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    Sema6b sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [ Mus musculus (house mouse) ]

    Gene ID: 20359, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sema6bprovided by MGI
    Official Full Name
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Bprovided by MGI
    Primary source
    MGI:MGI:1202889
    See related
    Ensembl:ENSMUSG00000001227 AllianceGenome:MGI:1202889
    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
    VIb; Sema; Seman; semaZ
    Summary
    Enables semaphorin receptor binding activity. Involved in axon guidance and hippocampus development. Predicted to be active in plasma membrane. Is expressed in several structures, including genitourinary system; liver; musculature; spinal cord; and spleen. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy. Orthologous to human SEMA6B (semaphorin 6B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in frontal lobe adult (RPKM 19.8), cortex adult (RPKM 18.3) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sema6b in Genome Data Viewer
    Location:
    17 29.17 cM; 17 D
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (56430085..56447343, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (56123085..56140343, complement)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene perilipin 5 Neighboring gene leucine-rich alpha-2-glycoprotein 1 Neighboring gene STARR-positive B cell enhancer ABC_E5621 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 1 Neighboring gene STARR-positive B cell enhancer ABC_E7547 Neighboring gene myeloid derived growth factor Neighboring gene dipeptidylpeptidase 9

    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. A novel transmembrane semaphorin can bind c-src. Eckhardt F, et al. Mol Cell Neurosci, 1997. PMID 9361278
    2. Cis interaction between Semaphorin6A and Plexin-A4 modulates the repulsive response to Sema6A. Haklai-Topper L, et al. EMBO J, 2010 Aug 4. PMID 20606624, Free PMC Article
    3. Sema6B, Sema6C, and Sema6D expression and function during mammalian retinal development. Matsuoka RL, et al. PLoS One, 2013. PMID 23646199, Free PMC Article
    4. Roles of semaphorin-6B and plexin-A2 in lamina-restricted projection of hippocampal mossy fibers. Tawarayama H, et al. J Neurosci, 2010 May 19. PMID 20484647, Free PMC Article
    5. On and off retinal circuit assembly by divergent molecular mechanisms. Sun LO, et al. Science, 2013 Nov 1. PMID 24179230, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • 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

    • MGC143995, MGC143996

    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
    		  
    enables semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in central nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in central nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in hippocampus development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-6B
    Names
    sema N
    sema VIB
    semaphorin VIB
    semaphorin-N

    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_001130456.1 → NP_001123928.1  semaphorin-6B precursor

      See identical proteins and their annotated locations for NP_001123928.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK139358, AK143229
      Consensus CDS
      CCDS28896.1
      UniProtKB/Swiss-Prot
      O54951
      UniProtKB/TrEMBL
      Q3TM84, Q3UTK5
      Related
      ENSMUSP00000001256.5, ENSMUST00000001256.11
      Conserved Domains (3) summary
      PHA03269
      Location:708 → 875
      PHA03269; envelope glycoprotein C; Provisional
      cd11267
      Location:58 → 526
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      smart00423
      Location:527 → 573
      PSI; domain found in Plexins, Semaphorins and Integrins

    2. NM_013662.2 → NP_038690.1  semaphorin-6B precursor

      See identical proteins and their annotated locations for NP_038690.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK139358, BY082811
      Consensus CDS
      CCDS28896.1
      UniProtKB/Swiss-Prot
      O54951
      UniProtKB/TrEMBL
      Q3TM84, Q3UTK5
      Related
      ENSMUSP00000130985.2, ENSMUST00000167545.3
      Conserved Domains (3) summary
      PHA03269
      Location:708 → 875
      PHA03269; envelope glycoprotein C; Provisional
      cd11267
      Location:58 → 526
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      smart00423
      Location:527 → 573
      PSI; domain found in Plexins, Semaphorins and Integrins

    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_000083.7 Reference GRCm39 C57BL/6J

      Range
      56430085..56447343 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006523930.5 → XP_006523993.1  semaphorin-6B isoform X1

      See identical proteins and their annotated locations for XP_006523993.1

      UniProtKB/Swiss-Prot
      O54951
      UniProtKB/TrEMBL
      Q3TM84, Q3UTK5
      Conserved Domains (3) summary
      PHA03269
      Location:708 → 875
      PHA03269; envelope glycoprotein C; Provisional
      cd11267
      Location:58 → 526
      Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
      smart00423
      Location:527 → 573
      PSI; domain found in Plexins, Semaphorins and Integrins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O54951.1 GenPept UniProtKB/Swiss-Prot:O54951

    Gene LinkOut

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

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