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SEMA3A semaphorin 3A [ Homo sapiens (human) ]

Gene ID: 10371, updated on 8-Jul-2018
Official Symbol
SEMA3Aprovided by HGNC
Official Full Name
semaphorin 3Aprovided by HGNC
Primary source
HGNC:HGNC:10723
See related
Ensembl:ENSG00000075213 MIM:603961; Vega:OTTHUMG00000023443
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
See SEMA3A in Genome Data Viewer
Location:
7q21.11
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (83956846..84515189, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (83587659..84122040, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RAD23 homolog B pseudogene 2 Neighboring gene uncharacterized LOC107986745 Neighboring gene uncharacterized LOC101927378 Neighboring gene ribosomal protein L7 pseudogene 30

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

NHGRI GWAS Catalog

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

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

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • CRMPs in Sema3A signaling, organism-specific biosystem (from REACTOME)
    CRMPs in Sema3A signaling, organism-specific biosystemCRMPs are a small family of plexinA-interacting cytosolic phosphoproteins identified as mediators of Sema3A signaling and neuronal differentiation. After Sema3A activation Plexin-A bound CRMP's under...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion, organism-specific biosystem (from REACTOME)
    SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion, organism-specific biosystemSema3A, a prototypical semaphorin, acts as a chemorepellent or a chemoattractant for axons by activating a receptor complex comprising neuropilin-1 as the ligand-binding subunit and plexin-A1 as the ...
  • Sema3A PAK dependent Axon repulsion, organism-specific biosystem (from REACTOME)
    Sema3A PAK dependent Axon repulsion, organism-specific biosystemActivated Rac1 bound to plexin-A might modulate actin dynamics through the sequential phosphorylation and activation of PAK, LIMK1 and cofilin.
  • Semaphorin interactions, organism-specific biosystem (from REACTOME)
    Semaphorin interactions, organism-specific biosystemSemaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphor...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC133243

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemorepellent activity TAS
Traceable Author Statement
more info
PubMed 
neuropilin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuropilin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin receptor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
axon guidance TAS
Traceable Author Statement
more info
PubMed 
axonal fasciculation IEA
Inferred from Electronic Annotation
more info
 
axonogenesis involved in innervation ISS
Inferred from Sequence or Structural Similarity
more info
 
basal dendrite arborization ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
basal dendrite arborization TAS
Traceable Author Statement
more info
PubMed 
branchiomotor neuron axon guidance IEA
Inferred from Electronic Annotation
more info
 
dichotomous subdivision of terminal units involved in salivary gland branching IEA
Inferred from Electronic Annotation
more info
 
facial nerve structural organization IEA
Inferred from Electronic Annotation
more info
 
facioacoustic ganglion development IEA
Inferred from Electronic Annotation
more info
 
gonadotrophin-releasing hormone neuronal migration to the hypothalamus IEA
Inferred from Electronic Annotation
more info
 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative chemotaxis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of axon extension involved in axon guidance IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial cell migration IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
nerve development ISS
Inferred from Sequence or Structural Similarity
more info
 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural crest cell migration involved in autonomic nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
 
neural crest cell migration involved in sympathetic nervous system development IEA
Inferred from Electronic Annotation
more info
 
neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
 
olfactory bulb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of JNK cascade TAS
Traceable Author Statement
more info
PubMed 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of male gonad development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of axon extension involved in axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
regulation of heart rate IEA
Inferred from Electronic Annotation
more info
 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway TAS
Traceable Author Statement
more info
PubMed 
semaphorin-plexin signaling pathway involved in axon guidance IEA
Inferred from Electronic Annotation
more info
 
semaphorin-plexin signaling pathway involved in neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
sensory system development TAS
Traceable Author Statement
more info
PubMed 
sympathetic ganglion development ISS
Inferred from Sequence or Structural Similarity
more info
 
sympathetic nervous system development TAS
Traceable Author Statement
more info
PubMed 
sympathetic neuron projection extension ISS
Inferred from Sequence or Structural Similarity
more info
 
sympathetic neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
trigeminal ganglion development IEA
Inferred from Electronic Annotation
more info
 
trigeminal nerve structural organization IEA
Inferred from Electronic Annotation
more info
 
ventral trunk neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
semaphorin-3A
Names
collapsin 1
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
semaphorin D
semaphorin III
semaphorin L

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_006080.2NP_006071.1  semaphorin-3A precursor

    See identical proteins and their annotated locations for NP_006071.1

    Status: REVIEWED

    Source sequence(s)
    AC006322, BM723807, BU186364, BX491494, CR748125, DR002146, L26081
    Consensus CDS
    CCDS5599.1
    UniProtKB/Swiss-Prot
    Q14563
    Related
    ENSP00000265362.3, OTTHUMP00000161379, ENST00000265362.8, OTTHUMT00000253355
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    83956846..84515189 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446633.1XP_024302401.1  semaphorin-3A isoform X1

    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. XM_011515734.3XP_011514036.1  semaphorin-3A isoform X1

    See identical proteins and their annotated locations for XP_011514036.1

    UniProtKB/Swiss-Prot
    Q14563
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
  3. XM_005250110.3XP_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
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
  4. XM_005250111.4XP_005250168.1  semaphorin-3A isoform X1

    See identical proteins and their annotated locations for XP_005250168.1

    UniProtKB/Swiss-Prot
    Q14563
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
  5. XM_017011673.1XP_016867162.1  semaphorin-3A isoform X1

    UniProtKB/Swiss-Prot
    Q14563
    Related
    ENSP00000415260.1, OTTHUMP00000208884, ENST00000436949.5, OTTHUMT00000342239
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
  6. XM_006715839.3XP_006715902.1  semaphorin-3A isoform X1

    See identical proteins and their annotated locations for XP_006715902.1

    UniProtKB/Swiss-Prot
    Q14563
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
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