Tbio SEMA4D Semaphorin-4D

Protein Classes

PANTHER Classes

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

DTO Classes

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

Protein Summary

Description

Cell surface receptor for PLXN1B and PLXNB2 that plays an important role in cell-cell signaling. Promotes reorganization of the actin cytoskeleton and plays a role in axonal growth cone guidance in the developing central nervous system. Regulates dendrite and axon branching and morphogenesis. Promotes the migration of cerebellar granule cells and of endothelial cells. Plays a role in the immune system; induces B-cells to aggregate and improves their viability (in vitro). Promotes signaling via SRC and PTK2B/PYK2, which then mediates activation of phosphatidylinositol 3-kinase and of the AKT1 signaling cascade. Interaction with PLXNB1 mediates activation of RHOA.

Uniprot Accession IDs

• Q92854
• B2RPM6
• Q7Z5S4
• Q8N8B0

Gene Name

• SEMA4D

Ensembl ID

• ENST00000339861
• ENSP00000344923
• ENSG00000187764
• ENST00000356444
• ENSP00000348822
• ENST00000420987
• ENSP00000391733
• ENST00000422704
• ENSP00000388768
• ENST00000438547
• ENSP00000405102
• ENST00000450295
• ENSP00000416523
• ENST00000455551
• ENSP00000411981

Symbol

• C9orf164
• CD100
• SEMAJ
• CD100
• COLL4
• SEMAJ
• coll-4
• C9orf164
• M-sema-G

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
protein domain	0.99
biological process	0.98
disease perturbation	0.83
microRNA	0.8
cell line	0.68

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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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: 280.26   (req: < 5)

Gene RIFs: 68   (req: <= 3)

Antibodies: 795   (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: 280.26   (req: >= 5)

Gene RIFs: 68   (req: > 3)

Antibodies: 795   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 31

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 (14)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 14

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
reticulocyte count	EFO_0007986	6	5	6		77
reticulocyte measurement	EFO_0010700	2	2	2		76.7
body mass index	EFO_0004340	3	3	2	2.9	67.1
triglyceride measurement	EFO_0004530	2	2	2		63.6
mean corpuscular volume	EFO_0004526	1	1	1		56.8

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 14

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
reticulocyte count	EFO_0007986	6		77
reticulocyte measurement	EFO_0010700	2		76.7
body mass index	EFO_0004340	2	2.9	67.1
triglyceride measurement	EFO_0004530	2		63.6
mean corpuscular volume	EFO_0004526	1		56.8

Reset Zoom  Beta Count   Odds Ratio

Orthologs (11)

1 – 5 of 11

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	semaphorin 4D	VGNC:13960	464584
Macaque	semaphorin 4D		697697
Mouse	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	MGI:109244	20354
Rat	semaphorin 4D	RGD:1310554	306790
Dog	semaphorin 4D	VGNC:53974	476350

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

Protein Structure (2 Structures, 1 AlphaFold Model)

tutorial

Representation

  axes   backbone   ball+stick   cartoon   rocket   rope   spacefill

Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

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

AF-Q92854-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 2 of 2

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 (9)

Reactome (7)

KEGG (1)

PathwayCommons (1)

Axon guidance (R-HSA-422475)

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Find Similar Targets

Items per page:

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1 – 5 of 7

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	Sema4D in semaphorin signaling	24 targets	R-HSA-400685
Reactome	Sema4D induced cell migration and growth-cone collapse	20 targets	R-HSA-416572

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
Sema4D in semaphorin signaling	24 targets	R-HSA-400685
Sema4D induced cell migration and growth-cone collapse	20 targets	R-HSA-416572

Gene Ontology Terms (34)

Functions (7)

Components (3)

Processes (24)

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Items per page:

10

1 – 7 of 7

GO Term	Evidence	Assigned by
signaling receptor activity	Inferred from Direct Assay (IDA)	HGNC
signaling receptor binding	Inferred from Direct Assay (IDA)	UniProtKB
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
semaphorin receptor binding	Inferred from Physical Interaction (IPI)	UniProtKB
transmembrane signaling receptor activity	Inferred from Mutant Phenotype (IMP)	UniProtKB
chemorepellent activity	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
neuropilin binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central

Protein-Protein Interactions (106)

Explore Interacting Targets

1 – 10 of 106

• See Interactions on String-DB

CST9L

Tdark

Novelty:  0.21941207

p_int:  0.999999047

p_ni:  9.53e-7

Data Source:  BioPlex

SCGB2A2

Tbio

Novelty:  0.01594053

p_int:  0.99996221

p_ni:  0.000009487

p_wrong:  0.000028302

Score:  0.198

Data Source:  BioPlex,STRINGDB

SCGB1D1

Tbio

Novelty:  0.04199997

p_int:  0.999743484

p_ni:  0.000217704

p_wrong:  0.000038812

Data Source:  BioPlex

VCAM1

Tchem

Novelty:  0.00022504

p_int:  0.999612167

p_ni:  0.000387833

Score:  0.261

Data Source:  BioPlex,STRINGDB

LCN6

Tbio

Novelty:  0.11406686

p_int:  0.999506993

p_ni:  0.00036848

p_wrong:  0.000124527

Data Source:  BioPlex

ST8SIA4

Tbio

Family:  Enzyme

Novelty:  0.00338436

p_int:  0.996746675

p_ni:  0.001443269

p_wrong:  0.001810055

Score:  0.278

Data Source:  BioPlex,STRINGDB

PLXNB1

Tbio

Novelty:  0.01073808

Score:  0.997

Data Source:  Reactome,STRINGDB

CD72

Tbio

Novelty:  0.00787437

Score:  0.986

Data Source:  Reactome,STRINGDB

RND1

Tbio

Family:  Enzyme

Novelty:  0.00834946

Score:  0.974

Data Source:  Reactome,STRINGDB

PLXNB3

Tbio

Novelty:  0.02948198

Score:  0.965

Data Source:  STRINGDB

Publication Statistics

PubMed Score  280.26

PubMed score by year

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PubTator Score  187.48

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

Show Full Sequence

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative splicing
Cell membrane
Complete proteome
Developmental protein
Differentiation
Disulfide bond
Glycoprotein
Immunoglobulin domain
Membrane

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein A 1 measurement
body mass index
chronotype measurement
cleft lip
Cleft palate
grip strength measurement
high density lipoprotein cholesterol measurement
mean corpuscular volume
metabolic syndrome
reticulocyte count

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
immune system phenotype