Details for: COL9A1

Gene ID: 1297

Symbol: COL9A1

Ensembl ID: ENSG00000112280

Description: collagen type IX alpha 1 chain

Associated with

Cells (max top 100)

(Marker Score score is uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 3.09
    Marker Score: 902
  • Cell Name: oligodendrocyte precursor cell (CL0002453)
    Fold Change: 1.65
    Marker Score: 2044
  • Cell Name: granulocyte monocyte progenitor cell (CL0000557)
    Fold Change: 1.37
    Marker Score: 868
  • Cell Name: type I pneumocyte (CL0002062)
    Fold Change: 1.34
    Marker Score: 1611
  • Cell Name: kidney proximal convoluted tubule epithelial cell (CL1000838)
    Fold Change: 1.21
    Marker Score: 2505
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 1.15
    Marker Score: 4810
  • Cell Name: enteric smooth muscle cell (CL0002504)
    Fold Change: 1.08
    Marker Score: 2538.5
  • Cell Name: early T lineage precursor (CL0002425)
    Fold Change: 1.04
    Marker Score: 795
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: 1.01
    Marker Score: 683.5
  • Cell Name: cerebral cortex GABAergic interneuron (CL0010011)
    Fold Change: 1
    Marker Score: 71820
  • Cell Name: forebrain radial glial cell (CL0013000)
    Fold Change: 1
    Marker Score: 48045
  • Cell Name: chondrocyte (CL0000138)
    Fold Change: 1
    Marker Score: 448
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.98
    Marker Score: 507
  • Cell Name: absorptive cell (CL0000212)
    Fold Change: 0.98
    Marker Score: 30408
  • Cell Name: BEST4+ intestinal epithelial cell, human (CL4030026)
    Fold Change: 0.97
    Marker Score: 460
  • Cell Name: epithelial cell of glomerular capsule (CL1000450)
    Fold Change: 0.97
    Marker Score: 247
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: 0.97
    Marker Score: 401.5
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.95
    Marker Score: 2412
  • Cell Name: epithelial cell of nephron (CL1000449)
    Fold Change: 0.94
    Marker Score: 1966
  • Cell Name: transit amplifying cell (CL0009010)
    Fold Change: 0.93
    Marker Score: 5331
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: 0.91
    Marker Score: 2737
  • Cell Name: epithelial cell of alveolus of lung (CL0010003)
    Fold Change: 0.91
    Marker Score: 407
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.9
    Marker Score: 324
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 0.87
    Marker Score: 5284
  • Cell Name: migratory enteric neural crest cell (CL0002607)
    Fold Change: 0.86
    Marker Score: 809
  • Cell Name: Mueller cell (CL0000636)
    Fold Change: 0.86
    Marker Score: 1186
  • Cell Name: mesodermal cell (CL0000222)
    Fold Change: 0.83
    Marker Score: 10961
  • Cell Name: immature innate lymphoid cell (CL0001082)
    Fold Change: 0.83
    Marker Score: 1688
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: 0.82
    Marker Score: 1395
  • Cell Name: cardiac endothelial cell (CL0010008)
    Fold Change: 0.8
    Marker Score: 1507
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.78
    Marker Score: 314
  • Cell Name: intestinal epithelial cell (CL0002563)
    Fold Change: 0.78
    Marker Score: 1259
  • Cell Name: brush cell (CL0002204)
    Fold Change: 0.77
    Marker Score: 706
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 0.77
    Marker Score: 12075
  • Cell Name: cortical thymic epithelial cell (CL0002364)
    Fold Change: 0.77
    Marker Score: 2842
  • Cell Name: Cajal-Retzius cell (CL0000695)
    Fold Change: 0.76
    Marker Score: 395
  • Cell Name: Sertoli cell (CL0000216)
    Fold Change: 0.76
    Marker Score: 4481
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: 0.74
    Marker Score: 782
  • Cell Name: near-projecting glutamatergic cortical neuron (CL4023012)
    Fold Change: 0.73
    Marker Score: 6869
  • Cell Name: neutrophil progenitor cell (CL0000834)
    Fold Change: 0.69
    Marker Score: 177
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.67
    Marker Score: 2807.5
  • Cell Name: neural crest cell (CL0011012)
    Fold Change: 0.65
    Marker Score: 694
  • Cell Name: renal alpha-intercalated cell (CL0005011)
    Fold Change: 0.64
    Marker Score: 339
  • Cell Name: lymphoid lineage restricted progenitor cell (CL0000838)
    Fold Change: 0.63
    Marker Score: 376
  • Cell Name: interstitial cell of Cajal (CL0002088)
    Fold Change: 0.61
    Marker Score: 212
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.59
    Marker Score: 378
  • Cell Name: intestinal enteroendocrine cell (CL1001516)
    Fold Change: 0.56
    Marker Score: 449
  • Cell Name: common myeloid progenitor (CL0000049)
    Fold Change: 0.55
    Marker Score: 147
  • Cell Name: megakaryocyte-erythroid progenitor cell (CL0000050)
