Gene info: ID 10371

Gene: SEMA3A

GENE ID: 10371

Description: semaphorin 3A

Gene type: protein-coding

Location: 7q21.11

dbXrefs: Ensembl:ENSG00000075213 MIM:603961 Vega:OTTHUMG00000023443 UniprotKB:Q14563

RefSeq: NG_011489.1

Retrived from: PubMed|SNP Mapped

SNPs: 3 ANCO-SNPs

Phenotype: ND|AD

# Publications: 1

Sherlock p-value : NA (AD) NA (ND) (Frontal_Cortex)

Pascal p-value : 7.856e-1 (AD) 9.717e-2 (ND)

ANCO-SNPs

SNP ID	Position	Alleles	Trait	Variation Type
rs10261069	chr7:84172336 (GRCh38.p7)	C>T	nicotine dependence	SNV(Single Nucleotide Variation)
rs7808864	chr7:84094031 (GRCh38.p7)	A>G	nicotine dependence	SNV(Single Nucleotide Variation)
rs139438618	chr7:84008281 (GRCh38.p7)	A>G	alcohol dependence	SNV(Single Nucleotide Variation)

DNA Methylation

There is no related methylation information for this gene.

Gene Expression in Different Tissues

Temporal and Spatial Expressions (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes average value of the expressions.

Top Co-expressed Genes in Brain-Frontal Cortex (BA9) (GTEx v7)

Top 10 positively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
EPHA7	0.803
OPRK1	0.798
SETDB2	0.794
DACH1	0.781
MCTP1	0.773
ATP8A1	0.772
SPEF2	0.77
PPP1R9A	0.765
RSPO3	0.76
LMLN	0.758

Top 10 negatively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
MTRNR2L8	-0.473
MTRNR2L2	-0.437
C4orf19	-0.412
KLRB1	-0.411
FOXL1	-0.407
TFPI2	-0.405
MDFI	-0.403
PLA2G5	-0.394
NKX6-1	-0.388
MTRNR2L9	-0.385

There is no DrugBank record for this gene !

