Tbio SEMA4A Semaphorin-4A

Protein Summary

Description

Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling. Plays a role in priming antigen-specific T-cells, promotes differentiation of Th1 T-helper cells, and thereby contributes to adaptive immunity. Promotes phosphorylation of TIMD2. Inhibits angiogenesis. Promotes axon growth cone collapse. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons (By similarity). This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

Uniprot Accession IDs

• Q9H3S1
• B2RDH8
• B3KR76
• Q5TCI5
• Q5TCJ6
• Q8WUA9

Gene Name

• SEMA4A

Ensembl ID

• ENST00000355014
• ENSP00000347117
• ENSG00000196189
• ENST00000368282
• ENSP00000357265
• ENST00000368284
• ENSP00000357267
• ENST00000368285
• ENSP00000357268

Symbol

• SEMAB
• SEMB
• RP35
• SEMB
• SEMAB
• CORD10

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
PubMedID	0.74
protein domain	0.73
transcription factor	0.71
disease perturbation	0.62
biological process	0.57

Protein Classes

PANTHER Classes

Protein / Signaling Molecule / Membrane-bound Signaling Molecule / Semaphorin-4a

DTO Classes

Protein / Signaling / Membrane-bound Signaling Molecule / Semaphorin-4a

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: 96.65   (req: < 5)

Gene RIFs: 20   (req: <= 3)

Antibodies: 344   (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: 96.65   (req: >= 5)

Gene RIFs: 20   (req: > 3)

Antibodies: 344   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 14

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

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

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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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (137)

Explore Interacting Targets

1 – 10 of 137

• See Interactions on String-DB

TMEM192

Tbio

Novelty:  0.30699087

p_int:  0.999339649

p_ni:  0.000660339

p_wrong:  1.2e-8

Data Source:  BioPlex

LEMD3

Tbio

Novelty:  0.00579701

p_int:  0.994464836

p_ni:  0.005535161

p_wrong:  3e-9

Data Source:  BioPlex

SEMA4C

Tbio

Novelty:  0.01237067

p_int:  0.993990505

p_ni:  0.006008961

p_wrong:  5.34e-7

Data Source:  BioPlex

SIRT5

Tchem

Family:  Epigenetic

Novelty:  0.00225239

p_int:  0.993663319

p_ni:  0.006091591

p_wrong:  0.00024509

Data Source:  BioPlex

SEMA4B

Tbio

Novelty:  0.01387522

p_int:  0.993488178

p_ni:  0.006506451

p_wrong:  0.000005371

Data Source:  BioPlex

GMCL1

Tbio

Novelty:  0.1543762

p_int:  0.981875529

p_ni:  0.000913325

p_wrong:  0.017211146

Data Source:  BioPlex

PLXND1

Tbio

Novelty:  0.01249713

Score:  0.994

Data Source:  Reactome,STRINGDB

NRP1

Tchem

Novelty:  0.00153628

Score:  0.868

Data Source:  STRINGDB

PLXNB3

Tbio

Novelty:  0.02948198

Score:  0.861

Data Source:  STRINGDB

PLXNB2

Tbio

Novelty:  0.01925055

Score:  0.861

Data Source:  STRINGDB

Nearest Tclin Targets (2)

Explore Nearest Tclin Targets

Downstream (2)

1 – 2 of 2

ROCK2

Tclin

Family:  Kinase

KEGG Distance:  4

Common Pathways:  1

1: Axon guidance

ROCK1

Tclin

Family:  Kinase

KEGG Distance:  4

Common Pathways:  1

1: Axon guidance

Pathways (6)

Reactome (4)

KEGG (1)

PathwayCommons (1)

Axon guidance (R-HSA-422475)

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Find Similar Targets

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1 – 4 of 4

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Axon guidance	533 targets	R-HSA-422475
Reactome	Developmental Biology	1055 targets	R-HSA-1266738
Reactome	Other semaphorin interactions	19 targets	R-HSA-416700
Reactome	Semaphorin interactions	64 targets	R-HSA-373755

Name	Explore in Pharos	Explore in Source
Axon guidance	533 targets	R-HSA-422475
Developmental Biology	1055 targets	R-HSA-1266738
Other semaphorin interactions	19 targets	R-HSA-416700
Semaphorin interactions	64 targets	R-HSA-373755

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (20)

Functions (3)

Components (6)

Processes (11)

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1 – 3 of 3

GO Term	Evidence	Assigned by
chemorepellent activity	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
neuropilin binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
semaphorin receptor binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central

Disease Associations (null)

No disease associations found

GWAS Traits (28)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 28

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mosaic loss of chromosome Y measurement	EFO_0007783	3	2	3		94.7
serum urea measurement	EFO_0009795	1	3	3		84.4
HbA1c measurement	EFO_0004541	2	2	2		82.4
body mass index	EFO_0004340	3	1	3		76.3
appendicular lean mass	EFO_0004980	3	2	4		76.2

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 28

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mosaic loss of chromosome Y measurement	EFO_0007783	3		94.7
serum urea measurement	EFO_0009795	3		84.4
HbA1c measurement	EFO_0004541	2		82.4
body mass index	EFO_0004340	3		76.3
appendicular lean mass	EFO_0004980	4		76.2

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
Adaptive immunity
Alternative splicing
Angiogenesis
Cell membrane
Complete proteome
Cone-rod dystrophy
Developmental protein
Differentiation
Disease mutation
Disulfide bond

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein A 1 measurement
appendicular lean mass
body height
body mass index
C-reactive protein measurement
creatinine measurement
glomerular filtration rate
HbA1c measurement
hemoglobin measurement
high density lipoprotein cholesterol measurement

MGI Phenotype Find Similar Targets

No Header	No Header
cellular phenotype
hematopoietic system phenotype
immune system phenotype
nervous system phenotype
pigmentation phenotype
vision/eye phenotype

IDG Resources

No IDG generated resources found

Orthologs (8)

1 – 5 of 8

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	semaphorin 4A	VGNC:10993	457386
Macaque	semaphorin 4A		718191
Mouse	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	MGI:107560	20351
Rat	semaphorin 4A	RGD:1304636	310630
Dog	semaphorin 4A	VGNC:45994	490416

Species	Name	OMA	EggNOG	Inparanoid
Chimp	semaphorin 4A
Macaque	semaphorin 4A
Mouse	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A
Rat	semaphorin 4A
Dog	semaphorin 4A

Publication Statistics

PubMed Score 96.65

PubMed score by year

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PubTator Score 36.85

PubTator score by year

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Related Publications

Text Mined References (32)

GeneRif Annotations (20)

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10

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PMID	Year	Title