col18a1a collagen type XVIII alpha 1 chain a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col18a1aprovided by ZNC
Official Full Name: collagen type XVIII alpha 1 chain aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030516-3
See related: Ensembl:ENSDARG00000036558 AllianceGenome:ZFIN:ZDB-GENE-030516-3
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb371; cb529; col18a1; fc96d06; sb:cb529; wu:fb47h10; wu:fb77g12; wu:fc50f04; wu:fc96d06; wu:fk02h12
Summary: Predicted to be an extracellular matrix structural constituent. Acts upstream of or within neural crest cell migration. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Is expressed in several structures, including anterior neural keel; digestive system; nervous system; neural plate; and pronephros. 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]
Orthologs: all
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Genomic context

Location:: chromosome: 9

Exon count:: 43

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (41821555..41979505)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (42112672..42176372)

Chromosome 9 - NC_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Together these data suggest that Lh3-Collagen18A1 dependent ECM modifications regulate the transition of trunk neural crest cells from a non-segmental sheet like migration mode to a segmental stream migration mode
Title: A novel role for Lh3 dependent ECM modifications during neural crest cell migration in zebrafish.
These results provide important insight into the biological function and regulation of COL18A1, and point to additional sequences that may contribute to complex diseases involving COL18A1.
Title: Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis.
diwanka (lh3) acts through myotomal type XVIII collagen, a ligand for neural-receptor protein tyrosine phosphatases that guide motor axons
Title: The myotomal diwanka (lh3) glycosyltransferase and type XVIII collagen are critical for motor growth cone migration.

Submit: New GeneRIF Correction

General gene information

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Markers

AI546073 (e-PCR)
- UniSTS:206266

AI545791 (e-PCR)
- UniSTS:206279

fb47h10.x1 (e-PCR)
- UniSTS:203227

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
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
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen type XVIII alpha 1 chain a; collagen type XVIII, alpha 1

Names: endostatin

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_001349195.1 → NP_001336124.1 collagen type XVIII alpha 1 chain a precursor

Status: VALIDATED

Source sequence(s)

BX927363, CT030212

UniProtKB/TrEMBL

B0S8G5

Related

ENSDARP00000002450.9, ENSDART00000007058.10

Conserved Domains (3) summary

pfam01391
Location:675 → 718

Collagen; Collagen triple helix repeat (20 copies)

pfam06482
Location:1209 → 1377

Endostatin; Collagenase NC10 and Endostatin

cl22861
Location:65 → 254

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: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007120.7 Reference GRCz11 Primary Assembly

Range

41821555..41979505

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021478722.1 → XP_021334397.1 collagen type XVIII, alpha 1 isoform X3

UniProtKB/TrEMBL

A0A8M9PS88

Related

ENSDARP00000088066.4, ENSDART00000097295.6

Conserved Domains (3) summary

pfam01391
Location:641 → 684

Collagen; Collagen triple helix repeat (20 copies)

pfam06482
Location:1175 → 1343

Endostatin; Collagenase NC10 and Endostatin

cl22861
Location:31 → 220

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 ...
XM_021478720.1 → XP_021334395.1 collagen type XVIII, alpha 1 isoform X1

UniProtKB/TrEMBL

A0A8M9QJR2

Related

ENSDARP00000108133.2, ENSDART00000130434.4

Conserved Domains (4) summary

cd07455
Location:203 → 340

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

pfam01391
Location:937 → 980

Collagen; Collagen triple helix repeat (20 copies)

pfam06482
Location:1471 → 1639

Endostatin; Collagenase NC10 and Endostatin

cl22861
Location:327 → 516

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 ...
XM_021478721.1 → XP_021334396.1 collagen type XVIII, alpha 1 isoform X2

UniProtKB/TrEMBL

A0A8M9QFI3

Conserved Domains (4) summary

cd07455
Location:6 → 143

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

pfam01391
Location:729 → 772

Collagen; Collagen triple helix repeat (20 copies)

pfam06482
Location:1263 → 1431

Endostatin; Collagenase NC10 and Endostatin

cl22861
Location:130 → 319

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 ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001039630.1: Suppressed sequence

Description

NM_001039630.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.