Tbio COL5A1 Collagen alpha-1(V) chain

Protein Summary

Description

Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin. This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]

Uniprot Accession IDs

• P20908
• A0A087WXW9
• Q15094
• Q5SUX4

Gene Name

• COL5A1

Ensembl ID

• ENST00000371817
• ENSP00000360882
• ENSG00000130635
• ENST00000618395
• ENSP00000481360

Symbol

• EDSC
• EDSCL1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
transcription factor perturbation	0.96
PubMedID	0.91
small molecule perturbation	0.8
molecular function	0.76
disease perturbation	0.74

Protein Classes

No PANTHER Classes or DTO Classes found

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: 208.94   (req: < 5)

Gene RIFs: 64   (req: <= 3)

Antibodies: 405   (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: 208.94   (req: >= 5)

Gene RIFs: 64   (req: > 3)

Antibodies: 405   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 22

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

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Expression Data (0 Tissues)

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No expression data found

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Target Illumination GWAS Analytics (TIGA)

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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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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (167)

Explore Interacting Targets

1 – 10 of 167

• See Interactions on String-DB

LAIR2

Tbio

Novelty:  0.06117644

p_int:  0.999999995

p_ni:  5e-9

Data Source:  BioPlex

COL8A2

Tbio

Novelty:  0.01672103

p_int:  0.999999863

p_ni:  1.32e-7

p_wrong:  5e-9

Score:  0.939

Data Source:  BioPlex,STRINGDB

PLOD1

Tbio

Family:  Enzyme

Novelty:  0.00905345

p_int:  0.99999971

p_ni:  2.9e-7

Score:  0.971

Data Source:  BioPlex,STRINGDB

PTPN2

Tchem

Family:  Enzyme

Novelty:  0.00372891

p_int:  0.999994591

p_ni:  0.000005125

p_wrong:  2.85e-7

Score:  0.455

Data Source:  BioPlex,STRINGDB

MMP9

Tchem

Family:  Enzyme

Novelty:  0.00008645

p_int:  0.99998814

p_ni:  0.000011821

p_wrong:  3.9e-8

Score:  0.421

Data Source:  BioPlex,STRINGDB

C1QTNF2

Tbio

Novelty:  0.18607978

p_int:  0.999926495

p_ni:  0.000043746

p_wrong:  0.000029758

Score:  0.324

Data Source:  BioPlex,STRINGDB

MMP2

Tchem

Family:  Enzyme

Novelty:  0.00012762

p_int:  0.993727212

p_ni:  0.000010308

p_wrong:  0.006262479

Score:  0.804

Data Source:  BioPlex,STRINGDB

PRSS23

Tbio

Family:  Enzyme

Novelty:  0.12685614

p_int:  0.943247269

p_ni:  0.000159095

p_wrong:  0.056593635

Score:  0.322

Data Source:  BioPlex,STRINGDB

COL6A2

Tbio

Novelty:  0.01275082

Score:  0.991

Data Source:  STRINGDB

COL6A1

Tbio

Novelty:  0.00644855

Score:  0.988

Data Source:  STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (16)

Reactome (5)

KEGG (1)

PathwayCommons (6)

WikiPathways (4)

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

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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

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (29)

Functions (7)

Components (7)

Processes (15)

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10

1 – 7 of 7

GO Term	Evidence	Assigned by
heparin binding	Inferred from Direct Assay (IDA)	UniProtKB
platelet-derived growth factor binding	Inferred from Direct Assay (IDA)	MGI
proteoglycan binding	Inferred from Physical Interaction (IPI)	UniProtKB
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
integrin binding	Non-traceable Author Statement (NAS)	UniProtKB
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Disease Associations ()

No disease associations found

GWAS Traits (5)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 5

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
central corneal thickness	EFO_0005213	6	7	2	4.7	96.6
corneal topography	EFO_0004345	1	2	2		74.7
eye measurement	EFO_0004731	3	3	3		41.9
Keratoconus	Orphanet_156071	1	1	1		28
intraocular pressure measurement	EFO_0004695	1	2	2		17.4

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 5

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
central corneal thickness	EFO_0005213	2	4.7	96.6
corneal topography	EFO_0004345	2		74.7
eye measurement	EFO_0004731	3		41.9
Keratoconus	Orphanet_156071	1		28
intraocular pressure measurement	EFO_0004695	2		17.4

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative splicing
Calcium
Collagen
Complete proteome
Direct protein sequencing
Disease mutation
Disulfide bond
Ehlers-Danlos syndrome
Extracellular matrix

GWAS Trait Find Similar Targets

No Header	No Header
central corneal thickness
corneal topography
eye measurement
intraocular pressure measurement
Keratoconus

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
embryo phenotype
integument phenotype
mortality/aging
vision/eye phenotype

IDG Resources

No IDG generated resources found

Orthologs (9)

1 – 5 of 9

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Mouse	collagen, type V, alpha 1	MGI:88457	12831
Rat	collagen type V alpha 1 chain	RGD:70920	85490
Dog	collagen type V alpha 1 chain	VGNC:51943	480684
Horse	collagen type V alpha 1 chain	VGNC:16744	100069057
Pig	collagen type V alpha 1 chain		397533

Species	Name	OMA	EggNOG	Inparanoid
Mouse	collagen, type V, alpha 1
Rat	collagen type V alpha 1 chain
Dog	collagen type V alpha 1 chain
Horse	collagen type V alpha 1 chain
Pig	collagen type V alpha 1 chain

Publication Statistics

PubMed Score 208.94

PubMed score by year

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PubTator Score 144.52

PubTator score by year

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Related Publications

Text Mined References (131)

GeneRif Annotations (64)

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10

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PMID	Year	Title