    Fold Change: 0.55
    Marker Score: 231
  • Cell Name: kidney cell (CL1000497)
    Fold Change: 0.54
    Marker Score: 362
  • Cell Name: mesothelial cell (CL0000077)
    Fold Change: 0.54
    Marker Score: 216
  • Cell Name: renal beta-intercalated cell (CL0002201)
    Fold Change: 0.52
    Marker Score: 165
  • Cell Name: vip GABAergic cortical interneuron (CL4023016)
    Fold Change: 0.46
    Marker Score: 17347
  • Cell Name: smooth muscle myoblast (CL0000514)
    Fold Change: 0.45
    Marker Score: 216
  • Cell Name: neural progenitor cell (CL0011020)
    Fold Change: 0.44
    Marker Score: 1687
  • Cell Name: neuroblast (sensu Vertebrata) (CL0000031)
    Fold Change: 0.42
    Marker Score: 264
  • Cell Name: pro-B cell (CL0000826)
    Fold Change: 0.4
    Marker Score: 390
  • Cell Name: sst GABAergic cortical interneuron (CL4023017)
    Fold Change: 0.39
    Marker Score: 7746
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: 0.36
    Marker Score: 115
  • Cell Name: kidney proximal straight tubule epithelial cell (CL1000839)
    Fold Change: 0.35
    Marker Score: 836
  • Cell Name: neuronal receptor cell (CL0000006)
    Fold Change: 0.35
    Marker Score: 153
  • Cell Name: fetal cardiomyocyte (CL0002495)
    Fold Change: 0.33
    Marker Score: 107
  • Cell Name: fraction A pre-pro B cell (CL0002045)
    Fold Change: 0.31
    Marker Score: 314
  • Cell Name: cerebellar granule cell precursor (CL0002362)
    Fold Change: 0.31
    Marker Score: 174
  • Cell Name: enteric neuron (CL0007011)
    Fold Change: 0.3
    Marker Score: 162
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.3
    Marker Score: 219
  • Cell Name: neural cell (CL0002319)
    Fold Change: 0.3
    Marker Score: 143
  • Cell Name: podocyte (CL0000653)
    Fold Change: 0.29
    Marker Score: 106
  • Cell Name: male germ cell (CL0000015)
    Fold Change: 0.28
    Marker Score: 81
  • Cell Name: ependymal cell (CL0000065)
    Fold Change: 0.28
    Marker Score: 98
  • Cell Name: glial cell (CL0000125)
    Fold Change: 0.27
    Marker Score: 301
  • Cell Name: precursor B cell (CL0000817)
    Fold Change: 0.27
    Marker Score: 180
  • Cell Name: chandelier pvalb GABAergic cortical interneuron (CL4023036)
    Fold Change: 0.27
    Marker Score: 1117
  • Cell Name: preosteoblast (CL0007010)
    Fold Change: 0.27
    Marker Score: 76
  • Cell Name: interneuron (CL0000099)
    Fold Change: 0.26
    Marker Score: 119
  • Cell Name: connective tissue cell (CL0002320)
    Fold Change: 0.26
    Marker Score: 67
  • Cell Name: cerebral cortex endothelial cell (CL1001602)
    Fold Change: 0.25
    Marker Score: 149
  • Cell Name: choroid plexus epithelial cell (CL0000706)
    Fold Change: 0.25
    Marker Score: 229
  • Cell Name: retina horizontal cell (CL0000745)
    Fold Change: 0.25
    Marker Score: 239
  • Cell Name: mature NK T cell (CL0000814)
    Fold Change: 0.25
    Marker Score: 115
  • Cell Name: osteoblast (CL0000062)
    Fold Change: 0.25
    Marker Score: 132.5
  • Cell Name: blood vessel endothelial cell (CL0000071)
    Fold Change: 0.25
    Marker Score: 248
  • Cell Name: regular atrial cardiac myocyte (CL0002129)
    Fold Change: 0.24
    Marker Score: 845
  • Cell Name: renal principal cell (CL0005009)
    Fold Change: 0.23
    Marker Score: 179
  • Cell Name: ventricular cardiac muscle cell (CL2000046)
    Fold Change: 0.23
    Marker Score: 96
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: 0.23
    Marker Score: 106
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 0.23
    Marker Score: 65
  • Cell Name: mesenchymal stem cell (CL0000134)
    Fold Change: 0.22
    Marker Score: 345
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.22
    Marker Score: 75
  • Cell Name: skeletal muscle satellite cell (CL0000594)
    Fold Change: 0.22
    Marker Score: 148
  • Cell Name: mononuclear cell (CL0000842)
    Fold Change: 0.22
    Marker Score: 71
  • Cell Name: lung ciliated cell (CL1000271)
    Fold Change: 0.21
    Marker Score: 101
  • Cell Name: neuron (CL0000540)
    Fold Change: 0.21
    Marker Score: 838
  • Cell Name: plasma cell (CL0000786)
    Fold Change: 0.2
    Marker Score: 227
  • Cell Name: parietal epithelial cell (CL1000452)
    Fold Change: 0.2
    Marker Score: 73
  • Cell Name: kidney interstitial cell (CL1000500)
    Fold Change: 0.2
    Marker Score: 141
  • Cell Name: kidney capillary endothelial cell (CL1000892)
    Fold Change: 0.2
    Marker Score: 62
  • Cell Name: plasmacytoid dendritic cell (CL0000784)
    Fold Change: 0.2
    Marker Score: 106
  • Cell Name: photoreceptor cell (CL0000210)
    Fold Change: 0.2
    Marker Score: 148
  • Cell Name: mesangial cell (CL0000650)
    Fold Change: 0.2
    Marker Score: 236

