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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 21-Apr-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 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 located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space. Predicted to be integral component of 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, Apr 2022]
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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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
  • 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. Plasmacytoid dendritic cells protect from viral bronchiolitis and asthma through semaphorin 4a-mediated T reg expansion. Lynch JP, et al. J Exp Med, 2018 Feb 5. PMID 29273643, Free PMC Article
  2. mTOR Complex Signaling through the SEMA4A-Plexin B2 Axis Is Required for Optimal Activation and Differentiation of CD8+ T Cells. Ito D, et al. J Immunol, 2015 Aug 1. PMID 26116513, Free PMC Article
  3. Semaphorin 4A is dynamically regulated during thymocyte development in mice. Linder GE, et al. Cell Immunol, 2013 Feb. PMID 23648820
  4. Neuroimmune semaphorin 4A downregulates the severity of allergic response. Nkyimbeng-Takwi EH, et al. Mucosal Immunol, 2012 Jul. PMID 22472774, Free PMC Article
  5. 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

See all (58) 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 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in T-helper 1 cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within 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 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
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 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
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 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
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
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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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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