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COL9A3 collagen type IX alpha 3 chain [ Homo sapiens (human) ]

Gene ID: 1299, updated on 4-Oct-2020

Summary

Official Symbol
COL9A3provided by HGNC
Official Full Name
collagen type IX alpha 3 chainprovided by HGNC
Primary source
HGNC:HGNC:2219
See related
Ensembl:ENSG00000092758 MIM:120270
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IDD; MED; EDM3; DJ885L7.4.1
Summary
This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
Expression
Broad expression in thyroid (RPKM 8.5), salivary gland (RPKM 6.2) and 17 other tissues See more
Orthologs

Genomic context

See COL9A3 in Genome Data Viewer
Location:
20q13.33
Exon count:
33
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (62817050..62841159)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61448414..61472511)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene MRG domain binding protein Neighboring gene OGFR antisense RNA 1 Neighboring gene opioid growth factor receptor Neighboring gene transcription factor like 5 Neighboring gene diphthamide biosynthesis 3 pseudogene 1 Neighboring gene uncharacterized LOC105372717 Neighboring gene ADP ribosylation factor 4 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ90759

Gene Ontology Provided by GOA

Process Evidence Code Pubs
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
female gonad development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
male gonad development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IX trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IX trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-3(IX) chain
Names
collagen IX, alpha-3 polypeptide
collagen type IX proteoglycan
collagen, type IX, alpha 3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_016353.1 RefSeqGene

    Range
    4989..29098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1253

mRNA and Protein(s)

  1. NM_001853.4NP_001844.3  collagen alpha-3(IX) chain precursor

    See identical proteins and their annotated locations for NP_001844.3

    Status: REVIEWED

    Source sequence(s)
    AK075240, AL035669, BC004412, BC011705
    Consensus CDS
    CCDS13505.1
    UniProtKB/Swiss-Prot
    Q14050
    Related
    ENSP00000496793.1, ENST00000649368.1
    Conserved Domains (1) summary
    pfam01391
    Location:289347
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    62817050..62841159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528545.1XP_011526847.1  collagen alpha-3(IX) chain isoform X1

    Conserved Domains (1) summary
    pfam01391
    Location:289347
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_017027666.1XP_016883155.1  collagen alpha-3(IX) chain isoform X2

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