Col18a1 collagen type XVIII alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col18a1provided by RGD
Official Full Name: collagen type XVIII alpha 1 chainprovided by RGD
Primary source: RGD:70936
See related: Ensembl:ENSRNOG00000001229 AllianceGenome:RGD:70936
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable identical protein binding activity. Predicted to be an extracellular matrix structural constituent. Involved in response to hydrostatic pressure and response to xenobiotic stimulus. Located in extracellular space. Used to study hepatocellular carcinoma. Biomarker of gastric ulcer and ulcerative colitis. Human ortholog(s) of this gene implicated in primary angle-closure glaucoma. Orthologous to human COL18A1 (collagen type XVIII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 645.8), Kidney (RPKM 341.4) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 20p12

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (11473645..11582111)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (11474104..11582593)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (12225202..12332858)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Specific collagen XVIII isoforms promote adipose tissue accrual via mechanisms determining
Title: Specific collagen XVIII isoforms promote adipose tissue accrual via mechanisms determining adipocyte number and affect fat deposition.
Reduced VEGF and increased endostatin result in the impaired angiogenesis and delayed injury healing in gastric mucosa of aging rats.
Title: An imbalance between VEGF and endostatin underlies impaired angiogenesis in gastric mucosa of aging rats.
Endogenous endostatin/collagen XVIII may suppress aberrant left ventricular remodeling and heart failure after myocardial infarction.
Title: Inhibition of endostatin/collagen XVIII deteriorates left ventricular remodeling and heart failure in rat myocardial infarction model.
Late increase in endostatin/collagen XVIII(+) microglia/macrophages and increased endostatin/collagen XVIII(+) subendothelial cells/vessels in areas of vascular remodeling. Role in termination of transient angiogenesis, linked to late inflammation.
Title: Lesional expression of the endogenous angiogenesis inhibitor endostatin/collagen XVIII following traumatic brain injury (TBI).
Expression of endostatin/collagen XVIII by macrophages in a "late" activated phagocytic mode suggests that this factor plays a role in counteracting the preceding "early" neoangiogenic response after spinal cord injury.
Title: Spinal cord injury-induced expression of the antiangiogenic endostatin/collagen XVIII in areas of vascular remodelling.
analysis of the correlation between the existence of disulfide bonds and the fibril formation of endostatin
Title: Deficiency of disulfide bonds facilitating fibrillogenesis of endostatin.
Spatial and temporal expression of endostatin/collagen XVIII in cartilaginous tissue and its inactivation of VEGF signalling suggests that it is important for development and maintenance of avascular zones in cartilage and fibrocartilage.
Title: Endostatin/collagen XVIII--an inhibitor of angiogenesis--is expressed in cartilage and fibrocartilage.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D20Rat3 (e-PCR)
- UniSTS:119361

RH135187 (e-PCR)
- UniSTS:218464

RH80498 (e-PCR)
- UniSTS:86200

RH137498 (e-PCR)
- UniSTS:219586

RH129672 (e-PCR)
- UniSTS:212969

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endothelial cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
involved_in notochord development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of vascular endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to hydrostatic pressure	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of vascular endothelial cell proliferation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type XVIII trimer	TAS Traceable Author Statement more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(XVIII) chain

Names: collagen, type XVIII, alpha 1; procollagen, type XVIII, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

NM_053489.2 → NP_445941.2 collagen alpha-1(XVIII) chain precursor

See identical proteins and their annotated locations for NP_445941.2

Status: PROVISIONAL

Source sequence(s)

CH473988

UniProtKB/TrEMBL

A0A8I5ZV54, A6JK98, F1LR02

Related

ENSRNOP00000047962.4, ENSRNOT00000045315.5

Conserved Domains (3) summary

pfam01391
Location:605 → 659

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:33 → 221

TSPN; Thrombospondin N-terminal -like domains

cd00247
Location:1135 → 1304

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; ...