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

Gene ID: 1298, updated on 2-Nov-2024

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; AllianceGenome:HGNC:2218
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
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Genomic context

See COL9A2 in Genome Data Viewer
Location:
1p34.2
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40300489..40317286, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40169995..40187371, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40766161..40782958, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 837 Neighboring gene transmembrane and coiled-coil domains 2 Neighboring gene zinc metallopeptidase STE24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 724 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 844 Neighboring gene small ArfGAP2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:40839657-40840156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 845

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
part_of collagen type IX trimer IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen type IX trimer IPI
Inferred from Physical Interaction
more info
PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 

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)

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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.

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
    B2RMP9, Q14055
    Related
    ENSP00000361834.3, ENST00000372748.8
    Conserved Domains (1) summary
    pfam01391
    Location:259316
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    40300489..40317286 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000332.2XP_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_011540715.3XP_011539017.1  collagen alpha-2(IX) chain isoform X2

    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)
  3. XM_017000333.2XP_016855822.1  collagen alpha-2(IX) chain isoform X3

    Conserved Domains (1) summary
    pfam01391
    Location:165222
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_011540716.3XP_011539018.1  collagen alpha-2(IX) chain isoform X2

    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)
  5. XM_047446392.1XP_047302348.1  collagen alpha-2(IX) chain isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    40169995..40187371 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334467.1XP_054190442.1  collagen alpha-2(IX) chain isoform X5

  2. XM_054334466.1XP_054190441.1  collagen alpha-2(IX) chain isoform X1

  3. XM_054334469.1XP_054190444.1  collagen alpha-2(IX) chain isoform X2

  4. XM_054334468.1XP_054190443.1  collagen alpha-2(IX) chain isoform X2

  5. XM_054334470.1XP_054190445.1  collagen alpha-2(IX) chain isoform X3