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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 11-Apr-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 and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to act upstream of or within cell differentiation and nervous system development. Located in plasma membrane and synapse. 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, Apr 2022]
    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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    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
    • 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. 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
    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 III can function as a selective chemorepellent to pattern sensory projections in the spinal cord. Messersmith EK, et al. Neuron, 1995 May. PMID 7748562
    5. Neuropilin is a receptor for the axonal chemorepellent Semaphorin III. He Z, et al. Cell, 1997 Aug 22. PMID 9288753

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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)
    • Gene trapped (4) 
    • Targeted (1)  1 citation
    • Endonuclease-mediated (2) 

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell differentiation 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
    		  
    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 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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