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Col5a2 collagen type V alpha 2 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 85250, updated on 6-May-2021

Summary

Official Symbol
Col5a2provided by RGD
Official Full Name
collagen type V alpha 2 chainprovided by RGD
Primary source
RGD:70921
See related
Ensembl:ENSRNOG00000003736
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
alpha chain of type V collagen; has a role in bone growth [RGD, Feb 2006]
Expression
Biased expression in Lung (RPKM 592.9), Uterus (RPKM 552.6) and 9 other tissues See more
Orthologs
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Genomic context

See Col5a2 in Genome Data Viewer
Location:
9q22
Exon count:
55
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (47448736..47598396, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (52091088..52238735, complement)

Chromosome 9 - NC_051344.1Genomic Context describing neighboring genes Neighboring gene similar to ribosomal protein S3 Neighboring gene collagen type III alpha 1 chain Neighboring gene U2 spliceosomal RNA Neighboring gene similar to Ctps protein Neighboring gene WD repeat domain 75

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables SMAD binding ISO
Inferred from Sequence Orthology
more info
 
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix structural constituent TAS
Traceable Author Statement
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to amino acid stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in collagen fibril organization ISO
Inferred from Sequence Orthology
more info
 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in eye morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of endodermal cell differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in ossification IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within skeletal system development ISO
Inferred from Sequence Orthology
more info
 
involved_in skin development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in skin development ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of collagen trimer ISO
Inferred from Sequence Orthology
more info
 
part_of collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen type V trimer ISO
Inferred from Sequence Orthology
more info
 
part_of collagen type V 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 

General protein information

Preferred Names
collagen alpha-2(V) chain
Names
collagen, type V, alpha 2
procollagen, type V, alpha 2

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_053488.1NP_445940.1  collagen alpha-2(V) chain precursor

    Status: VALIDATED

    Source sequence(s)
    EV773139, FQ222447, JACYVU010000214
    Related
    ENSRNOP00000005073.7, ENSRNOT00000005073.7
    Conserved Domains (3) summary
    pfam01391
    Location:493551
    Collagen; Collagen triple helix repeat (20 copies)
    smart00214
    Location:4095
    VWC; von Willebrand factor (vWF) type C domain
    pfam01410
    Location:12651496
    COLFI; Fibrillar collagen C-terminal domain

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_051344.1 Reference mRatBN7.2 Primary Assembly

    Range
    47448736..47598396 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039084297.1XP_038940225.1  collagen alpha-2(V) chain isoform X1

    Conserved Domains (5) summary
    smart00214
    Location:4095
    VWC; von Willebrand factor (vWF) type C domain
    PHA03307
    Location:7451145
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam09606
    Location:282643
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam01391
    Location:10431099
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:12641497
    COLFI; Fibrillar collagen C-terminal domain
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