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COL9A2 collagen type IX alpha 2 chain [ Homo sapiens (human) ]

Gene ID: 1298, updated on 4-Oct-2020

Summary

Official Symbol
COL9A2provided by HGNC
Official Full Name
collagen type IX alpha 2 chainprovided by HGNC
Primary source
HGNC:HGNC:2218
See related
Ensembl:ENSG00000049089 MIM:120260
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
MED; EDM2; STL5; DJ39G22.4
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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
Expression
Broad expression in prostate (RPKM 5.8), brain (RPKM 5.5) and 20 other tissues See more
Orthologs

Genomic context

See COL9A2 in Genome Data Viewer
Location:
1p34.2
Exon count:
35
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (40300487..40317653, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40766162..40782939, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transmembrane and coiled-coil domains 2 Neighboring gene zinc metallopeptidase STE24 Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene uncharacterized LOC107984945

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?

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2013-10-09)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2013-10-09)

ClinGen Genome Curation Page

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength IC
Inferred by Curator
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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
 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
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-2(IX) chain
Names
alpha 2 type IX collagen
collagen IX, alpha-2 polypeptide
collagen, type IX, alpha 2

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_008031.1 RefSeqGene

    Range
    4982..21779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001852.4NP_001843.1  collagen alpha-2(IX) chain precursor

    See identical proteins and their annotated locations for NP_001843.1

    Status: REVIEWED

    Source sequence(s)
    BC136326, CB305733, CD722372
    Consensus CDS
    CCDS450.1
    UniProtKB/Swiss-Prot
    Q14055
    Related
    ENSP00000361834.3, ENST00000372748.8
    Conserved Domains (1) summary
    pfam01391
    Location:259316
    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_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    40300487..40317653 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000332.1XP_016855821.1  collagen alpha-2(IX) chain isoform X1

    Conserved Domains (1) summary
    pfam01391
    Location:263320
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_006710365.3XP_006710428.1  collagen alpha-2(IX) chain isoform X2

    See identical proteins and their annotated locations for XP_006710428.1

    UniProtKB/Swiss-Prot
    Q14055
    Conserved Domains (1) summary
    pfam01391
    Location:259316
    Collagen; Collagen triple helix repeat (20 copies)
  3. XM_011540715.2XP_011539017.1  collagen alpha-2(IX) chain isoform X3

    See identical proteins and their annotated locations for XP_011539017.1

    Conserved Domains (1) summary
    pfam01391
    Location:169226
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_011540717.2XP_011539019.1  collagen alpha-2(IX) chain isoform X5

    See identical proteins and their annotated locations for XP_011539019.1

    Conserved Domains (1) summary
    pfam01391
    Location:78135
    Collagen; Collagen triple helix repeat (20 copies)
  5. XM_011540716.2XP_011539018.1  collagen alpha-2(IX) chain isoform X3

    See identical proteins and their annotated locations for XP_011539018.1

    Conserved Domains (1) summary
    pfam01391
    Location:169226
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_017000333.1XP_016855822.1  collagen alpha-2(IX) chain isoform X4

    UniProtKB/TrEMBL
    D3DPU8
    Conserved Domains (1) summary
    pfam01391
    Location:165222
    Collagen; Collagen triple helix repeat (20 copies)
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