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

    Gene ID: 29751, updated on 3-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, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 34.4), Brain (RPKM 32.2) and 9 other tissues See more
    Orthologs
    NEW
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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

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chemorepellent activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables neuropilin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables semaphorin receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables semaphorin receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within axon guidance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within axonal fasciculation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in axonogenesis involved in innervation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in basal dendrite arborization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in branchiomotor neuron axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dendrite morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of epithelial cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in facial nerve structural organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in facioacoustic ganglion development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in maintenance of synapse structure ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in motor neuron axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in motor neuron axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of epithelial cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nerve development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within nervous system development ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neural crest cell migration involved in sympathetic nervous system development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory bulb development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of male gonad development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of axon extension involved in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of heart rate ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of plasma membrane bounded cell projection organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sympathetic ganglion development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sympathetic neuron projection extension ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sympathetic neuron projection guidance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic target recognition ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in trigeminal ganglion development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in trigeminal nerve structural organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ventral trunk neural crest cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in axon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cerebellar climbing fiber to Purkinje cell synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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