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

Gene ID: 564123, updated on 2-Nov-2024

Summary

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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 conferring tensile strength. Acts upstream of or within neural crest cell migration. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing 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, Nov 2024]
Orthologs
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Genomic context

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See col18a1a in Genome Data Viewer
Location:
chromosome: 9
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (41821613..41979505)
105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (42112672..42176372)

Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene si:dkeyp-30e7.2 Neighboring gene uncharacterized LOC137496416 Neighboring gene poly(rC) binding protein 3 Neighboring gene leucine rich repeat containing 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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Related articles in PubMed

  1. Sequence and embryonic expression of collagen XVIII NC1 domain (endostatin) in the zebrafish. Haftek Z, et al. Gene Expr Patterns, 2003 Jun. PMID 12799084
  2. The myotomal diwanka (lh3) glycosyltransferase and type XVIII collagen are critical for motor growth cone migration. Schneider VA, et al. Neuron, 2006 Jun 1. PMID 16731508
  3. A novel role for Lh3 dependent ECM modifications during neural crest cell migration in zebrafish. Banerjee S, et al. PLoS One, 2013. PMID 23349938, Free PMC Article
  4. Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis. Kague E, et al. Dev Biol, 2010 Jan 15. PMID 19895802
  5. The lh3 Glycosyltransferase Directs Target-Selective Peripheral Nerve Regeneration. Isaacman-Beck J, et al. Neuron, 2015 Nov 18. PMID 26549330, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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

Homology

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
  
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
Names
collagen type XVIII, alpha 1
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)

  1. 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: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007120.7 Reference GRCz11 Primary Assembly

    Range
    41821613..41979505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021478722.2 → XP_021334397.1  collagen type XVIII alpha 1 chain a 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 ...

  2. XM_068223431.1 → XP_068079532.1  collagen type XVIII alpha 1 chain a isoform X4

  3. XM_021478720.2 → XP_021334395.1  collagen type XVIII alpha 1 chain a 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 ...

  4. XM_068223430.1 → XP_068079531.1  collagen type XVIII alpha 1 chain a isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.
Nucleotide Protein Strain
Heading Accession and Version

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