Col18a1 collagen, type XVIII, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col18a1provided by MGI
Official Full Name: collagen, type XVIII, alpha 1provided by MGI
Primary source: MGI:MGI:88451
See related: Ensembl:ENSMUSG00000001435 AllianceGenome:MGI:88451
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable identical protein binding activity. Predicted to be an extracellular matrix structural constituent. Acts upstream of or within several processes, including angiogenesis; endothelial cell morphogenesis; and positive regulation of endothelial cell apoptotic process. Located in basement membrane. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Used to study pigment dispersion syndrome. 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: Broad expression in liver adult (RPKM 128.4), liver E18 (RPKM 40.0) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 39.72 cM

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (76888013..77002351, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (77052178..77166530, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Microvascular damage, neuroinflammation and extracellular matrix remodeling in Col18a1 knockout mice as a model for early cerebral small vessel disease.
Title: Microvascular damage, neuroinflammation and extracellular matrix remodeling in Col18a1 knockout mice as a model for early cerebral small vessel disease.
Lack of collagen XVIII leads to lipodystrophy and perturbs hepatic glucose and lipid homeostasis.
Title: Lack of collagen XVIII leads to lipodystrophy and perturbs hepatic glucose and lipid homeostasis.
Collagen XVIII plays a role in the formation of the dermal-epidermal junction during re-epithelialization.
Title: Collagen XVIII Deposition in the Basement Membrane Zone beneath the Newly Forming Epidermis during Wound Healing in Mice.
This study examined the staining levels of proteasomal and autophagy markers in the RPE of different ages of the Col18a1 (-/-) mice. Eyes from 3, 6-7, 10-13 and 18 months old mice were enucleated and embedded in paraffin according to the routine protocol.
Title: Absence of collagen XVIII in mice causes age-related insufficiency in retinal pigment epithelium proteostasis.
Kidney fibrosis in aging may represent a natural outcome of upregulated endostatin (EST) and transglutaminase 2 (TG2), but more likely it appears to be a result of cumulative stresses occurring on the background of synergistically acting geronic (aging) proteins, EST and TG2.
Title: Endostatin and transglutaminase 2 are involved in fibrosis of the aging kidney.
Basement membrane zone collagens XV and XVIII mediate leukocyte influx in renal ischemia-reperfusion.
Title: Basement membrane zone collagens XV and XVIII/proteoglycans mediate leukocyte influx in renal ischemia/reperfusion.
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.
There are correlations between the elevation of endostatin levels and parallel microvascular rarefaction and induction of renal fibrosis in aging mice.
Title: Endostatin and kidney fibrosis in aging: a case for antagonistic pleiotropy?
An excess of the collagen XVIII Tsp-1 domain is deleterious in the eye, possibly by impairing certain functions of the full-length molecule.
Title: Collagen XVIII short isoform is critical for retinal vascularization, and overexpression of the Tsp-1 domain affects eye growth and cataract formation.
The results of the present study indicate endostatin promotes soft callus formation but inhibits callus remodeling during fracture healing most probably by an inhibition of angiogenesis.
Title: Endostatin inhibits Callus remodeling during fracture healing in mice.

Submit: New GeneRIF Correction See all GeneRIFs (44)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Col18a1 (e-PCR), detects polymorphism
- UniSTS:141368

PMC125362P1 (e-PCR)
- UniSTS:270495

Col18a1 (e-PCR), detects polymorphism
- UniSTS:532421

Col18a1 (e-PCR), detects polymorphism
- UniSTS:259058

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within angiogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of blood vessel endothelial cell migration	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of endothelial cell apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in endothelial cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endothelial cell morphogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within extracellular matrix organization	IMP Inferred from Mutant Phenotype more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of endothelial cell apoptotic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of vascular endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of vascular endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed

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

General protein information

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Preferred Names: collagen alpha-1(XVIII) chain

Names: alpha-1(XVIII) collagen; endostatin; procollagen, type XVIII, alpha 1

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)