ID	Drug Name	Action	PubMed
C548651	2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester	2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester results in decreased expression of SEMA3A mRNA	19933214
C029790	2,2',3',4,4',5-hexachlorobiphenyl	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C081766	2,4,4'-trichlorobiphenyl	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C014024	2,4,5,2',4',5'-hexachlorobiphenyl	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C009828	2,4,5,2',5'-pentachlorobiphenyl	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C009407	2,5,2',5'-tetrachlorobiphenyl	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with trichostatin A co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with trichostatin A co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
D000082	Acetaminophen	Acetaminophen results in increased expression of SEMA3A mRNA	26690555
D019342	Acetic Acid	Acetic Acid results in decreased expression of SEMA3A protein	21296659
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased methylation of SEMA3A gene	27153756
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of SEMA3A mRNA	16483693
D018501	Antirheumatic Agents	Antirheumatic Agents results in decreased expression of SEMA3A mRNA	24449571
D001151	Arsenic	Arsenic affects the methylation of SEMA3A gene	25304211
C006632	arsenic trioxide	arsenic trioxide results in decreased expression of SEMA3A mRNA	26705709
D017638	Asbestos, Crocidolite	"Asbestos, Crocidolite results in increased expression of SEMA3A mRNA"	25351596
D001280	Atrazine	Atrazine results in decreased expression of SEMA3A mRNA	25929836
D001280	Atrazine	Atrazine results in increased expression of SEMA3A mRNA	18585445
D001374	Azacitidine	Azacitidine results in increased expression of SEMA3A mRNA	20823114
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in decreased expression of SEMA3A mRNA	20713471
D004958	Estradiol	[Estradiol co-treated with Bucladesine co-treated with Medroxyprogesterone Acetate] results in increased expression of SEMA3A mRNA	20823114
D004958	Estradiol	Estradiol results in decreased expression of SEMA3A mRNA	21185374
C006780	bisphenol A	bisphenol A results in increased expression of SEMA3A mRNA	25594700
C006780	bisphenol A	bisphenol A results in decreased expression of SEMA3A mRNA	25181051
C006780	bisphenol A	bisphenol A results in increased expression of SEMA3A mRNA	29097150
C099813	bromochloroacetic acid	bromochloroacetic acid results in decreased expression of SEMA3A protein	21296659
D002104	Cadmium	Cadmium results in increased expression of SEMA3A mRNA	21120746
D019256	Cadmium Chloride	Cadmium Chloride results in increased methylation of SEMA3A promoter	22457795
D002330	Carmustine	SEMA3A mRNA affects the susceptibility to Carmustine	16365179
D003042	Cocaine	Cocaine results in decreased expression of SEMA3A mRNA	27899881
D019327	Copper Sulfate	Copper Sulfate results in decreased expression of SEMA3A mRNA	19549813
D016572	Cyclosporine	Cyclosporine results in decreased expression of SEMA3A mRNA	20106945
D000069439	Dasatinib	Dasatinib results in decreased expression of SEMA3A mRNA	20579391
C007262	deoxynivalenol	deoxynivalenol results in decreased expression of SEMA3A mRNA	26763390
D003994	Bucladesine	[Estradiol co-treated with Bucladesine co-treated with Medroxyprogesterone Acetate] results in increased expression of SEMA3A mRNA	20823114
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in increased expression of SEMA3A mRNA	29097150
D005472	Fluorouracil	Fluorouracil results in increased expression of SEMA3A mRNA	16510598
D005947	Glucose	Glucose results in decreased expression of SEMA3A mRNA	17178593
C409722	hexaconazole	hexaconazole affects the expression of SEMA3A mRNA	22045034
C492448	ICG 001	ICG 001 results in decreased expression of SEMA3A mRNA	26191083
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in decreased expression of SEMA3A mRNA	24796395\|2675264
C561695	(+)-JQ1 compound	[PD 0325901 co-treated with (+)-JQ1 compound] results in decreased expression of SEMA3A mRNA	25119042
D017258	Medroxyprogesterone Acetate	[Estradiol co-treated with Bucladesine co-treated with Medroxyprogesterone Acetate] results in increased expression of SEMA3A mRNA	20823114
D008727	Methotrexate	Methotrexate results in increased expression of SEMA3A mRNA	21678067
C004925	methylmercuric chloride	methylmercuric chloride results in decreased expression of SEMA3A mRNA	28001369
D037742	Nanotubes, Carbon	"Nanotubes, Carbon analog results in decreased expression of SEMA3A mRNA"	25554681
D037742	Nanotubes, Carbon	"Nanotubes, Carbon results in decreased expression of SEMA3A mRNA"	25554681
C009618	O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate	"O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate results in increased expression of SEMA3A mRNA"	21673326
C009618	O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate	"PON1 protein affects the reaction [O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate results in increased expression of SEMA3A mRNA]"	21673326
C410127	PCB 180	"[2,4,4'-trichlorobiphenyl co-treated with 2,5,2',5'-tetrachlorobiphenyl co-treated with 2,4,5,2',5'-pentachlorobiphenyl co-treated with 2,2',3',4,4',5-hexachlorobiphenyl co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with PCB 180] results in decreased expression of SEMA3A mRNA"	25510870
C506614	PD 0325901	[PD 0325901 co-treated with (+)-JQ1 compound] results in decreased expression of SEMA3A mRNA	25119042
C506614	PD 0325901	PD 0325901 results in decreased expression of SEMA3A mRNA	25119042
C027373	potassium chromate(VI)	potassium chromate(VI) results in decreased expression of SEMA3A mRNA	22714537
D020849	Raloxifene Hydrochloride	Raloxifene Hydrochloride results in decreased expression of SEMA3A mRNA	21185374
C017947	sodium arsenite	sodium arsenite results in increased expression of and affects the splicing of SEMA3A mRNA	25879800
C047246	temozolomide	SEMA3A mRNA affects the susceptibility to temozolomide	16365179
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of SEMA3A mRNA	21570461
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in decreased expression of SEMA3A mRNA	19933214
C012589	trichostatin A	"[NOG protein co-treated with trichostatin A co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
C012589	trichostatin A	trichostatin A results in decreased expression of SEMA3A mRNA	24935251\|2627250
C012589	trichostatin A	trichostatin A results in increased expression of SEMA3A mRNA	27188386
C012589	trichostatin A	trichostatin A results in decreased expression of SEMA3A mRNA	15901671
C016805	tris(1,3-dichloro-2-propyl)phosphate	"tris(1,3-dichloro-2-propyl)phosphate results in decreased expression of SEMA3A mRNA"	26179874
D014520	Urethane	Urethane results in decreased expression of SEMA3A mRNA	28818685
D014635	Valproic Acid	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in decreased expression of SEMA3A mRNA"	27188386
D014635	Valproic Acid	Valproic Acid affects the expression of SEMA3A mRNA	25979313
D014635	Valproic Acid	Valproic Acid results in decreased expression of SEMA3A mRNA	23179753\|2627250
D014635	Valproic Acid	Valproic Acid results in increased expression of SEMA3A mRNA	23179753
D014635	Valproic Acid	Valproic Acid affects the expression of SEMA3A mRNA	22045034
D014635	Valproic Acid	Valproic Acid results in decreased expression of SEMA3A mRNA	15901671
D014638	Vanadates	Vanadates results in increased expression of SEMA3A mRNA	22714537
D001335	Vehicle Emissions	Vehicle Emissions results in increased methylation of SEMA3A gene	25560391
C111237	vorinostat	vorinostat results in increased expression of SEMA3A mRNA	27188386