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Other Information

**Key characteristics:** - Col9a1 is a single-exon gene with a predicted protein length of approximately 180 amino acids. - It is expressed in a wide range of cell types, including epithelial cells, neurons, and immune cells. - The protein is highly conserved across species. **Pathways and functions:** - Col9a1 is involved in the assembly and maintenance of collagen fibrils and other multimeric structures in the ECM. - It is also involved in axon guidance, as it is expressed in neurons and is essential for the stability and integrity of axons. - Col9a1 is a key regulator of collagen biosynthesis and modifying enzymes, which are involved in the production and degradation of collagen. - It also plays a role in the degradation of the extracellular matrix, developmental biology, and immune responses. **Clinical significance:** - Mutations in COL9A1 have been linked to several human diseases, including Marfan syndrome, which is characterized by weakened and fragile skin and blood vessels. - Col9a1 is also involved in the pathogenesis of some cancers, such as breast cancer and lung cancer. - Targeting Col9a1 signaling has emerged as a potential therapeutic strategy for these diseases.

Genular Protein ID: 2001509862

Symbol: CO9A1_HUMAN

Name: Collagen alpha-1(IX) chain

UniProtKB Accession Codes:

P20849 Q13699 Q13700 Q5TF52 Q6P467 Q96BM8 Q99225 Q9H151 Q9H152 Q9Y6P2 Q9Y6P3

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 3 CTD 1 ChEBI 3 ChiTaRS 1 ComplexPortal 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 50 Ensembl 3 EvolutionaryTrace 1 ExpressionAtlas 1 GO 11 Gene3D 1 GeneCards 1 GeneReviews 1 GeneTree 1 GeneWiki 1 Genevisible 1 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MIM 5 MINT 1 MalaCards 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 Orphanet 2 OrthoDB 1 PANTHER 2 PDB 7 PDBsum 5 PIR 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 3 RNAct 1 Reactome 8 RefSeq 2 SAM 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 2209617

Title: The complete primary structure of two distinct forms of human alpha 1 (IX) collagen chains.

