Format

Send to:

Choose Destination

COL7A1 collagen type VII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1294, updated on 12-May-2019

Summary

Official Symbol
COL7A1provided by HGNC
Official Full Name
collagen type VII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2214
See related
Ensembl:ENSG00000114270 MIM:120120
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
EBD1; EBR1; EBDCT; NDNC8
Summary
This gene encodes the alpha chain of type VII collagen. The type VII collagen fibril, composed of three identical alpha collagen chains, is restricted to the basement zone beneath stratified squamous epithelia. It functions as an anchoring fibril between the external epithelia and the underlying stroma. Mutations in this gene are associated with all forms of dystrophic epidermolysis bullosa. In the absence of mutations, however, an acquired form of this disease can result from an autoimmune response made to type VII collagen. [provided by RefSeq, Jul 2008]
Expression
Biased expression in skin (RPKM 63.4), endometrium (RPKM 13.0) and 5 other tissues See more
Orthologs

Genomic context

See COL7A1 in Genome Data Viewer
Location:
3p21.31
Exon count:
120
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (48564073..48595302, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48601506..48632593, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Neighboring gene microRNA 6823 Neighboring gene urocortin 2 Neighboring gene microRNA 711 Neighboring gene ubiquinol-cytochrome c reductase core protein 1 Neighboring gene small nucleolar RNA, H/ACA box 94 Neighboring gene transmembrane protein 89

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Anchoring fibril formation, organism-specific biosystem (from REACTOME)
    Anchoring fibril formation, organism-specific biosystemCollagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009, Has & Kern 2010). During fibrillogenesis, the nascent type VII ...
  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • 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...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • Cargo concentration in the ER, organism-specific biosystem (from REACTOME)
    Cargo concentration in the ER, organism-specific biosystemComputational analysis suggests that ~25% of the proteome may be exported from the ER in human cells (Kanapin et al, 2003). These cargo need to be recognized and concentrated into COPII vesicles, wh...
  • 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...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • 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...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • 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...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
ER to Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
endodermal cell differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
epidermis development TAS
Traceable Author Statement
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
growth plate cartilage chondrocyte morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
COPII-coated ER to Golgi transport vesicle TAS
Traceable Author Statement
more info
 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
basement membrane IEA
Inferred from Electronic Annotation
more info
 
collagen type VII trimer TAS
Traceable Author Statement
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with collagen-containing extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
endoplasmic reticulum-Golgi intermediate compartment membrane TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(VII) chain
Names
LC collagen
collagen VII, alpha-1 polypeptide
collagen, type VII, alpha 1
long-chain collagen

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_007065.1 RefSeqGene

    Range
    5093..36180
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_286

mRNA and Protein(s)

  1. NM_000094.3NP_000085.1  collagen alpha-1(VII) chain precursor

    See identical proteins and their annotated locations for NP_000085.1

    Status: REVIEWED

    Source sequence(s)
    AB209645, BQ300155, L02870, M65158, S51236
    Consensus CDS
    CCDS2773.1
    UniProtKB/Swiss-Prot
    Q02388
    UniProtKB/TrEMBL
    Q59F16
    Related
    ENSP00000332371.8, ENST00000328333.12
    Conserved Domains (6) summary
    pfam01391
    Location:21082166
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:687771
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00109
    Location:28742930
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01482
    Location:37201
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:233317
    fn3; Fibronectin type III domain
    pfam00092
    Location:10541227
    VWA; von Willebrand factor type A domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    48564073..48595302 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005688.1XP_016861177.1  collagen alpha-1(VII) chain isoform X2

  2. XM_011533337.1XP_011531639.1  collagen alpha-1(VII) chain isoform X1

    See identical proteins and their annotated locations for XP_011531639.1

    UniProtKB/Swiss-Prot
    Q02388
    Conserved Domains (6) summary
    pfam01391
    Location:21082166
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:687771
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00109
    Location:28742930
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01482
    Location:37201
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:233317
    fn3; Fibronectin type III domain
    pfam00092
    Location:10541227
    VWA; von Willebrand factor type A domain
  3. XM_017005689.1XP_016861178.1  collagen alpha-1(VII) chain isoform X3

  4. XM_017005692.1XP_016861181.1  collagen alpha-1(VII) chain isoform X6

  5. XM_017005691.1XP_016861180.1  collagen alpha-1(VII) chain isoform X5

  6. XM_017005690.1XP_016861179.1  collagen alpha-1(VII) chain isoform X4

RNA

  1. XR_001740005.1 RNA Sequence

  2. XR_001740004.1 RNA Sequence

  3. XR_001740003.1 RNA Sequence

  4. XR_001740006.1 RNA Sequence

  5. XR_001740007.1 RNA Sequence

  6. XR_001740008.1 RNA Sequence

  7. XR_001740009.1 RNA Sequence

Support Center