GO/Pathway

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0030215	semaphorin receptor binding	-	IBA	21873635
GO:0030215	semaphorin receptor binding	-	IEA	-
GO:0038191	neuropilin binding	-	IBA	21873635
GO:0038191	neuropilin binding	-	ISS	-
GO:0045499	chemorepellent activity	-	IBA	21873635
GO:0045499	chemorepellent activity	-	TAS	19909241

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0001755	neural crest cell migration	-	IBA	21873635
GO:0001764	neuron migration	-	ISS	-
GO:0002027	regulation of heart rate	-	IEA	-
GO:0006915	apoptotic process	-	IEA	-
GO:0007411	axon guidance	-	TAS	19909241
GO:0007413	axonal fasciculation	-	IEA	-
GO:0010633	negative regulation of epithelial cell migration	-	IEA	-
GO:0010977	negative regulation of neuron projection development	-	IMP	21593320
GO:0021612	facial nerve structural organization	-	IEA	-
GO:0021637	trigeminal nerve structural organization	-	IEA	-
GO:0021675	nerve development	-	ISS	-
GO:0021772	olfactory bulb development	-	IMP	22416012
GO:0021785	branchiomotor neuron axon guidance	-	IEA	-
GO:0021828	gonadotrophin-releasing hormone neuronal migration to the hypothalamus	-	IEA	-
GO:0030335	positive regulation of cell migration	-	IBA	21873635
GO:0036486	ventral trunk neural crest cell migration	-	IEA	-
GO:0046330	positive regulation of JNK cascade	-	TAS	22683681
GO:0048485	sympathetic nervous system development	-	TAS	19909241
GO:0048841	regulation of axon extension involved in axon guidance	-	IDA	18053124
GO:0048843	negative regulation of axon extension involved in axon guidance	-	IBA	21873635
GO:0048843	negative regulation of axon extension involved in axon guidance	-	IEA	-
GO:0048846	axon extension involved in axon guidance	-	ISS	-
GO:0048880	sensory system development	-	TAS	19909241
GO:0050919	negative chemotaxis	-	IBA	21873635
GO:0050919	negative chemotaxis	-	IEA	-
GO:0060385	axonogenesis involved in innervation	-	ISS	-
GO:0060666	dichotomous subdivision of terminal units involved in salivary gland branching	-	IEA	-
GO:0061549	sympathetic ganglion development	-	ISS	-
GO:0061551	trigeminal ganglion development	-	IEA	-
GO:0071526	semaphorin-plexin signaling pathway	-	IBA	21873635
GO:0071526	semaphorin-plexin signaling pathway	-	TAS	19909241
GO:0097490	sympathetic neuron projection extension	-	ISS	-
GO:0097491	sympathetic neuron projection guidance	-	ISS	-
GO:0150020	basal dendrite arborization	-	ISS	22683681
GO:0150020	basal dendrite arborization	-	TAS	22683681
GO:1901166	neural crest cell migration involved in autonomic nervous system development	-	ISS	-
GO:1902285	semaphorin-plexin signaling pathway involved in neuron projection guidance	-	ISS	-
GO:1902287	semaphorin-plexin signaling pathway involved in axon guidance	-	IEA	-
GO:1903045	neural crest cell migration involved in sympathetic nervous system development	-	IEA	-
GO:1903375	facioacoustic ganglion development	-	IEA	-
GO:2000020	positive regulation of male gonad development	-	IEA	-
GO:2001224	positive regulation of neuron migration	-	IBA	21873635

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0005576	extracellular region	-	TAS	-
GO:0005615	extracellular space	-	IBA	21873635
GO:0005887	integral component of plasma membrane	-	IBA	21873635
GO:0030424	axon	-	IBA	21873635
GO:0030425	dendrite	-	IEA	-

KEGG ID	KEGG Term
hsa04360	Axon guidance

Reactome ID	Reactome Term	Evidence
R-HSA-1266738	Developmental Biology	TAS
R-HSA-1266738	Developmental Biology	IEA
R-HSA-373755	Semaphorin interactions	TAS
R-HSA-373755	Semaphorin interactions	IEA
R-HSA-399954	Sema3A PAK dependent Axon repulsion	TAS
R-HSA-399955	SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion	IEA
R-HSA-399955	SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion	TAS
R-HSA-399956	CRMPs in Sema3A signaling	TAS
R-HSA-399956	CRMPs in Sema3A signaling	IEA
R-HSA-422475	Axon guidance	TAS
R-HSA-422475	Axon guidance	IEA

Interactions (STRING v10.5, Interaction Score >= 0.400)

Publications (Co-occurrence of gene symbol strings and ANCO-Dependence terms)

PMID	Title (Year)	Author	Journal
29071344	Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression. (2017 Dec 1)	Zhou H	JAMA Psychiatry