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COL9A1 collagen, type IX, alpha 1 [ Homo sapiens (human) ]

Gene ID: 1297, updated on 6-Jul-2014
Official Symbol
COL9A1provided by HGNC
Official Full Name
collagen, type IX, alpha 1provided by HGNC
Primary source
HGNC:2217
Locus tag
RP1-138F4.2
See related
Ensembl:ENSG00000112280; HPRD:00367; MIM:120210; Vega:OTTHUMG00000014988
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; EDM6; STL4; DJ149L1.1.2
Summary
This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
See COL9A1 in Epigenomics, MapViewer
Location:
6q13
Exon count :
40
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 6 NC_000006.12 (70216040..70303083, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70925743..71012786, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LMBR1 domain containing 1 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene collagen, type XIX, alpha 1 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene uncharacterized LOC101928353 Neighboring gene family with sequence similarity 135, member A

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Multiple epiphyseal dysplasia 6
MedGen: CN071420 OMIM: 614135 GeneReviews: Not available
Compare labs
Stickler syndrome, type 4
MedGen: C1852831 OMIM: 614134 GeneReviews: Stickler Syndrome
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2013-11-06)

ISCA Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2013-11-06)

ISCA Genome Curation Page
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Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent conferring tensile strength IC
Inferred by Curator
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
axon guidance TAS
Traceable Author Statement
more info
 
collagen catabolic process TAS
Traceable Author Statement
more info
 
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
growth plate cartilage development IEA
Inferred from Electronic Annotation
more info
 
organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
tissue homeostasis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen type IX trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen type IX trimer TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
Preferred Names
collagen alpha-1(IX) chain
Names
collagen alpha-1(IX) chain
alpha-1(IX) collagen chain
collagen IX, alpha-1 polypeptide
cartilage-specific short collagen

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_011654.1 

    Range
    5001..92044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001851.4NP_001842.3  collagen alpha-1(IX) chain isoform 1 precursor

    See proteins identical to NP_001842.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1, also known as the long form).
    Source sequence(s)
    AU118474, AW021120, BC015409, BC063646, BF196880, X54412
    Consensus CDS
    CCDS4971.1
    UniProtKB/Swiss-Prot
    P20849
    Conserved Domains (2) summary
    pfam01391
    Location:493552
    Blast Score: 120
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50244
    Blast Score: 531
    TSPN; Thrombospondin N-terminal -like domains
  2. NM_078485.3NP_511040.2  collagen alpha-1(IX) chain isoform 2 precursor

    See proteins identical to NP_511040.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks several exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a unique AUG and an isoform (2, also known as the short form) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AW021120, BC063646, BF196880, CA392556, X54412
    Consensus CDS
    CCDS47447.1
    UniProtKB/Swiss-Prot
    P20849
    Related
    ENSP00000315252, OTTHUMP00000016699, ENST00000320755, OTTHUMT00000041132
    Conserved Domains (1) summary
    pfam01391
    Location:250309
    Blast Score: 118
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000006.12 

    Range
    70216040..70303083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715331.1XP_006715394.1  

    Conserved Domains (1) summary
    pfam01391
    Location:199258
    Blast Score: 118
    Collagen; Collagen triple helix repeat (20 copies)

Alternate HuRef

Genomic

  1. AC_000138.1 

    Range
    68124097..68211118
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018917.2 

    Range
    71092075..71179110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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