U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 20347, updated on 21-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Alleles

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

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
semaphorin-3B
Names
sema A
semaphorin-A

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_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.

Other Literature Sources
Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous