembl:ENSXETG00000010783 AllianceGenome:Xenbase:XB-GENE-5864292
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
Summary
Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. 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 dermal system. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome; Ehlers-Danlos syndrome hypermobility type; end stage renal disease; and vascular type Ehlers-Danlos syndrome. Orthologous to human COL3A1 (collagen type III alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2025]
Orthologs
human mouse all
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Genomic context

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See col3a1 in Genome Data Viewer
Location:
chromosome: 9
Exon count:
51
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 9 NC_030685.2 (48129571..48189114, complement)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 9 NC_030685.1 (39803845..39864240, complement)

Chromosome 9 - NC_030685.2Genomic Context describing neighboring genes Neighboring gene tumorhead Neighboring gene collagen, type V, alpha 2 Neighboring gene GULP PTB domain containing engulfment adaptor 1 Neighboring gene keratin-associated protein 10-2-like Neighboring gene cilia and flagella associated protein 410

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. 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

General gene information

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Homology

Gene Ontology Provided by Xenbase

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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
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-1(III) chain

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_001142907.1 → NP_001136379.1  collagen alpha-1(III) chain precursor

    See identical proteins and their annotated locations for NP_001136379.1

    Status: PROVISIONAL

    Source sequence(s)
    BC168784
    UniProtKB/TrEMBL
    B5DES3
    Related
    ENSXETP00000116358.1, ENSXETT00000122572.1
    Conserved Domains (4) summary
    pfam01391
    Location:402 → 460
    Collagen; Collagen triple helix repeat (20 copies)
    PRK07764
    Location:942 → 1151
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam00093
    Location:34 → 90
    VWC; von Willebrand factor type C domain
    pfam01410
    Location:1235 → 1467
    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_030685.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    48129571..48189114 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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