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]

Uniprot Accession IDs

• P02458
• A6NGA0
• Q12985
• Q14009
• Q14044
• Q14045
• Q14046
• Q14047
• Q14056
• Q14058
• Q16672
• Q1JQ82
• Q2V4X7
• Q6LBY1
• Q6LBY2
• Q6LBY3
• Q96IT5
• Q99227
• Q9UE38
• Q9UE39
• Q9UE40
• Q9UE41
• Q9UE42
• Q9UE43

Gene Name

• COL2A1

Ensembl ID

• ENST00000337299
• ENSP00000338213
• ENSG00000139219
• ENST00000380518
• ENSP00000369889

Symbol

• AOM
• ANFH
• SEDC
• STL1
• COL11A3

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

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: 891.97   (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: 891.97   (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

Protein Sequence and Structure

Residue Counts

Protein Sequence

Show Full Sequence

ProtVista Viewer

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.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Protein-Protein Interactions (207)

Explore Interacting Targets

1 – 10 of 207

• See Interactions on String-DB

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

Pathways (22)

Reactome (5)

KEGG (5)

PathwayCommons (5)

WikiPathways (7)

Assembly of collagen fibrils and other multimeric structures (R-HSA-2022090)

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Items per page:

5

1 – 5 of 5

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Assembly of collagen fibrils and other multimeric structures	57 targets	R-HSA-2022090
Reactome	Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Reactome	Collagen chain trimerization	44 targets	R-HSA-8948216
Reactome	Collagen formation	90 targets	R-HSA-1474290
Reactome	Extracellular matrix organization	297 targets	R-HSA-1474244

Name	Explore in Pharos	Explore in Source
Assembly of collagen fibrils and other multimeric structures	57 targets	R-HSA-2022090
Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Collagen chain trimerization	44 targets	R-HSA-8948216
Collagen formation	90 targets	R-HSA-1474290
Extracellular matrix organization	297 targets	R-HSA-1474244

Gene Ontology Terms (40)

Functions (7)

Components (8)

Processes (25)

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10

1 – 7 of 7

GO Term	Evidence	Assigned by
platelet-derived growth factor binding	Inferred from Direct Assay (IDA)	MGI
proteoglycan binding	Inferred from Direct Assay (IDA)	MGI
MHC class II protein binding	Inferred from Physical Interaction (IPI)	CAFA
extracellular matrix structural constituent conferring tensile strength	Inferred from High Throughput Direct Assay (HDA)	BHF-UCL
extracellular matrix structural constituent	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
identical protein binding	Non-traceable Author Statement (NAS)	BHF-UCL
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

GWAS Traits (17)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 17

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
HbA1c measurement	EFO_0004541	3	8	8		96.6
hemoglobin measurement	EFO_0004509	2	3	3		95.4
mean corpuscular volume	EFO_0004526	1	1	1		73.6
hematocrit	EFO_0004348	1	2	2		72.9
reticulocyte count	EFO_0007986	2	2	2		69.1

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 17

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
HbA1c measurement	EFO_0004541	8		96.6
hemoglobin measurement	EFO_0004509	3		95.4
mean corpuscular volume	EFO_0004526	1		73.6
hematocrit	EFO_0004348	2		72.9
reticulocyte count	EFO_0007986	2		69.1

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative splicing
Calcium
Cataract
Collagen
Complete proteome
Deafness
Direct protein sequencing
Disease mutation
Disulfide bond

GWAS Trait Find Similar Targets

No Header	No Header
appendicular lean mass
Calcium channel blocker use measurement
eosinophil percentage of leukocytes
gut microbiome measurement
HbA1c measurement
hematocrit
hemoglobin measurement
inflammatory biomarker measurement
lymphocyte count
lymphocyte percentage of leukocytes

MGI Phenotype Find Similar Targets

No Header	No Header
adipose tissue phenotype
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
craniofacial phenotype
digestive/alimentary phenotype
embryo phenotype
growth/size/body region phenotype
hearing/vestibular/ear phenotype
homeostasis/metabolism phenotype

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	collagen, type II, alpha 1	MGI:88452	12824
Rat	collagen type II alpha 1 chain	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	collagen, type II, alpha 1
Rat	collagen type II alpha 1 chain
Dog	collagen type II alpha 1 chain
Horse	collagen type II alpha 1 chain

Publication Statistics

PubMed Score 891.97

PubMed score by year

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PubTator Score 588.73

PubTator score by year

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