PubMed ID: 2209617

DOI: 10.1111/j.1432-1033.1990.tb19279.x

PubMed ID: 9707347

Title: Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule.

PubMed ID: 9707347

DOI: 10.1016/s0945-053x(98)90063-4

PubMed ID: 14574404

Title: The DNA sequence and analysis of human chromosome 6.

PubMed ID: 14574404

DOI: 10.1038/nature02055

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 8660302

Title: Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites.

PubMed ID: 8660302

DOI: 10.1042/bj3140327

PubMed ID: 2465149

Title: Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6.

PubMed ID: 2465149

DOI: 10.1111/j.1432-1033.1989.tb14522.x

PubMed ID: 1690886

Title: The alpha 1 (IX) collagen gene gives rise to two different transcripts in both mouse embryonic and human fetal RNA.

PubMed ID: 1690886

DOI: 10.1073/pnas.87.7.2400

PubMed ID: 17553797

Title: Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family.

PubMed ID: 17553797

DOI: 10.1074/jbc.m702514200

PubMed ID: 11565064

Title: A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity.

PubMed ID: 11565064

DOI: 10.1086/324023

PubMed ID: 16909383

Title: A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene.

PubMed ID: 16909383

DOI: 10.1086/506478

PubMed ID: 21421862

Title: Autosomal recessive Stickler syndrome in two families is caused by mutations in the COL9A1 gene.

PubMed ID: 21421862

DOI: 10.1167/iovs.10-7128

PubMed ID: 31090205

Title: Homozygous Type IX collagen variants (COL9A1, COL9A2, and COL9A3) causing recessive Stickler syndrome-Expanding the phenotype.

PubMed ID: 31090205

DOI: 10.1002/ajmg.a.61191

Sequence Information:

  • Length: 921
  • Mass: 91869
  • Checksum: A69BF076127283D0
  • Sequence:
    • MKTCWKIPVF FFVCSFLEPW ASAAVKRRPR FPVNSNSNGG NELCPKIRIG QDDLPGFDLI 
SQFQVDKAAS RRAIQRVVGS ATLQVAYKLG NNVDFRIPTR NLYPSGLPEE YSFLTTFRMT 
GSTLKKNWNI WQIQDSSGKE QVGIKINGQT QSVVFSYKGL DGSLQTAAFS NLSSLFDSQW 
HKIMIGVERS SATLFVDCNR IESLPIKPRG PIDIDGFAVL GKLADNPQVS VPFELQWMLI 
HCDPLRPRRE TCHELPARIT PSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP 
PGPPGPAGEP GKPGAPGKPG TPGADGLTGP DGSPGSIGSK GQKGEPGVPG SRGFPGRGIP 
GPPGPPGTAG LPGELGRVGP VGDPGRRGPP GPPGPPGPRG TIGFHDGDPL CPNACPPGRS 
GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE GDQGELGEVG AQGPPGAQGL RGITGIVGDK 
GEKGARGLDG EPGPQGLPGA PGDQGQRGPP GEAGPKGDRG AEGARGIPGL PGPKGDTGLP 
GVDGRDGIPG MPGTKGEPGK PGPPGDAGLQ GLPGVPGIPG AKGVAGEKGS TGAPGKPGQM 
GNSGKPGQQG PPGEVGPRGP QGLPGSRGEL GPVGSPGLPG KLGSLGSPGL PGLPGPPGLP 
GMKGDRGVVG EPGPKGEQGA SGEEGEAGER GELGDIGLPG PKGSAGNPGE PGLRGPEGSR 
GLPGVEGPRG PPGPRGVQGE QGATGLPGVQ GPPGRAPTDQ HIKQVCMRVI QEHFAEMAAS 
LKRPDSGATG LPGRPGPPGP PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK 
GERGPPGRGP NGLPGAIGLP GDPGPASYGR NGRDGERGPP GVAGIPGVPG PPGPPGLPGF 
CEPASCTMQA GQRAFNKGPD P

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. For the full schema, download it here.