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Col9a2 collagen type IX alpha 2 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 362584, updated on 2-Nov-2024

Summary

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Official Symbol
Col9a2provided by RGD
Official Full Name
collagen type IX alpha 2 chainprovided by RGD
Primary source
RGD:1307029
See related
EnsemblRapid:ENSRNOG00000011502 AllianceGenome:RGD:1307029
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
Predicted to enable protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to be part of collagen type IX trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 2; and osteochondrodysplasia. Orthologous to human COL9A2 (collagen type IX alpha 2 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Brain (RPKM 33.2), Lung (RPKM 12.0) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Col9a2 in Genome Data Viewer
Location:
5q36
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (139892798..139910131)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (134607616..134624678)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (139962684..139979865)

Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene small ArfGAP2 Neighboring gene ribosomal protein L10A like 3 Neighboring gene uncharacterized LOC108351024 Neighboring gene zinc metallopeptidase STE24 Neighboring gene transmembrane and coiled-coil domains 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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Related articles in PubMed

  1. A mutation in the gene encoding the alpha 2 chain of the fibril-associated collagen IX, COL9A2, causes multiple epiphyseal dysplasia (EDM2). Muragaki Y, et al. Nat Genet, 1996 Jan. PMID 8528240
  2. Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites. Diab M, et al. Biochem J, 1996 Feb 15. PMID 8660302, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of collagen type IX trimer ISO
Inferred from Sequence Orthology
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 alpha-2(IX) chain
Names
alpha 1 type IX collagen
collagen, type IX, alpha 2
procollagen, type IX, 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_001108675.1 → NP_001102145.1  collagen alpha-2(IX) chain precursor

    See identical proteins and their annotated locations for NP_001102145.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473968
    UniProtKB/TrEMBL
    A6IS03, D3ZNT5
    Related
    ENSRNOP00000049994.3, ENSRNOT00000048506.5
    Conserved Domains (1) summary
    pfam01391
    Location:360 → 418
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086023.1 Reference GRCr8

    Range
    139892798..139910131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039110306.2 → XP_038966234.1  collagen alpha-2(IX) chain isoform X1

    Conserved Domains (1) summary
    pfam01391
    Location:144 → 199
    Collagen; Collagen triple helix repeat (20 copies)
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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