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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 3-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Sema3b in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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
     
    involved_in semaphorin-plexin signaling pathway IEA
    Inferred from Electronic Annotation
    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

    Preferred Names
    semaphorin-3B
    Names
    sema A
    semaphorin-A

    NCBI Reference Sequences (RefSeq)

    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_001042779.3NP_001036244.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001036244.1

      Status: REVIEWED

      Source sequence(s)
      AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099591.4, ENSMUST00000102532.10
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. NM_001291537.1NP_001278466.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278466.1

      Status: REVIEWED

      Source sequence(s)
      AK014333, AK037034, AK048364, AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. NM_001291538.1NP_001278467.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278467.1

      Status: REVIEWED

      Source sequence(s)
      AK014333, AK037034, AK048364, AL672219, BC090669
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. NM_001291539.2NP_001278468.1  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_001278468.1

      Status: REVIEWED

      Source sequence(s)
      AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099590.2, ENSMUST00000102531.7
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    5. NM_001433897.1NP_001420826.1  semaphorin-3B precursor

      Status: REVIEWED

      Source sequence(s)
      AL672219
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
    6. NM_001433898.1NP_001420827.1  semaphorin-3B precursor

      Status: REVIEWED

      Source sequence(s)
      AL672219
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
    7. NM_001433899.1NP_001420828.1  semaphorin-3B precursor

      Status: REVIEWED

      Source sequence(s)
      AL672219
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
    8. NM_001433900.1NP_001420829.1  semaphorin-3B precursor

      Status: REVIEWED

      Source sequence(s)
      AL672219
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
    9. NM_009153.4NP_033179.2  semaphorin-3B precursor

      See identical proteins and their annotated locations for NP_033179.2

      Status: REVIEWED

      Source sequence(s)
      AL672219
      Consensus CDS
      CCDS23501.1
      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Related
      ENSMUSP00000099588.4, ENSMUST00000102529.10
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. NR_111986.1 RNA Sequence

      Status: REVIEWED

      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_011242865.4XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. XM_036154742.1XP_036010635.1  semaphorin-3B isoform X1

      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. XM_011242864.4XP_011241166.1  semaphorin-3B isoform X1

      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. XM_011242862.4XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    5. XM_017313225.3XP_017168714.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    6. XM_011242863.4XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    7. XM_006511665.5XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    8. XM_036154743.1XP_036010636.1  semaphorin-3B isoform X1

      UniProtKB/TrEMBL
      M9MMK0, Q0VGP2
      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    9. XM_006511666.5XP_006511729.1  semaphorin-3B isoform X1

      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    10. XM_006511671.5XP_006511734.1  semaphorin-3B isoform X1

      Conserved Domains (4) summary
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    11. XM_006511664.5XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    12. XM_011242867.4XP_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:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:575580
      Ig; Ig strand A [structural motif]
      cl11960
      Location:575665
      Ig; Immunoglobulin domain
      cl15693
      Location:46516
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    13. XM_006511673.1XP_006511736.1  semaphorin-3B isoform X2

      Conserved Domains (3) summary
      smart00423
      Location:322358
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:382472
      Ig; Immunoglobulin domain
      cl15693
      Location:1323
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins