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Tbio
COL2A1
Collagen alpha-1(II) chain

Protein Summary
Description
Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces. This gene encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED congenita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. [provided by RefSeq, Jul 2008]
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
gene perturbation
0.99
biological term
0.94
PubMedID
0.92
disease
0.86
phenotype
0.86


Related Tools
Target Illumination GWAS Analytics (TIGA)
TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
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GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 859.43   (req: < 5)
Gene RIFs: 182   (req: <= 3)
Antibodies: 668   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 859.43   (req: >= 5)
Gene RIFs: 182   (req: > 3)
Antibodies: 668   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 32
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
GWAS Traits (4)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
appendicular lean mass
1
1
1
66.2
neutrophil percentage of leukocytes
1
1
1
19.2
monocyte count
1
1
1
16.4
lymphocyte count
1
1
1
16.4
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
appendicular lean mass
1
66.2
neutrophil percentage of leukocytes
1
19.2
monocyte count
1
16.4
lymphocyte count
1
16.4
Orthologs (9)
1 – 5 of 9
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
collagen type II alpha 1 chain
VGNC:10704
451860
Mouse
MGI:88452
12824
Rat
RGD:2375
25412
Dog
collagen type II alpha 1 chain
VGNC:39471
403826
Horse
collagen type II alpha 1 chain
VGNC:16737
791241
Species
Name
OMA
EggNOG
Inparanoid
Chimp
collagen type II alpha 1 chain
Mouse
Rat
Dog
collagen type II alpha 1 chain
Horse
collagen type II alpha 1 chain
Protein Structure (7 Structures, 1 AlphaFold Model)
RepresentationColor Scheme

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-P02458-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 7
PDB Structure Id
Ligand
Method
Resolution (Å)
Residues
Fraction of Total Protein
Pub Year
Title
PDB Structure Id
Fraction of Total Protein
Resolution
Pub Year
Pathways (22)
Assembly of collagen fibrils and other multimeric structures (R-HSA-2022090)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 5 of 5
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Assembly of collagen fibrils and other multimeric structures
Reactome
Collagen biosynthesis and modifying enzymes
Reactome
Collagen chain trimerization
Reactome
Collagen formation
Reactome
Extracellular matrix organization
Name
Explore in Pharos
Explore in Source
Assembly of collagen fibrils and other multimeric structures
Collagen biosynthesis and modifying enzymes
Collagen chain trimerization
Collagen formation
Extracellular matrix organization
Gene Ontology Terms (40)
Items per page:
10
1 – 7 of 7
GO Term
Evidence
Assigned by
Inferred from Direct Assay (IDA)
MGI
Inferred from Direct Assay (IDA)
MGI
Inferred from Physical Interaction (IPI)
CAFA
Inferred from High Throughput Direct Assay (HDA)
BHF-UCL
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Non-traceable Author Statement (NAS)
BHF-UCL
Inferred from Electronic Annotation (IEA)
UniProtKB-KW
Protein-Protein Interactions (207)
1 – 10 of 207
LAIR2
Tbio
Novelty: 0.06117644
p_int: 0.999999986
p_ni: 1.4e-8
p_wrong: 1e-9
Data Source: BioPlex
PLOD1
Tbio
Family: Enzyme
Novelty: 0.00905345
p_int: 0.999999588
p_ni: 4.12e-7
Score: 0.936
Data Source: BioPlex,STRINGDB
MMP9
Tchem
Family: Enzyme
Novelty: 0.00008645
p_int: 0.999998423
p_ni: 0.000001576
Score: 0.506
Data Source: BioPlex,STRINGDB
COL8A2
Tbio
Novelty: 0.01672103
p_int: 0.999996793
p_ni: 0.000003207
Score: 0.97
Data Source: BioPlex,STRINGDB
P4HA1
Tchem
Family: Enzyme
Novelty: 0.01624726
p_int: 0.99998342
p_ni: 0.000016579
p_wrong: 1e-9
Score: 0.924
Data Source: BioPlex,STRINGDB
COLGALT2
Tbio
Family: Enzyme
Novelty: 0.15981994
p_int: 0.999953598
p_ni: 0.000046384
p_wrong: 1.7e-8
Score: 0.952
Data Source: BioPlex,STRINGDB
MMP2
Tchem
Family: Enzyme
Novelty: 0.00012762
p_int: 0.999937648
p_ni: 0.000062306
p_wrong: 4.6e-8
Score: 0.497
Data Source: BioPlex,STRINGDB
C1QTNF2
Tbio
Novelty: 0.18607978
p_int: 0.99992905
p_ni: 0.000070949
Score: 0.297
Data Source: BioPlex,STRINGDB
COL9A1
Tbio
Novelty: 0.0160066
p_int: 0.999114226
p_ni: 0.000885767
p_wrong: 8e-9
Score: 0.963
Data Source: BioPlex,STRINGDB
FKBP9
Tbio
Family: Enzyme
Novelty: 0.16472204
p_int: 0.998671448
p_ni: 0.001328548
p_wrong: 4e-9
Score: 0.202
Data Source: BioPlex,STRINGDB
Publication Statistics
PubMed Score  859.43

PubMed score by year
PubTator Score  588.73

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer
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