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COL18A1 collagen type XVIII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 80781, updated on 29-May-2016
Official Symbol
COL18A1provided by HGNC
Official Full Name
collagen type XVIII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2195
See related
Ensembl:ENSG00000182871 HPRD:00382; MIM:120328; Vega:OTTHUMG00000090407
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
KS; KNO; KNO1
Summary
This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Orthologs
Location:
21q22.3
Exon count:
43
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 21 NC_000021.9 (45405137..45513720)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46825058..46933634)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372839 Neighboring gene uncharacterized LOC101928745 Neighboring gene MT-CO1 pseudogene 3 Neighboring gene COL18A1 antisense RNA 2 Neighboring gene COL18A1 antisense RNA 1 Neighboring gene microRNA 6815 Neighboring gene solute carrier family 19 member 1 Neighboring gene uncharacterized LOC105372840 Neighboring gene uncharacterized LOC100129027

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Knobloch syndrome 1
MedGen: C1849409 OMIM: 267750 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
Multiple loci influencing hippocampal degeneration identified by genome scan.
NHGRI GWA Catalog
  • Activation of Matrix Metalloproteinases, organism-specific biosystem (from REACTOME)
    Activation of Matrix Metalloproteinases, organism-specific biosystemThe matrix metalloproteinases (MMPs), previously known as matrixins, are classically known to be involved in the turnover of extracellular matrix (ECM) components. However, recent high throughput pro...
  • 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...
  • 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 degradation, organism-specific biosystem (from REACTOME)
    Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
  • 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...
  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • 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...
  • FOXA1 transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    FOXA1 transcription factor network, organism-specific biosystem
    FOXA1 transcription factor network
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • Laminin interactions, organism-specific biosystem (from REACTOME)
    Laminin interactions, organism-specific biosystemLaminins are a large family of conserved, multidomain trimeric basement membrane proteins. There are many theoretical trimer combinations but only 18 have been described (Domogatskaya et al. 2012, Mi...
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ27325, FLJ34914, MGC74745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
collagen catabolic process TAS
Traceable Author Statement
more info
 
endothelial cell morphogenesis IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
negative regulation of cell proliferation TAS
Traceable Author Statement
more info
PubMed 
organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
positive regulation of cell migration IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of endothelial cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to hydrostatic pressure IEA
Inferred from Electronic Annotation
more info
 
visual perception TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
more info
 
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with extracellular matrix TAS
Traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
collagen alpha-1(XVIII) chain
Names
antiangiogenic agent
collagen, type XVIII, alpha 1
endostatin
multi-functional protein MFP

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_011903.1 RefSeqGene

    Range
    5001..113529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_030582.3NP_085059.2  collagen alpha-1(XVIII) chain isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_085059.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as NCI-493) uses an alternate splice donor in the 5' terminal exon compared to variant 3. The encoded isoform (1) is shorter than isoform 3.
    Source sequence(s)
    AF018082, BC063833, BX322561
    Consensus CDS
    CCDS42972.1
    UniProtKB/Swiss-Prot
    P39060
    UniProtKB/TrEMBL
    D3DSM5
    Related
    ENSP00000347665, OTTHUMP00000115472, ENST00000355480, OTTHUMT00000206827
    Conserved Domains (5) summary
    pfam01391
    Location:822872
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:221409
    TSPN; Thrombospondin N-terminal -like domains
    cd00247
    Location:13401510
    Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
    pfam06121
    Location:22195
    DUF959; Domain of Unknown Function (DUF959)
    pfam06482
    Location:12021516
    Endostatin; Collagenase NC10 and Endostatin
  2. NM_130444.2NP_569711.2  collagen alpha-1(XVIII) chain isoform 3 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as NCI-728) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AF018082, BC063833, BX322561
    Consensus CDS
    CCDS77643.1
    UniProtKB/Swiss-Prot
    P39060
    Related
    ENSP00000352798, ENST00000359759
    Conserved Domains (6) summary
    cd07455
    Location:330452
    CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )
    pfam01391
    Location:10571107
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:456644
    TSPN; Thrombospondin N-terminal -like domains
    cd00247
    Location:15751745
    Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
    pfam06121
    Location:22195
    DUF959; Domain of Unknown Function (DUF959)
    pfam06482
    Location:14371751
    Endostatin; Collagenase NC10 and Endostatin
  3. NM_130445.3NP_569712.2  collagen alpha-1(XVIII) chain isoform 2 preproprotein

    See identical proteins and their annotated locations for NP_569712.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as NCI-303) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon compared to variant 3. The encoded isoform (2) has a distinct and shorter N-terminus compared to isoform 3.
    Source sequence(s)
    AF018082, BC063833, CN389577
    Consensus CDS
    CCDS42971.1
    UniProtKB/Swiss-Prot
    P39060
    UniProtKB/TrEMBL
    D3DSM4
    Related
    ENSP00000383191, OTTHUMP00000115473, ENST00000400337, OTTHUMT00000206828
    Conserved Domains (4) summary
    pfam01391
    Location:642692
    Collagen; Collagen triple helix repeat (20 copies)
    cd00247
    Location:11601330
    Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
    pfam06482
    Location:10221336
    Endostatin; Collagenase NC10 and Endostatin
    cl22861
    Location:41229
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p2 Primary Assembly

    Range
    45405137..45513720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018932.2 Alternate CHM1_1.1

    Range
    46385890..46494464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)