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Sema4b sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [ Mus musculus (house mouse) ]

Gene ID: 20352, updated on 2-Nov-2024

Summary

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Official Symbol
Sema4bprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Bprovided by MGI
Primary source
MGI:MGI:107559
See related
Ensembl:ENSMUSG00000030539 AllianceGenome:MGI:107559
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
SemC; Semac; sema C; mKIAA1745
Summary
Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Located in plasma membrane and synapse. Is active in glutamatergic synapse and postsynaptic density membrane. Is expressed in several structures, including back musculature; central nervous system; peripheral nervous system ganglion; and retina. Orthologous to human SEMA4B (semaphorin 4B). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in spleen adult (RPKM 31.2), duodenum adult (RPKM 28.9) and 27 other tissues See more
Orthologs
human all
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Genomic context

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See Sema4b in Genome Data Viewer
Location:
7 D2; 7 45.51 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (79836618..79876394)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (80186870..80226646)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene isocitrate dehydrogenase 2 (NADP+), mitochondrial Neighboring gene predicted gene, 53380 Neighboring gene STARR-seq mESC enhancer starr_19312 Neighboring gene STARR-positive B cell enhancer ABC_E3729 Neighboring gene STARR-positive B cell enhancer ABC_E6564 Neighboring gene predicted gene 45202 Neighboring gene STARR-positive B cell enhancer ABC_E8182 Neighboring gene STARR-seq mESC enhancer starr_19316 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:87337544-87337745 Neighboring gene STARR-seq mESC enhancer starr_19318 Neighboring gene STARR-seq mESC enhancer starr_19319 Neighboring gene STARR-seq mESC enhancer starr_19320 Neighboring gene STARR-seq mESC enhancer starr_19323 Neighboring gene STARR-positive B cell enhancer ABC_E10446 Neighboring gene calcium and integrin binding 1 Neighboring gene GDP-D-glucose phosphorylase 1

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. Improved neuron protection following cortical injury in the absence of Semaphorin4B. Sweetat S, et al. Front Cell Neurosci, 2022. PMID 36531136, Free PMC Article
  2. Astrogliosis Induced by Brain Injury Is Regulated by Sema4B Phosphorylation. Ben-Gigi L, et al. eNeuro, 2015 May-Jun. PMID 26464987, Free PMC Article
  3. Identification of semaphorin 4B as a negative regulator of basophil-mediated immune responses. Nakagawa Y, et al. J Immunol, 2011 Mar 1. PMID 21270411
  4. Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis. Amin A, et al. Mol Metab, 2023 Jul. PMID 37121509, Free PMC Article
  5. Astrocyte-to-microglia communication via Sema4B-Plexin-B2 modulates injury-induced reactivity of microglia. Casden N, et al. Proc Natl Acad Sci U S A, 2024 May 28. PMID 38781210, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Astrocyte-to-microglia communication via Sema4B-Plexin-B2 modulates injury-induced reactivity of microglia.
    Title: Astrocyte-to-microglia communication via Sema4B-Plexin-B2 modulates injury-induced reactivity of microglia.
  2. Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis.
    Title: Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis.
  3. Sema4B negatively regulates basophil-mediated T helper type (Th)2 cell and humoral memory responses.
    Title: Identification of semaphorin 4B as a negative regulator of basophil-mediated immune responses.
  4. Sema4B co-localizes with PSD-95 at synaptic contacts between cultured hippocampal neurons.
    Title: Semaphorin 4B interacts with the post-synaptic density protein PSD-95/SAP90 and is recruited to synapses through a C-terminal PDZ-binding motif.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Gene trapped (4) 
  • Targeted (1)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1745

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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in 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 semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic density membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic density membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in postsynaptic membrane ISO
Inferred from Sequence Orthology
more info
 PubMed 
located_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
semaphorin-4B
Names
semaphorin-C

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_001360135.2 → NP_001347064.1  semaphorin-4B precursor

    Status: VALIDATED

    Source sequence(s)
    AC109232
    Consensus CDS
    CCDS21391.1
    UniProtKB/Swiss-Prot
    Q4PKI6, Q62179, Q69ZB7
    UniProtKB/TrEMBL
    Q8BIR6
    Related
    ENSMUSP00000145622.2, ENSMUST00000205822.2
    Conserved Domains (3) summary
    pfam01437
    Location:512 → 558
    PSI; Plexin repeat
    cd05872
    Location:579 → 663
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:48 → 511
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  2. NM_013659.5 → NP_038687.2  semaphorin-4B precursor

    See identical proteins and their annotated locations for NP_038687.2

    Status: VALIDATED

    Source sequence(s)
    AC109232
    Consensus CDS
    CCDS21391.1
    UniProtKB/Swiss-Prot
    Q4PKI6, Q62179, Q69ZB7
    UniProtKB/TrEMBL
    Q8BIR6
    Related
    ENSMUSP00000032754.8, ENSMUST00000032754.9
    Conserved Domains (3) summary
    pfam01437
    Location:512 → 558
    PSI; Plexin repeat
    cd05872
    Location:579 → 663
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:48 → 511
    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_000073.7 Reference GRCm39 C57BL/6J

    Range
    79836618..79876394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036152820.1 → XP_036008713.1  semaphorin-4B isoform X1

    UniProtKB/Swiss-Prot
    Q4PKI6, Q62179, Q69ZB7
    UniProtKB/TrEMBL
    Q8BIR6
    Conserved Domains (3) summary
    pfam01437
    Location:512 → 558
    PSI; Plexin repeat
    cd05872
    Location:579 → 663
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:48 → 511
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  2. XM_030242259.2 → XP_030098119.2  semaphorin-4B isoform X1

    UniProtKB/Swiss-Prot
    Q4PKI6, Q62179, Q69ZB7
    UniProtKB/TrEMBL
    Q8BIR6
    Conserved Domains (3) summary
    pfam01437
    Location:512 → 558
    PSI; Plexin repeat
    cd05872
    Location:579 → 663
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:48 → 511
    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
Q62179.2 GenPept UniProtKB/Swiss-Prot:Q62179

Gene LinkOut

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