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    Sema4a sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [ Mus musculus (house mouse) ]

    Gene ID: 20351, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Sema4aprovided by MGI
    Official Full Name
    sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Aprovided by MGI
    Primary source
    MGI:MGI:107560
    See related
    Ensembl:ENSMUSG00000028064 AllianceGenome:MGI:107560
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    SemB; Semab
    Summary
    Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in several processes, including T-helper 1 cell differentiation; negative regulation of angiogenesis; and positive regulation of synapse assembly. Predicted to be active in plasma membrane. Is expressed in several structures, including blood vessel; central nervous system; primitive ventricle; retina; and ureteric trunk. 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, Nov 2024]
    Expression
    Broad expression in colon adult (RPKM 43.5), duodenum adult (RPKM 41.8) and 25 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sema4a in Genome Data Viewer
    Location:
    3 F1; 3 38.83 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (88343266..88368500, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (88435959..88461182, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 25, member 44 Neighboring gene STARR-positive B cell enhancer ABC_E2076 Neighboring gene 60S ribosomal protein L21 pseudogene Neighboring gene microRNA 7011 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:88257320-88257473 Neighboring gene predicted gene, 40089 Neighboring gene high mobility group box 3 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Involvement of Sema4A in the progression of experimental autoimmune myocarditis. Makino N, et al. FEBS Lett, 2008 Nov 26. PMID 18977352
    2. Semaphorin 4A exerts a proangiogenic effect by enhancing vascular endothelial growth factor-A expression in macrophages. Meda C, et al. J Immunol, 2012 Apr 15. PMID 22442441
    3. Neuroimmune semaphorin 4A downregulates the severity of allergic response. Nkyimbeng-Takwi EH, et al. Mucosal Immunol, 2012 Jul. PMID 22472774, Free PMC Article
    4. Semaphorin 4A is dynamically regulated during thymocyte development in mice. Linder GE, et al. Cell Immunol, 2013 Feb. PMID 23648820
    5. Semaphorin 4A induces growth cone collapse of hippocampal neurons in a Rho/Rho-kinase-dependent manner. Yukawa K, et al. Int J Mol Med, 2005 Jul. PMID 15942687

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sema4A is implicated in the acceleration of Th17 cell-mediated neuroinflammation in the effector phase.
      Title: Sema4A is implicated in the acceleration of Th17 cell-mediated neuroinflammation in the effector phase.
    2. We highlight a common but age-related Sema4a-mediated pathway by which plasmacytoid dendritic cells and microbial colonization induce T reg cell expansion to protect against severe bronchiolitis and subsequent asthma.
      Title: Plasmacytoid dendritic cells protect from viral bronchiolitis and asthma through semaphorin 4a-mediated T reg expansion.
    3. Sema4A functions through postsynaptic Plexin-B2 for excitatory synapse development.
      Title: Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus.
    4. Suggest a role for Plexin-B1 as a ligand and Sema4A as a receptor and characterize a reverse signaling pathway downstream of Sema4A regulating cell migration via Scrib.
      Title: A reverse signaling pathway downstream of Sema4A controls cell migration via Scrib.
    5. SEMA4A is required for optimal activation of mTORC1 in CD8+ T cells.
      Title: mTOR Complex Signaling through the SEMA4A-Plexin B2 Axis Is Required for Optimal Activation and Differentiation of CD8+ T Cells.
    6. Treg-cell stability can be subverted in certain inflammatory sites, but is maintained by a Sema4a-Nrp1 axis-- this pathway is a potential therapeutic target that could limit Treg-cell-mediated tumour-induced tolerance without inducing autoimmunity
      Title: Stability and function of regulatory T cells is maintained by a neuropilin-1-semaphorin-4a axis.
    7. Data indicate that both semaphorin 4A mRNA and protein were clearly detected on the earliest progenitors and were downregulated through thymic development.
      Title: Semaphorin 4A is dynamically regulated during thymocyte development in mice.
    8. These results indicate the importance of the Sema4A protein conformation in human and mouse retina homeostasis.
      Title: A point mutation in Semaphorin 4A associates with defective endosomal sorting and causes retinal degeneration.
    9. A fraction of Sema4a-deficient transgenic BALB/c mice spontaneously develop skin lesions resembling atopic dermatitis (AD) in humans.
      Title: An inhibitory role for Sema4A in antigen-specific allergic asthma.
    10. These data provide a new insight into Sema4A biology and define Sema4A as an important regulator of Th2-driven lung pathophysiology.
      Title: Neuroimmune semaphorin 4A downregulates the severity of allergic response.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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
    		  
    enables semaphorin receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in T cell differentiation involved in immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in T-helper 1 cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of inhibitory synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell shape IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of endothelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in semaphorin-plexin signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-4A
    Names
    sema B
    semaphorin-B

