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    Sema3a semaphorin 3A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 29751, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sema3aprovided by RGD
    Official Full Name
    semaphorin 3Aprovided by RGD
    Primary source
    RGD:3657
    See related
    EnsemblRapid:ENSRNOG00000023337 AllianceGenome:RGD:3657
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in negative regulation of axon extension. Acts upstream of or within axon guidance. Located in axon and dendrite. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 34.4), Brain (RPKM 32.2) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Sema3a in Genome Data Viewer
    Location:
    4q12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (22239418..22709907, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (21282398..21754834, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (18170375..18545190, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120102217 Neighboring gene uncharacterized LOC134486717 Neighboring gene uncharacterized LOC120102218 Neighboring gene uncharacterized LOC134486718

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity  
    enables chemorepellent activity  
    enables neuropilin binding  
    enables neuropilin binding  
    enables semaphorin receptor binding  
    enables semaphorin receptor binding  
    enables semaphorin receptor binding  
    Items 1 - 25 of 50
    Process Evidence Code Pubs
    acts_upstream_of axon extension  
    acts_upstream_of axon extension involved in axon guidance  
    involved_in axon extension involved in axon guidance  
    involved_in axon guidance  
    acts_upstream_of_or_within axon guidance PubMed 
    acts_upstream_of_or_within axon guidance  
    acts_upstream_of_or_within axonal fasciculation  
    involved_in axonogenesis involved in innervation  
    involved_in basal dendrite arborization  
    involved_in branchiomotor neuron axon guidance  
    acts_upstream_of_or_within dendrite morphogenesis  
    acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching  
    acts_upstream_of epithelial cell migration  
    involved_in facial nerve structural organization  
    involved_in facioacoustic ganglion development  
    involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus  
    involved_in maintenance of synapse structure  
    involved_in motor neuron axon guidance  
    involved_in motor neuron axon guidance  
    involved_in negative chemotaxis  
    acts_upstream_of_or_within negative chemotaxis  
    involved_in negative regulation of axon extension PubMed 
    acts_upstream_of_or_within negative regulation of axon extension  
    acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance  
    acts_upstream_of_or_within negative regulation of epithelial cell migration  
    involved_in negative regulation of neuron projection development  
    involved_in nerve development  
    acts_upstream_of_or_within nervous system development  
    involved_in neural crest cell migration  
    involved_in neural crest cell migration involved in autonomic nervous system development  
    involved_in neural crest cell migration involved in sympathetic nervous system development  
    involved_in neuron migration  
    involved_in olfactory bulb development  
    involved_in olfactory bulb development  
    involved_in positive regulation of cell migration  
    involved_in positive regulation of male gonad development  
    involved_in positive regulation of neuron migration  
    involved_in regulation of axon extension involved in axon guidance  
    acts_upstream_of_or_within regulation of heart rate  
    involved_in regulation of plasma membrane bounded cell projection organization  
    involved_in semaphorin-plexin signaling pathway  
    acts_upstream_of_or_within semaphorin-plexin signaling pathway  
    involved_in semaphorin-plexin signaling pathway  
    involved_in sympathetic ganglion development  
    involved_in sympathetic neuron projection extension  
    involved_in sympathetic neuron projection guidance  
    involved_in synaptic target recognition  
    involved_in trigeminal ganglion development  
    involved_in trigeminal nerve structural organization  
    involved_in ventral trunk neural crest cell migration  
    Items 1 - 25 of 50
    Component Evidence Code Pubs
    is_active_in axon  
    located_in axon PubMed 
    is_active_in cerebellar climbing fiber to Purkinje cell synapse  
    located_in dendrite PubMed 
    located_in extracellular region  
    is_active_in extracellular space  
    located_in extracellular space PubMed 
    is_active_in glutamatergic synapse  
    is_active_in glutamatergic synapse  
    is_active_in plasma membrane  

    General protein information

    Preferred Names
    semaphorin-3A
    Names
    sema III
    sema domain, immunoglobulin domain (Ig), short basic domain, sec
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
    semaphorin III

    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.

    mRNA and Protein(s)

    1. NM_017310.2NP_059006.1  semaphorin-3A precursor

      See identical proteins and their annotated locations for NP_059006.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      Q63548
      UniProtKB/TrEMBL
      A0A8L2QL58, A6K213
      Related
      ENSRNOP00000036472.3, ENSRNOT00000034692.5
      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:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      22239418..22709907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008762702.3XP_008760924.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_008760924.1

      UniProtKB/Swiss-Prot
      Q63548
      UniProtKB/TrEMBL
      A0A8L2QL58, A6K213
      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:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
    2. XM_063285863.1XP_063141933.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q63548
      UniProtKB/TrEMBL
      A0A8L2QL58, A6K213
    3. XM_006235990.5XP_006236052.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_006236052.1

      UniProtKB/Swiss-Prot
      Q63548
      UniProtKB/TrEMBL
      A0A8L2QL58, A6K213
      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:580671
      Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
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