Details for: COL9A1

Gene ID: 1297

Symbol: COL9A1

Ensembl ID: ENSG00000112280

Description: collagen type IX alpha 1 chain

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 34.1902
    Cell Significance Index: -13.8900
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 2.6523
    Cell Significance Index: 1684.5100
  • Cell Name: chondroblast (CL0000058)
    Fold Change: 2.1738
    Cell Significance Index: 12.7600
  • Cell Name: epithelial cell of pancreas (CL0000083)
    Fold Change: 1.3035
    Cell Significance Index: 21.4800
  • Cell Name: mesonephric nephron tubule epithelial cell (CL1000022)
    Fold Change: 1.2525
    Cell Significance Index: 43.5300
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 1.0765
    Cell Significance Index: 60.4100
  • Cell Name: skeletal muscle myoblast (CL0000515)
    Fold Change: 1.0063
    Cell Significance Index: 10.9400
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.6506
    Cell Significance Index: 123.8100
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.5718
    Cell Significance Index: 25.9200
  • Cell Name: kidney cell (CL1000497)
    Fold Change: 0.4559
    Cell Significance Index: 3.6400
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.4354
    Cell Significance Index: 43.0800
  • Cell Name: fibroblast of dermis (CL0002551)
    Fold Change: 0.3473
    Cell Significance Index: 7.2700
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.3172
    Cell Significance Index: 286.4400
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.2288
    Cell Significance Index: 37.2100
  • Cell Name: Sertoli cell (CL0000216)
    Fold Change: 0.2068
    Cell Significance Index: 2.9000
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: 0.1918
    Cell Significance Index: 3.2100
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.1883
    Cell Significance Index: 20.4800
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.1004
    Cell Significance Index: 6.0300
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.0752
    Cell Significance Index: 1.6300
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: 0.0733
    Cell Significance Index: 10.6500
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.0718
    Cell Significance Index: 135.2500
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 0.0521
    Cell Significance Index: 28.4500
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: 0.0459
    Cell Significance Index: 1.4700
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0433
    Cell Significance Index: 1.5200
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 0.0388
    Cell Significance Index: 26.8500
  • Cell Name: CD14-low, CD16-positive monocyte (CL0002396)
    Fold Change: 0.0182
    Cell Significance Index: 0.4400
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.0168
    Cell Significance Index: 1.1700
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.0042
    Cell Significance Index: 0.1200
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: -0.0095
    Cell Significance Index: -17.5500
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: -0.0147
    Cell Significance Index: -22.6600
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: -0.0174
    Cell Significance Index: -23.6700
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: -0.0176
    Cell Significance Index: -0.4400
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: -0.0178
    Cell Significance Index: -13.0200
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0228
    Cell Significance Index: -16.9100
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: -0.0234
    Cell Significance Index: -2.7300
  • Cell Name: pancreatic PP cell (CL0002275)
    Fold Change: -0.0238
    Cell Significance Index: -14.8500
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0247
    Cell Significance Index: -11.1900
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: -0.0261
    Cell Significance Index: -5.2400
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: -0.0290
    Cell Significance Index: -10.3900
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0295
    Cell Significance Index: -16.6500
  • Cell Name: radial glial cell (CL0000681)
    Fold Change: -0.0320
    Cell Significance Index: -0.1900
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0464
    Cell Significance Index: -13.3700
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: -0.0564
    Cell Significance Index: -1.1700
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: -0.0597
    Cell Significance Index: -11.8500
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: -0.0736
    Cell Significance Index: -13.2600
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: -0.0767
    Cell Significance Index: -13.1000
  • Cell Name: tendon cell (CL0000388)
    Fold Change: -0.0780
    Cell Significance Index: -1.0600
  • Cell Name: Mueller cell (CL0000636)
    Fold Change: -0.0796
    Cell Significance Index: -0.6100
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.0807
    Cell Significance Index: -16.9900
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: -0.0832
    Cell Significance Index: -5.1000
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: -0.0934
    Cell Significance Index: -12.8200
  • Cell Name: BEST4+ enteroycte (CL4030026)
    Fold Change: -0.0975
    Cell Significance Index: -1.4700
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: -0.1020
    Cell Significance Index: -2.8500
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: -0.1057
    Cell Significance Index: -6.6700
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: -0.1126
    Cell Significance Index: -13.8400
  • Cell Name: lactocyte (CL0002325)
    Fold Change: -0.1171
    Cell Significance Index: -15.1300
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.1215
    Cell Significance Index: -13.9200
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: -0.1226
    Cell Significance Index: -3.6100
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.1297
    Cell Significance Index: -13.5100
  • Cell Name: oligodendrocyte precursor cell (CL0002453)
    Fold Change: -0.1303
    Cell Significance Index: -1.7000
  • Cell Name: cerebellar granule cell (CL0001031)
    Fold Change: -0.1371
    Cell Significance Index: -2.3500
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.1411
    Cell Significance Index: -14.4100
  • Cell Name: medial ganglionic eminence derived interneuron (CL4023063)
    Fold Change: -0.1431
    Cell Significance Index: -2.0500
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: -0.1474
    Cell Significance Index: -3.1400
  • Cell Name: basal cell of epidermis (CL0002187)
    Fold Change: -0.1771
    Cell Significance Index: -2.6900
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: -0.1816
    Cell Significance Index: -11.1600
  • Cell Name: hippocampal granule cell (CL0001033)
    Fold Change: -0.1856
    Cell Significance Index: -12.4800
  • Cell Name: melanocyte of skin (CL1000458)
    Fold Change: -0.1891
    Cell Significance Index: -2.6500
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: -0.1898
    Cell Significance Index: -14.5700
  • Cell Name: fallopian tube secretory epithelial cell (CL4030006)
    Fold Change: -0.1946
    Cell Significance Index: -3.0100
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.1948
    Cell Significance Index: -15.4300
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.2033
    Cell Significance Index: -15.1500
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: -0.2233
    Cell Significance Index: -11.6300
  • Cell Name: near-projecting glutamatergic cortical neuron (CL4023012)
    Fold Change: -0.2806
    Cell Significance Index: -7.0000
  • Cell Name: Purkinje cell (CL0000121)
    Fold Change: -0.3074
    Cell Significance Index: -6.7300
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: -0.3104
    Cell Significance Index: -13.7300
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.3199
    Cell Significance Index: -15.0400
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.3237
    Cell Significance Index: -17.0000
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: -0.3287
    Cell Significance Index: -8.4500
  • Cell Name: VIP GABAergic cortical interneuron (CL4023016)
    Fold Change: -0.3327
    Cell Significance Index: -6.6800
  • Cell Name: L5 extratelencephalic projecting glutamatergic cortical neuron (CL4023041)
    Fold Change: -0.3468
    Cell Significance Index: -12.1500
  • Cell Name: epithelial cell of nephron (CL1000449)
    Fold Change: -0.3471
    Cell Significance Index: -2.9500
  • Cell Name: cortical thymic epithelial cell (CL0002364)
    Fold Change: -0.3506
    Cell Significance Index: -2.9000
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: -0.3655
    Cell Significance Index: -13.8400
  • Cell Name: mesodermal cell (CL0000222)
    Fold Change: -0.3722
    Cell Significance Index: -2.3300
  • Cell Name: eukaryotic cell (CL0000255)
    Fold Change: -0.3836
    Cell Significance Index: -16.6800
  • Cell Name: sst GABAergic cortical interneuron (CL4023017)
    Fold Change: -0.3932
    Cell Significance Index: -7.7800
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.4029
    Cell Significance Index: -13.1900
  • Cell Name: forebrain radial glial cell (CL0013000)
    Fold Change: -0.4085
    Cell Significance Index: -2.9700
  • Cell Name: chandelier pvalb GABAergic cortical interneuron (CL4023036)
    Fold Change: -0.4178
    Cell Significance Index: -8.7200
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.4286
    Cell Significance Index: -13.6500
  • Cell Name: muscle fibroblast (CL1001609)
    Fold Change: -0.4310
    Cell Significance Index: -2.6400
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: -0.4420
    Cell Significance Index: -20.6100
  • Cell Name: neuron associated cell (CL0000095)
    Fold Change: -0.4591
    Cell Significance Index: -18.8100
  • Cell Name: hippocampal pyramidal neuron (CL1001571)
    Fold Change: -0.4608
    Cell Significance Index: -13.1500
  • Cell Name: neutrophil progenitor cell (CL0000834)
    Fold Change: -0.4824
    Cell Significance Index: -12.9100
  • Cell Name: hepatoblast (CL0005026)
    Fold Change: -0.5018
    Cell Significance Index: -8.4400
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: -0.5057
    Cell Significance Index: -13.5500
  • Cell Name: obsolete epithelial cell of alveolus of lung (CL0010003)
    Fold Change: -0.5185
    Cell Significance Index: -12.9300
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: -0.5264
    Cell Significance Index: -26.6000

