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COL3A1 collagen type III alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1281, updated on 6-Dec-2019

Summary

Official Symbol
COL3A1provided by HGNC
Official Full Name
collagen type III alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2201
See related
Ensembl:ENSG00000168542 MIM:120180
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EDS4A; EDSVASC; PMGEDSV
Summary
This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome types IV, and with aortic and arterial aneurysms. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
Expression
Biased expression in gall bladder (RPKM 1491.0), placenta (RPKM 1173.3) and 12 other tissues See more
Orthologs

Genomic context

See COL3A1 in Genome Data Viewer
Location:
2q32.2
Exon count:
51
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (188974373..189012746)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (189839099..189877472)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8257 Neighboring gene GULP PTB domain containing engulfment adaptor 1 Neighboring gene uncharacterized LOC105373790 Neighboring gene disrupted in renal carcinoma 1 Neighboring gene uncharacterized LOC105373791 Neighboring gene microRNA 1245a Neighboring gene microRNA 1245b Neighboring gene microRNA 3606 Neighboring gene collagen type V alpha 2 chain Neighboring gene microRNA 3129 Neighboring gene keratin 18 pseudogene 19

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Professional guidelines

Description
Professional guideline
ACMG 2013

The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in COL3A1 that are pathogenic or expected to be pathogenic.

GuidelinePubMed

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2017-01-12)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2017-01-12)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates the steady-state RNA levels for fibronectin and types I and III collagen in glioblastoma cells and salivary gland cell lines PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • AGE-RAGE signaling pathway in diabetic complications, conserved biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, conserved biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • Amoebiasis, organism-specific biosystem (from KEGG)
    Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Amoebiasis, conserved biosystem (from KEGG)
    Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
  • Binding and Uptake of Ligands by Scavenger Receptors, organism-specific biosystem (from REACTOME)
    Binding and Uptake of Ligands by Scavenger Receptors, organism-specific biosystemScavenger receptors bind free extracellular ligands as the initial step in clearance of the ligands from the body (reviewed in Ascenzi et al. 2005, Areschoug and Gordon 2009, Nielsen et al. 2010). So...
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Endothelins, organism-specific biosystem (from Pathway Interaction Database)
    Endothelins, organism-specific biosystem
    Endothelins
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Inflammatory Response Pathway, organism-specific biosystem (from WikiPathways)
    Inflammatory Response Pathway, organism-specific biosystem
    Inflammatory Response Pathway
  • Platelet activation, organism-specific biosystem (from KEGG)
    Platelet activation, organism-specific biosystemPlatelets play a key and beneficial role for primary hemostasis on the disruption of the integrity of vessel wall. Platelet adhesion and activation at sites of vascular wall injury is initiated by ad...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Scavenging by Class A Receptors, organism-specific biosystem (from REACTOME)
    Scavenging by Class A Receptors, organism-specific biosystemClass A scavenger receptors contain an intracellular domain, a transmembrane region, a coiled-coil domain, a collagenous domain, and the SR cysteine-rich domain (reviewed in Areschoug and Gordon 2009...
  • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
    Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
    miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34534

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SMAD binding IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent IMP
Inferred from Mutant Phenotype
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength HDA PubMed 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
integrin binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
integrin binding NAS
Non-traceable Author Statement
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor binding IDA
Inferred from Direct Assay
more info
PubMed 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
aorta smooth muscle tissue morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cell-matrix adhesion IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
cerebral cortex development ISS
Inferred from Sequence or Structural Similarity
more info
 
collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization NAS
Non-traceable Author Statement
more info
PubMed 
digestive tract development IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
integrin-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
 
peptide cross-linking IDA
Inferred from Direct Assay
more info
PubMed 
platelet activation NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of Rho protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of immune response TAS
Traceable Author Statement
more info
 
response to cytokine IDA
Inferred from Direct Assay
more info
PubMed 
response to mechanical stimulus IEA
Inferred from Electronic Annotation
more info
 
response to radiation IDA
Inferred from Direct Assay
more info
PubMed 
skeletal system development IEA
Inferred from Electronic Annotation
more info
 
skin development IMP
Inferred from Mutant Phenotype
more info
PubMed 
supramolecular fiber organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
transforming growth factor beta receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
wound healing IDA
Inferred from Direct Assay
more info
PubMed 
wound healing NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
collagen type III trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type III trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen type III trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen type III trimer NAS
Non-traceable Author Statement
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
collagen-containing extracellular matrix IMP
Inferred from Mutant Phenotype
more info
PubMed 
colocalizes_with collagen-containing extracellular matrix TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(III) chain
Names
Ehlers-Danlos syndrome type IV, autosomal dominant
alpha-1 type III collagen
alpha1 (III) collagen
collagen, fetal
collagen, type III, alpha 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_007404.1 RefSeqGene

    Range
    5001..43374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_3

mRNA and Protein(s)

  1. NM_000090.4NP_000081.2  collagen alpha-1(III) chain preproprotein

    Status: REVIEWED

    Source sequence(s)
    AC066694
    Consensus CDS
    CCDS2297.1
    Related
    ENSP00000304408.3, ENST00000304636.7

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    188974373..189012746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001376916.1: Suppressed sequence

    Description
    NM_001376916.1: This RefSeq is removed as it is redundant with another RefSeq.
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