NM_001109991.2 → NP_001103461.1 collagen alpha-1(XVIII) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_001103461.1

Status: VALIDATED

Source sequence(s)

AC055777, AC159334

Consensus CDS

CCDS48604.1

UniProtKB/Swiss-Prot

P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63

Related

ENSMUSP00000101049.2, ENSMUST00000105409.8

Conserved Domains (4) summary

pfam01391
Location:822 → 881

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:245 → 433

TSPN; Thrombospondin N-terminal -like domains

cd00247
Location:1350 → 1520

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:22 → 218

DUF959; Domain of Unknown Function (DUF959)
NM_001406250.1 → NP_001393179.1 collagen alpha-1(XVIII) chain isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_001406251.1 → NP_001393180.1 collagen alpha-1(XVIII) chain isoform 4 precursor

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_001406252.1 → NP_001393181.1 collagen alpha-1(XVIII) chain isoform 5

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_001406253.1 → NP_001393182.1 collagen alpha-1(XVIII) chain isoform 5

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_001406254.1 → NP_001393183.1 collagen alpha-1(XVIII) chain isoform 5

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_001406255.1 → NP_001393184.1 collagen alpha-1(XVIII) chain isoform 6

Status: VALIDATED

Source sequence(s)

AC055777, AC159334
NM_009929.4 → NP_034059.2 collagen alpha-1(XVIII) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_034059.2

Status: VALIDATED

Source sequence(s)

AC055777, AC159334

Consensus CDS

CCDS23953.1

UniProtKB/Swiss-Prot

P39061

Related

ENSMUSP00000080358.7, ENSMUST00000081654.13

Conserved Domains (3) summary

pfam01391
Location:610 → 669

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:33 → 221

TSPN; Thrombospondin N-terminal -like domains

cd00247
Location:1138 → 1308

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; ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

76888013..77002351 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006513174.4 → XP_006513237.1 collagen alpha-1(XVIII) chain isoform X2

UniProtKB/Swiss-Prot

P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63

Conserved Domains (5) summary

cd07455
Location:366 → 488

CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )

pfam01391
Location:1069 → 1128

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:492 → 680

TSPN; Thrombospondin N-terminal -like domains

pfam06121
Location:37 → 218

DUF959; Domain of Unknown Function (DUF959)

pfam06482
Location:1462 → 1764

Endostatin; Collagenase NC10 and Endostatin
XM_006513173.5 → XP_006513236.1 collagen alpha-1(XVIII) chain isoform X1

UniProtKB/Swiss-Prot

P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63

UniProtKB/TrEMBL

E9QPX1

Related

ENSMUSP00000072538.5, ENSMUST00000072755.12

Conserved Domains (5) summary

cd07455
Location:366 → 488

CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )

pfam01391
Location:1069 → 1128

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:492 → 680

TSPN; Thrombospondin N-terminal -like domains

pfam06121
Location:37 → 218

DUF959; Domain of Unknown Function (DUF959)

pfam06482
Location:1463 → 1765

Endostatin; Collagenase NC10 and Endostatin
XM_006513176.4 → XP_006513239.1 collagen alpha-1(XVIII) chain isoform X6

UniProtKB/Swiss-Prot

P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63

Conserved Domains (4) summary

pfam01391
Location:822 → 881

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:245 → 433

TSPN; Thrombospondin N-terminal -like domains

pfam06121
Location:37 → 218

DUF959; Domain of Unknown Function (DUF959)

pfam06482
Location:1215 → 1517

Endostatin; Collagenase NC10 and Endostatin
XM_011243347.4 → XP_011241649.1 collagen alpha-1(XVIII) chain isoform X5

Conserved Domains (4) summary

cd07455
Location:366 → 488

CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )

pfam01391
Location:840 → 875

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:492 → 680

TSPN; Thrombospondin N-terminal -like domains

pfam06121
Location:37 → 218

DUF959; Domain of Unknown Function (DUF959)