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** COL9A1 is a member of the collagen family, specifically a type IX collagen, which is composed of three alpha chains (α1, α2, and α3). The COL9A1 gene encodes for the α1 chain, which is essential for the formation of collagen IX trimer. This trimer is a crucial component of the ECM, providing structural integrity and mechanical strength to tissues. COL9A1 is also involved in the assembly of collagen fibrils, which are essential for tissue development and remodeling. **Pathways and Functions:** COL9A1 is involved in various signaling pathways, including: 1. **Assembly of collagen fibrils and other multimeric structures**: COL9A1 plays a critical role in the formation of collagen fibrils, which are essential for tissue development and remodeling. 2. **Axon guidance**: COL9A1 is involved in the guidance of axons during nervous system development, where it interacts with Ncam1 and regulates neurite out-growth. 3. **Degradation of the extracellular matrix**: COL9A1 is involved in the degradation of the ECM, where it interacts with metalloproteases and regulates ECM remodeling. 4. **Developmental biology**: COL9A1 is essential for tissue development, where it interacts with other ECM components to regulate tissue morphogenesis. 5. **Signaling by receptor tyrosine kinases**: COL9A1 interacts with receptor tyrosine kinases, such as PDGF receptor, to regulate signaling pathways involved in tissue development and remodeling. **Clinical Significance:** Dysregulation of COL9A1 has been implicated in various diseases, including: 1. **Osteogenesis imperfecta**: A genetic disorder characterized by fragile bones and ECM defects, where COL9A1 mutations are commonly found. 2. **Limb-girdle muscular dystrophy**: A genetic disorder characterized by muscle weakness and ECM defects, where COL9A1 mutations are implicated. 3. **Neuropathic pain**: COL9A1 has been implicated in neuropathic pain, where it interacts with Ncam1 and regulates axon guidance. 4. **Cancer**: COL9A1 has been implicated in cancer, where it interacts with metalloproteases and regulates ECM remodeling. In conclusion, COL9A1 is a crucial component of the ECM, playing a vital role in maintaining tissue structure and function. Its dysregulation has been implicated in various diseases, highlighting the importance of COL9A1 in human health and disease. Further research is necessary to fully understand the mechanisms by which COL9A1 regulates tissue development and remodeling, and to develop therapeutic strategies for diseases associated with COL9A1 dysfunction.

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 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 4 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 5 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 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. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.