U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Sema4a semaphorin 4A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310630, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Sema4aprovided by RGD
    Official Full Name
    semaphorin 4Aprovided by RGD
    Primary source
    RGD:1304636
    See related
    EnsemblRapid:ENSRNOG00000019737 AllianceGenome:RGD:1304636
    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. Predicted to be involved in several processes, including T-helper 1 cell differentiation; positive regulation of synapse assembly; and regulation of cell migration. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in cone-rod dystrophy 10 and retinitis pigmentosa 35. Orthologous to human SEMA4A (semaphorin 4A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 102.1), Lung (RPKM 88.2) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Sema4a in Genome Data Viewer
    Location:
    2q34
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (176194248..176215752, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (173896432..173917903, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (187799568..187823014, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485637 Neighboring gene solute carrier family 25, member 44 Neighboring gene uncharacterized LOC134485636 Neighboring gene lamin A/C Neighboring gene uncharacterized LOC120100862

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Sema4A induces cell morphological changes through B-type plexin-mediated signaling. Yukawa K, et al. Int J Mol Med, 2010 Feb. PMID 20043131
    2. Nonredundant roles of Sema4A in the immune system: defective T cell priming and Th1/Th2 regulation in Sema4A-deficient mice. Kumanogoh A, et al. Immunity, 2005 Mar. PMID 15780988
    3. Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus. McDermott JE, et al. Mol Cell Neurosci, 2018 Oct. PMID 29981480, Free PMC Article
    4. Semaphorin-4A, an activator for T-cell-mediated immunity, suppresses angiogenesis via Plexin-D1. Toyofuku T, et al. EMBO J, 2007 Mar 7. PMID 17318185, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in T cell differentiation involved in immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in T-helper 1 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axonogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of excitatory synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of inhibitory synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell shape ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of endothelial cell migration 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
    		  
    involved_in semaphorin-plexin signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    semaphorin-4A
    Names
    sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001012078.2 → NP_001012078.2  semaphorin-4A precursor

      See identical proteins and their annotated locations for NP_001012078.2

      Status: VALIDATED

      Source sequence(s)
      BC081943, JAXUCZ010000002
      UniProtKB/TrEMBL
      A0A1B0GWV9, A6J676, F7F3I7
      Related
      ENSRNOP00000053704.3, ENSRNOT00000056862.6
      Conserved Domains (3) summary
      smart00423
      Location:498 → 542
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:567 → 639
      Ig; Immunoglobulin domain
      cl15693
      Location:57 → 497
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    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_086020.1 Reference GRCr8

      Range
      176194248..176215752 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006232639.5 → XP_006232701.1  semaphorin-4A isoform X1

      See identical proteins and their annotated locations for XP_006232701.1

      UniProtKB/TrEMBL
      A0A1B0GWV9, A6J676, F7F3I7
      Conserved Domains (3) summary
      smart00423
      Location:498 → 542
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:567 → 639
      Ig; Immunoglobulin domain
      cl15693
      Location:57 → 497
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_063281836.1 → XP_063137906.1  semaphorin-4A isoform X1

      UniProtKB/TrEMBL
      A0A1B0GWV9, A6J676, F7F3I7

    3. XM_063281837.1 → XP_063137907.1  semaphorin-4A isoform X1

      UniProtKB/TrEMBL
      A0A1B0GWV9, A6J676, F7F3I7

    4. XM_006232641.5 → XP_006232703.1  semaphorin-4A isoform X1

      See identical proteins and their annotated locations for XP_006232703.1

      UniProtKB/TrEMBL
      A0A1B0GWV9, A6J676, F7F3I7
      Conserved Domains (3) summary
      smart00423
      Location:498 → 542
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:567 → 639
      Ig; Immunoglobulin domain
      cl15693
      Location:57 → 497
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. XM_039102308.2 → XP_038958236.1  semaphorin-4A isoform X2

      UniProtKB/TrEMBL
      A0A1B0GWV9
      Conserved Domains (4) summary
      smart00423
      Location:305 → 349
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:381 → 389
      Ig; Ig strand B [structural motif]
      cl11960
      Location:379 → 446
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 304
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    6. XM_039102309.2 → XP_038958237.1  semaphorin-4A isoform X2

      UniProtKB/TrEMBL
      A0A1B0GWV9
      Conserved Domains (4) summary
      smart00423
      Location:305 → 349
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:381 → 389
      Ig; Ig strand B [structural motif]
      cl11960
      Location:379 → 446
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 304
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous