U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Col9a1 collagen type IX alpha 1 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 305104, updated on 10-Jul-2024

Summary

Go to the top of the page Help
Official Symbol
Col9a1provided by RGD
Official Full Name
collagen type IX alpha 1 chainprovided by RGD
Primary source
RGD:1309425
See related
EnsemblRapid:ENSRNOG00000012920 AllianceGenome:RGD:1309425
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
Predicted to be an extracellular matrix structural constituent. Involved in chondrocyte differentiation. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane and extracellular space. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 6; and osteochondrodysplasia. Orthologous to human COL9A1 (collagen type IX alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 6.6), Kidney (RPKM 4.9) and 4 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Col9a1 in Genome Data Viewer
Location:
9q21
Exon count:
39
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (34081364..34164552)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (26585034..26668222)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (30419001..30502307)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 135, member A Neighboring gene uncharacterized LOC102553447 Neighboring gene uncharacterized LOC134480563 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene ADP-ribosylation factor-like protein 3 pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Establishment of bone morphogenetic protein 2 responsive chondrogenic cell line. Aikawa T, et al. J Bone Miner Res, 1996 Apr. PMID 8992886
  2. Altered cartilage phenotype expressed during intramembranous bone formation. Ting K, et al. J Bone Miner Res, 1993 Nov. PMID 8266829
  3. Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6. Kimura T, et al. Eur J Biochem, 1989 Jan 15. PMID 2465149
  4. Mice lacking alpha 1 (IX) collagen develop noninflammatory degenerative joint disease. Fässler R, et al. Proc Natl Acad Sci U S A, 1994 May 24. PMID 8197187, Free PMC Article
  5. Ablation of collagen IX and COMP disrupts epiphyseal cartilage architecture. Blumbach K, et al. Matrix Biol, 2008 May. PMID 18191556

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Collagen type IX alpha1 was found within the tectorial membrane as well as fibrocytes in the spiral ligament.
    Title: The localization of proteins encoded by CRYM, KIAA1199, UBA52, COL9A3, and COL9A1, genes highly expressed in the cochlea.
Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables carbohydrate binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within bone morphogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cartilage development ISO
Inferred from Sequence Orthology
more info
  
involved_in chondrocyte differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within chondrocyte proliferation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within growth plate cartilage development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within skeletal system development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within tissue homeostasis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type IX trimer IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type IX trimer ISO
Inferred from Sequence Orthology
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
collagen alpha-1(IX) chain
Names
collagen, type IX, alpha 1
procollagen, type IX, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001100842.1 → NP_001094312.1  collagen alpha-1(IX) chain precursor

    Status: VALIDATED

    Source sequence(s)
    BQ191679, DY313373, DY316977, JAXUCZ010000009
    UniProtKB/TrEMBL
    F1LQ93
    Related
    ENSRNOP00000018116.6, ENSRNOT00000018116.8
    Conserved Domains (2) summary
    pfam01391
    Location:506 → 565
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:63 → 257
    TSPN; Thrombospondin N-terminal -like domains

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_086027.1 Reference GRCr8

    Range
    34081364..34164552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039083449.1 → XP_038939377.1  collagen alpha-1(IX) chain isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZSW9
    Related
    ENSRNOP00000081771.1, ENSRNOT00000115769.2
    Conserved Domains (1) summary
    pfam01391
    Location:342 → 396
    Collagen; Collagen triple helix repeat (20 copies)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P20850.1 GenPept UniProtKB/Swiss-Prot:P20850

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools