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

    Gene ID: 29751, updated on 28-Oct-2018

    Summary

    Official Symbol
    Sema3aprovided by RGD
    Official Full Name
    semaphorin 3Aprovided by RGD
    Primary source
    RGD:3657
    See related
    Ensembl:ENSRNOG00000023337
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    induces neuronal cell death; induces apoptosis of retinal ganglion cells in response to injury [RGD, Feb 2006]
    Expression
    Biased expression in Lung (RPKM 34.4), Brain (RPKM 32.2) and 9 other tissues See more
    Orthologs

    Genomic context

    See Sema3a in Genome Data Viewer
    Location:
    4q12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (18170375..18545190, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (18133300..18444520, complement)

    Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene MLV-related proviral Env polyprotein-like Neighboring gene rCG50794-like Neighboring gene uncharacterized LOC108350657 Neighboring gene semaphorin 3D Neighboring gene MLV-related proviral Env polyprotein-like

    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 FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

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

    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)

    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_017310.1NP_059006.1  semaphorin-3A precursor

      See identical proteins and their annotated locations for NP_059006.1

      Status: PROVISIONAL

      Source sequence(s)
      X95286
      UniProtKB/Swiss-Prot
      Q63548
      Related
      ENSRNOP00000036472.1, ENSRNOT00000034692.2
      Conserved Domains (4) summary
      cd05871
      Location:581671
      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)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

      Range
      18170375..18545190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      See identical proteins and their annotated locations for XP_008760924.1

      UniProtKB/Swiss-Prot
      Q63548
      Conserved Domains (4) summary
      cd05871
      Location:581671
      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)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. XM_006235989.3XP_006236051.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_006236051.1

      UniProtKB/Swiss-Prot
      Q63548
      Conserved Domains (4) summary
      cd05871
      Location:581671
      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)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    3. XM_017592568.1XP_017448057.1  semaphorin-3A isoform X1

      UniProtKB/Swiss-Prot
      Q63548
      Conserved Domains (4) summary
      cd05871
      Location:581671
      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)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins
    4. XM_006235990.3XP_006236052.1  semaphorin-3A isoform X1

      See identical proteins and their annotated locations for XP_006236052.1

      UniProtKB/Swiss-Prot
      Q63548
      Conserved Domains (4) summary
      cd05871
      Location:581671
      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)
      smart00410
      Location:586664
      IG_like; Immunoglobulin like
      smart00423
      Location:516552
      PSI; domain found in Plexins, Semaphorins and Integrins

    Alternate Rn_Celera

    Genomic

    1. AC_000072.1 Alternate Rn_Celera

      Range
      16810716..17013648 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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