    NCBI Reference Sequences (RefSeq)

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    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_001163489.2 → NP_001156961.1  semaphorin-4A precursor

      See identical proteins and their annotated locations for NP_001156961.1

      Status: VALIDATED

      Source sequence(s)
      AC102388
      Consensus CDS
      CCDS17475.1
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Related
      ENSMUSP00000125909.2, ENSMUST00000166237.8
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001163490.2 → NP_001156962.1  semaphorin-4A precursor

      See identical proteins and their annotated locations for NP_001156962.1

      Status: VALIDATED

      Source sequence(s)
      AC102388
      Consensus CDS
      CCDS17475.1
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Related
      ENSMUSP00000128510.2, ENSMUST00000165898.8
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. NM_001163491.2 → NP_001156963.1  semaphorin-4A precursor

      See identical proteins and their annotated locations for NP_001156963.1

      Status: VALIDATED

      Source sequence(s)
      AC102388
      Consensus CDS
      CCDS17475.1
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Related
      ENSMUSP00000128887.2, ENSMUST00000169222.8
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. NM_001428657.1 → NP_001415586.1  semaphorin-4A precursor

      Status: VALIDATED

      Source sequence(s)
      AC102388
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178

    5. NM_001428658.1 → NP_001415587.1  semaphorin-4A precursor

      Status: VALIDATED

      Source sequence(s)
      AC102388
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178

    6. NM_013658.3 → NP_038686.3  semaphorin-4A precursor

      See identical proteins and their annotated locations for NP_038686.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. All four variants encode the same protein.
      Source sequence(s)
      AK077976, AK153164, BY201883
      Consensus CDS
      CCDS17475.1
      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Related
      ENSMUSP00000029700.6, ENSMUST00000029700.12
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      88343266..88368500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162974.1 → XP_036018867.1  semaphorin-4A isoform X3

      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_006501190.4 → XP_006501253.1  semaphorin-4A isoform X4

      See identical proteins and their annotated locations for XP_006501253.1

      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (3) summary
      smart00423
      Location:327 → 371
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:396 → 468
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 326
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_036162971.1 → XP_036018864.1  semaphorin-4A isoform X2

      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (4) summary
      smart00423
      Location:520 → 564
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:596 → 604
      Ig; Ig strand B [structural motif]
      cl11960
      Location:594 → 661
      Ig; Immunoglobulin domain
      cl15693
      Location:79 → 519
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. XM_036162972.1 → XP_036018865.1  semaphorin-4A isoform X3

      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. XM_006501187.4 → XP_006501250.1  semaphorin-4A isoform X1

      Conserved Domains (3) summary
      smart00423
      Location:534 → 578
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:603 → 675
      Ig; Immunoglobulin domain
      cl15693
      Location:93 → 533
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    6. XM_006501189.3 → XP_006501252.1  semaphorin-4A isoform X3

      See identical proteins and their annotated locations for XP_006501252.1

      UniProtKB/Swiss-Prot
      D3Z5L2, Q62178
      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    7. XM_011240051.3 → XP_011238353.1  semaphorin-4A isoform X3

      Conserved Domains (4) summary
      smart00423
      Location:496 → 540
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:572 → 580
      Ig; Ig strand B [structural motif]
      cl11960
      Location:570 → 637
      Ig; Immunoglobulin domain
      cl15693
      Location:55 → 495
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    8. XM_006501191.4 → XP_006501254.1  semaphorin-4A isoform X4

      See identical proteins and their annotated locations for XP_006501254.1

      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (3) summary
      smart00423
      Location:327 → 371
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:396 → 468
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 326
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    9. XM_006501188.5 → XP_006501251.1  semaphorin-4A isoform X2

      UniProtKB/TrEMBL
      D3YWV5
      Conserved Domains (4) summary
      smart00423
      Location:520 → 564
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:596 → 604
      Ig; Ig strand B [structural motif]
      cl11960
      Location:594 → 661
      Ig; Immunoglobulin domain
      cl15693
      Location:79 → 519
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    10. XM_036162975.1 → XP_036018868.1  semaphorin-4A isoform X5

      UniProtKB/TrEMBL
      D3YWV5
      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
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q62178.2 GenPept UniProtKB/Swiss-Prot:Q62178

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