SEMA3A semaphorin 3A [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEMA3Aprovided by HGNC
Official Full Name: semaphorin 3Aprovided by HGNC
Primary source: HGNC:HGNC:10723
See related: Ensembl:ENSG00000075213 MIM:603961; AllianceGenome:HGNC:10723
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HH16; SemD; COLL1; SEMA1; SEMAD; SEMAL; coll-1; Hsema-I; SEMAIII; Hsema-III
Summary: This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 2.5), gall bladder (RPKM 2.0) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q21.11

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (83955777..84492725, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (85206156..85764887, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (83585093..83824105, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PIEZO1 Promotes Odontoblast-Mediated Reactionary Dentinogenesis via SEMA3A.
Title: PIEZO1 Promotes Odontoblast-Mediated Reactionary Dentinogenesis via SEMA3A.
Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
Title: Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
Hypoxia-induced Semaphorin 3A promotes the development of endometriosis through regulating macrophage polarization.
Title: Hypoxia-induced Semaphorin 3A promotes the development of endometriosis through regulating macrophage polarization.
Role of Semaphorin 3A in common psychiatric illnesses such as schizophrenia, depression, and anxiety.
Title: Role of Semaphorin 3A in common psychiatric illnesses such as schizophrenia, depression, and anxiety.
Sema3A Alleviates the Malignant Behaviors of Gastric Cancer Cells by Inhibiting NRP-1.
Title: Sema3A Alleviates the Malignant Behaviors of Gastric Cancer Cells by Inhibiting NRP-1.
Semaphorin 3 a restores the ability of type 1 regulatory T cells to suppress food allergy.
Title: Semaphorin 3 a restores the ability of type 1 regulatory T cells to suppress food allergy.
Semmaphorin 3 A causes immune suppression by inducing cytoskeletal paralysis in tumour-specific CD8[+] T cells.
Title: Semmaphorin 3 A causes immune suppression by inducing cytoskeletal paralysis in tumour-specific CD8(+) T cells.
Expression of semaphorin 3A (SEMA3A) in breast cancer subtypes.
Title: Expression of semaphorin 3A (SEMA3A) in breast cancer subtypes.
Sema3A secreted by sensory nerve induces bone formation under mechanical loads.
Title: Sema3A secreted by sensory nerve induces bone formation under mechanical loads.
Semaphorin 3A inhibits tumor progression via the downregulation of Lin28B in ovarian cancer.
Title: Semaphorin 3A inhibits tumor progression via the downregulation of Lin28B in ovarian cancer.

Submit: New GeneRIF Correction See all GeneRIFs (165)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hypogonadotropic hypogonadism 16 with or without anosmia MedGen: C3554021 OMIM: 614897 GeneReviews: Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2017-08-07) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2017-08-07) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of the child behavior checklist dysregulation profile. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS findings for human iris patterns: associations with variants in genes that influence normal neuronal pattern development. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef upregulates VEGFR2 and its co-receptor neuropilin-1 and downregulates the expression of semaphorin 3a in podocytes	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-56119 (e-PCR)
- UniSTS:74775

RH69031 (e-PCR)
- UniSTS:62231

RH119383 (e-PCR)
- UniSTS:132923

RH122163 (e-PCR)
- UniSTS:134723

SHGC-53494 (e-PCR)
- UniSTS:1610

D7S820 (e-PCR), detects polymorphism
- UniSTS:29516

SHGC-82891 (e-PCR)
- UniSTS:96086

D7S2366 (e-PCR)
- UniSTS:68954

G42165 (e-PCR)
- UniSTS:93294

D7S1598 (e-PCR)
- UniSTS:33146

SEMIII (e-PCR)
- UniSTS:32126

GDB:1317948 (e-PCR)
- UniSTS:61826

D7S820 (e-PCR), detects polymorphism
- UniSTS:74895

G42251 (e-PCR)
- UniSTS:93354

SHGC-106937 (e-PCR)
- UniSTS:184500

SEMA3A_1309 (e-PCR)
- UniSTS:277698

SEMA3A_v396 (e-PCR)
- UniSTS:277698

SHGC-33736 (e-PCR)
- UniSTS:8190

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemorepellent activity	TAS Traceable Author Statement more info	PubMed
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	ISS Inferred from Sequence or Structural Similarity more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in axon extension involved in axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in axon guidance	TAS Traceable Author Statement more info	PubMed
involved_in axonogenesis involved in innervation	ISS Inferred from Sequence or Structural Similarity more info
involved_in basal dendrite arborization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in basal dendrite arborization	TAS Traceable Author Statement more info	PubMed
involved_in branchiomotor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in facial nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in motor neuron axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in motor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of axon extension	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nerve development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in neural crest cell migration involved in autonomic nervous system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in olfactory bulb development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of JNK cascade	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in semaphorin-plexin signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in sensory system development	TAS Traceable Author Statement more info	PubMed
involved_in sympathetic ganglion development	ISS Inferred from Sequence or Structural Similarity more info
involved_in sympathetic nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in sympathetic neuron projection extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in sympathetic neuron projection guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in trigeminal nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-3A

Names: collapsin 1; sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A; semaphorin D; semaphorin III; semaphorin L

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011489.1 RefSeqGene

Range

5001..241559

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006080.3 → NP_006071.1 semaphorin-3A precursor

See identical proteins and their annotated locations for NP_006071.1

Status: REVIEWED

Source sequence(s)

AC006322, BM723807, BX491494, CR748125, DR002146, L26081

Consensus CDS

CCDS5599.1

UniProtKB/Swiss-Prot

Q14563

Related

ENSP00000265362.3, ENST00000265362.9

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:579 → 670

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

83955777..84492725 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005250110.4 → XP_005250167.1 semaphorin-3A isoform X1

See identical proteins and their annotated locations for XP_005250167.1

UniProtKB/Swiss-Prot

Q14563

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:579 → 670

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_047419751.1 → XP_047275707.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

85206156..85764887 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357047.1 → XP_054213022.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357048.1 → XP_054213023.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357046.1 → XP_054213021.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357044.1 → XP_054213019.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357049.1 → XP_054213024.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357051.1 → XP_054213026.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357045.1 → XP_054213020.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563
XM_054357050.1 → XP_054213025.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q14563