U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 1299, updated on 5-Mar-2024

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; AllianceGenome:HGNC:2219
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; STL6; 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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See COL9A3 in Genome Data Viewer
Location:
20q13.33
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (62816213..62841159)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (64616007..64640720)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61448402..61472511)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13120 Neighboring gene MRG domain binding protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61435960-61436865 Neighboring gene OGFR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13125 Neighboring gene opioid growth factor receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61446582-61447268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61447957-61448642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61449331-61450016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61450017-61450704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61454586-61455274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61455275-61455962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61461792-61462748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61462749-61463704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61463705-61464661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61464662-61465617 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:61467141-61468340 Neighboring gene Sharpr-MPRA regulatory region 13411 Neighboring gene transcription factor like 5 Neighboring gene diphthamide biosynthesis 3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13127 Neighboring gene uncharacterized LOC105372717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61492967-61493621 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

Clone Names

  • FLJ90759

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)

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.

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
    Q13681, Q14050, Q9H4G9, Q9UPE2
    Related
    ENSP00000496793.1, ENST00000649368.1
    Conserved Domains (1) summary
    pfam01391
    Location:289347
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    62816213..62841159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439894.1XP_047295850.1  collagen alpha-3(IX) chain isoform X2

  2. XM_047439893.1XP_047295849.1  collagen alpha-3(IX) chain isoform X1

  3. XM_047439895.1XP_047295851.1  collagen alpha-3(IX) chain isoform X4

  4. XM_017027666.2XP_016883155.1  collagen alpha-3(IX) chain isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    64616007..64640720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322984.1XP_054178959.1  collagen alpha-3(IX) chain isoform X1

  2. XM_054322986.1XP_054178961.1  collagen alpha-3(IX) chain isoform X4

  3. XM_054322985.1XP_054178960.1  collagen alpha-3(IX) chain isoform X3