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    SEMA3A semaphorin 3A [ Homo sapiens (human) ]

    Gene ID: 10371, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SEMA3A in Genome Data Viewer
    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_000007.14Genomic 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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

    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)

    NEW Try the new Transcript table

    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_006080.3NP_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: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
      cd05871
      Location:579670
      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

    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_005250110.4XP_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: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
      cd05871
      Location:579670
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    2. XM_047419751.1XP_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_054357047.1XP_054213022.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    2. XM_054357048.1XP_054213023.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    3. XM_054357046.1XP_054213021.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    4. XM_054357044.1XP_054213019.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    5. XM_054357049.1XP_054213024.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    6. XM_054357051.1XP_054213026.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    7. XM_054357045.1XP_054213020.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563
    8. XM_054357050.1XP_054213025.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q14563