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SEMA3A semaphorin 3A [ Homo sapiens (human) ]

Gene ID: 10371, updated on 17-Apr-2024

Summary

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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

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Location:
7q21.11
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (83955777..84492725, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (85206156..85764887, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (83585093..83824105, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83314287-83314786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83315470-83315977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:83320326-83320837 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83322516-83323158 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:83337804-83339003 Neighboring gene RAD23B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83463173-83463673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18337 Neighboring gene uncharacterized LOC107986745 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83623841-83624402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83624403-83624963 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:83631626-83632189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26218 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83684723-83685314 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83684131-83684722 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:83720483-83720983 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83779267-83779791 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83779792-83780315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:83795422-83795922 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:83824219-83825026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83835322-83836064 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chr7:83857426-83857944 and GRCh37_chr7:83857945-83858461 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:83880131-83881330 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83906806-83907406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26219 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:84001008-84002207 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100327 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100336 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100364 Neighboring gene long intergenic non-protein coding RNA 3017 Neighboring gene ribosomal protein L7 pseudogene 30

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Semaphorin 3A Levels in Lupus with and without Secondary Antiphospholipid Antibody Syndrome and Renal Involvement. Kart Bayram GS, et al. Lab Med, 2022 May 5. PMID 34927690
  2. Low Urine Secretion of Semaphorin3A in Lupus Patients with Proteinuria. Doron R, et al. Inflammation, 2022 Apr. PMID 34562225
  3. [Expression of Semaphorin 3A after spinal cord injury]. Wang GY, et al. Zhongguo Gu Shang, 2021 Apr 25. PMID 33896139
  4. Immunosuppressive Regulation of Dendritic Cells and T Cells in Allergic Rhinitis by Semaphorin 3A. Liu H, et al. Am J Rhinol Allergy, 2021 Nov. PMID 33761786
  5. Further delineation of a recognizable type of syndromic short stature caused by biallelic SEMA3A loss-of-function variants. Gileta AF, et al. Am J Med Genet A, 2021 Mar. PMID 33369061, Free PMC Article

See all (191) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Expression of semaphorin 3A (SEMA3A) in breast cancer subtypes.
    Title: Expression of semaphorin 3A (SEMA3A) in breast cancer subtypes.
  3. Sema3A secreted by sensory nerve induces bone formation under mechanical loads.
    Title: Sema3A secreted by sensory nerve induces bone formation under mechanical loads.
  4. 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.
  5. CD72-semaphorin3A axis: A new regulatory pathway in systemic lupus erythematosus.
    Title: CD72-semaphorin3A axis: A new regulatory pathway in systemic lupus erythematosus.
  6. Semaphorin 3A-Neuropilin-1 Signaling Modulates MMP13 Expression in Human Osteoarthritic Chondrocytes.
    Title: Semaphorin 3A-Neuropilin-1 Signaling Modulates MMP13 Expression in Human Osteoarthritic Chondrocytes.
  7. Semaphorin 3A protects against alveolar bone loss during orthodontic tooth movement in mice with periodontitis.
    Title: Semaphorin 3A protects against alveolar bone loss during orthodontic tooth movement in mice with periodontitis.
  8. The possible involvement of sema3A and sema4A in the pathogenesis of multiple sclerosis.
    Title: The possible involvement of sema3A and sema4A in the pathogenesis of multiple sclerosis.
  9. Semaphorin 3A Levels in Lupus with and without Secondary Antiphospholipid Antibody Syndrome and Renal Involvement.
    Title: Semaphorin 3A Levels in Lupus with and without Secondary Antiphospholipid Antibody Syndrome and Renal Involvement.
  10. Low Urine Secretion of Semaphorin3A in Lupus Patients with Proteinuria.
    Title: Low Urine Secretion of Semaphorin3A in Lupus Patients with Proteinuria.
Submit: New GeneRIF Correction See all GeneRIFs (159)

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC133243

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 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

  1. NG_011489.1 RefSeqGene

    Range
    5001..241559
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    83955777..84492725 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_047419751.1 → XP_047275707.1  semaphorin-3A isoform X1

    UniProtKB/Swiss-Prot
    Q14563

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    85206156..85764887 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563

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

    UniProtKB/Swiss-Prot
    Q14563
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14563.1 GenPept UniProtKB/Swiss-Prot:Q14563

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