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

Gene ID: 85251, updated on 22-Aug-2021

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
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
intermediate filament protein; a precursor of the angiogenesis inhibitor endostatin [RGD, Feb 2006]
Expression
Biased expression in Liver (RPKM 645.8), Kidney (RPKM 341.4) and 9 other tissues See more
Orthologs
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Genomic context

See Col18a1 in Genome Data Viewer
Location:
20p12
Exon count:
41
Annotation release Status Assembly Chr Location
108 current 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_051355.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120098894 Neighboring gene transfer RNA threonine (anticodon AGU) Neighboring gene uncharacterized LOC120098958 Neighboring gene peptidyl-prolyl cis-trans isomerase NIMA-interacting 4-like Neighboring gene solute carrier family 19 member 1 Neighboring gene uncharacterized LOC100912209

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
more info
 
Component Evidence Code Pubs
located_in basement membrane ISO
Inferred from Sequence Orthology
more info
 
part_of collagen type XVIII trimer TAS
Traceable Author Statement
more info
PubMed 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(XVIII) chain
Names
collagen, type XVIII, alpha 1
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)

  1. NM_053489.2NP_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
    F1LR02
    Related
    ENSRNOP00000047962.4, ENSRNOT00000045315.4
    Conserved Domains (3) summary
    pfam01391
    Location:605659
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:33221
    TSPN; Thrombospondin N-terminal -like domains
    cd00247
    Location:11351304
    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: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051355.1 Reference mRatBN7.2 Primary Assembly

    Range
    11474104..11582593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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