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    Sema3b sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [ Mus musculus (house mouse) ]

    Gene ID: 20347, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Sema3bprovided by MGI
    Official Full Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Bprovided by MGI
    Primary source
    MGI:MGI:107561
    See related
    Ensembl:ENSMUSG00000057969 AllianceGenome:MGI:107561
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    SemA; Semaa; sema5; semaV
    Summary
    This gene encodes a secreted protein that belongs to the class 3 semaphorin/collapsin family. Members of this family play a role in growth cone guidance during neurogenesis. The encoded protein inhibits axonal extension. This protein is thought to be an osteoblast protein that regulates bone mass and affects skeletal homeostasis. A similar gene in humans functions as a tumor suppressor gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in colon adult (RPKM 23.8), lung adult (RPKM 21.6) and 15 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    9 F1; 9 58.31 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (107474868..107486440, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (107597674..107609241, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene hyaluronoglucosaminidase 1 Neighboring gene STARR-positive B cell enhancer ABC_E300 Neighboring gene N(alpha)-acetyltransferase 80, NatH catalytic subunit Neighboring gene hyaluronoglucosaminidase 3 Neighboring gene interferon-related developmental regulator 2 Neighboring gene leucine-rich single-pass membrane protein 2 Neighboring gene STARR-positive B cell enhancer ABC_E11753 Neighboring gene STARR-positive B cell enhancer ABC_E8314 Neighboring gene G protein subunit alpha i2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:107527067-107527220 Neighboring gene STARR-seq mESC enhancer starr_25181 Neighboring gene predicted gene, 53518 Neighboring gene STARR-seq mESC enhancer starr_25182 Neighboring gene STARR-positive B cell enhancer ABC_E5103 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:107546963-107547072 Neighboring gene STARR-positive B cell enhancer ABC_E8315 Neighboring gene solute carrier family 38, member 3

    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. Hippocampal semaphorin 3B improves depression-like behaviours in mice by upregulating synaptic plasticity and inhibiting neuronal apoptosis. Du Y, et al. J Neurochem, 2022 Oct. PMID 35892177
    2. Semaphorin-3D and semaphorin-3E inhibit the development of tumors from glioblastoma cells implanted in the cortex of the brain. Sabag AD, et al. PLoS One, 2012. PMID 22936999, Free PMC Article
    3. Null and conditional semaphorin 3B alleles using a flexible puroDeltatk loxP/FRT vector. van der Weyden L, et al. Genesis, 2005 Apr. PMID 15789413
    4. Reciprocal modulation of Ca(v) 2.3 voltage-gated calcium channels by copper(II) ions and kainic acid. Neumaier F, et al. J Neurochem, 2018 Nov. PMID 29972687
    5. Tumor necrosis factor alpha suppresses osteogenic differentiation of MSCs by inhibiting semaphorin 3B via Wnt/β-catenin signaling in estrogen-deficiency induced osteoporosis. Sang C, et al. Bone, 2016 Mar. PMID 26723579

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Hippocampal semaphorin 3B improves depression-like behaviours in mice by upregulating synaptic plasticity and inhibiting neuronal apoptosis.
      Title: Hippocampal semaphorin 3B improves depression-like behaviours in mice by upregulating synaptic plasticity and inhibiting neuronal apoptosis.
    2. CHL1 mediated spine pruning in response to Sema3B and associated with receptor subunits Neuropilin-2 and PlexinA4. Sema3B protein eliminated spines on apical dendrites of cortical neurons cultured from wild-type but not CHL1-null embryos. Sema3B was secreted by cortical neuron cultures.In vivo CHL1 was coexpressed with Sema3B in pyramidal neuron subpopulations and formed a complex with Neuropilin-2 and PlexinA4.
      Title: Close Homolog of L1 Regulates Dendritic Spine Density in the Mouse Cerebral Cortex Through Semaphorin 3B.
    3. Semaphorin3B may contribute to impaired bone formation by elevated TNF-alpha in estrogen-deficiency-induced osteoporosis.
      Title: Tumor necrosis factor alpha suppresses osteogenic differentiation of MSCs by inhibiting semaphorin 3B via Wnt/β-catenin signaling in estrogen-deficiency induced osteoporosis.
    4. Cerebrospinal fluid-derived Semaphorin3B orients neuroepithelial cell divisions in the apicobasal axis.
      Title: Cerebrospinal fluid-derived Semaphorin3B orients neuroepithelial cell divisions in the apicobasal axis.
    5. The human ortholog of this gene functions as a tumor suppressor gene.
      Title: Inhibition of lung cancer cell growth and induction of apoptosis after reexpression of 3p21.3 candidate tumor suppressor gene SEMA3B.
    6. Dual functional activity of semaphorin 3B is required for positioning the anterior commissure.
      Title: Dual functional activity of semaphorin 3B is required for positioning the anterior commissure.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (5)  1 citation
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 

    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 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
    located_in extracellular region 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-3B
    Names
    sema A
    semaphorin-A

    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_001042779.2 → NP_001036244.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001036244.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. Variants 1 through 5 encode the same protein.
      Source sequence(s)
      AK014333, AK037034, AL672219, BY138852
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099591.4, ENSMUST00000102532.10
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001291537.1 → NP_001278466.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278466.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript. Variants 1 through 5 encode the same protein.
      Source sequence(s)
      AK014333, AK037034, AK048364, AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. NM_001291538.1 → NP_001278467.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278467.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 3. Variants 1 through 5 encode the same protein.
      Source sequence(s)
      AK014333, AK037034, AK048364, AL672219, BC090669
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. NM_001291539.1 → NP_001278468.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278468.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 3. Variants 1 through 5 encode the same protein.
      Source sequence(s)
      AK014333, AK043634, BY138852
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099590.2, ENSMUST00000102531.7
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. NM_009153.4 → NP_033179.2  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_033179.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. Variants 1 through 5 encode the same protein.
      Source sequence(s)
      AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099588.4, ENSMUST00000102529.10
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. NR_111986.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in an internal exon compared to variant 3. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK014333, AK037034, AL672219
      Related
      ENSMUST00000123926.8

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      107474868..107486440 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011242865.4 → XP_011241167.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_011241167.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_036154742.1 → XP_036010635.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_011242864.4 → XP_011241166.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_011241166.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. XM_011242862.4 → XP_011241164.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_011241164.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. XM_017313225.3 → XP_017168714.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    6. XM_011242863.4 → XP_011241165.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_011241165.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    7. XM_006511665.5 → XP_006511728.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_006511728.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099589.2, ENSMUST00000102530.8
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    8. XM_036154743.1 → XP_036010636.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    9. XM_006511666.5 → XP_006511729.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_006511729.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    10. XM_006511671.5 → XP_006511734.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_006511734.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    11. XM_006511664.5 → XP_006511727.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_006511727.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    12. XM_011242867.4 → XP_011241169.1  semaphorin-3B isoform X1

      See identical proteins and their annotated locations for XP_011241169.1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000073152.6, ENSMUST00000073448.12
      Conserved Domains (4) summary
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575 → 580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575 → 665
      Ig; Immunoglobulin domain
      cl15693
      Location:46 → 516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    13. XM_006511673.1 → XP_006511736.1  semaphorin-3B isoform X2

      Conserved Domains (3) summary
      smart00423
      Location:322 → 358
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:382 → 472
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 323
      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
    Q62177.2 GenPept UniProtKB/Swiss-Prot:Q62177

    Gene LinkOut

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

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