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    Sema6a sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [ Mus musculus (house mouse) ]

    Gene ID: 20358, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sema6aprovided by MGI
    Official Full Name
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Aprovided by MGI
    Primary source
    MGI:MGI:1203727
    See related
    Ensembl:ENSMUSG00000019647 AllianceGenome:MGI:1203727
    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
    VIa; Semaq; Sema6A-1; A730020P05Rik
    Summary
    Enables identical protein binding activity; semaphorin receptor binding activity; and transmembrane signaling receptor activity. Involved in generation of neurons; positive regulation of neuron migration; and semaphorin-plexin signaling pathway. Acts upstream of or within cell surface receptor signaling pathway and centrosome localization. Located in plasma membrane. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Orthologous to human SEMA6A (semaphorin 6A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 13.8), lung adult (RPKM 13.8) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Sema6a in Genome Data Viewer
    Location:
    18 C; 18 25.08 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (47378321..47504267, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (47245254..47371200, complement)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene heat shock protein 1 (chaperonin 10), related sequence 1 Neighboring gene ADP-ribosylation factor interacting protein 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_44536 Neighboring gene STARR-seq mESC enhancer starr_44538 Neighboring gene ribosomal protein L6 pseudogene Neighboring gene RIKEN cDNA 9130209A04 gene

    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)

    Pathways from PubChem

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables semaphorin receptor binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transmembrane signaling receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 axon guidance NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within cell surface receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to vascular endothelial growth factor stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within centrosome localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of ERK1 and ERK2 cascade ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell adhesion involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of vascular endothelial growth factor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in semaphorin-plexin signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in axon NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    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 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    semaphorin-6A
    Names
    Mutant line 997
    sema Q
    sema VIA
    semaphorin Q
    semaphorin VIA
    semaphorin-6A-1

    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_001311097.1NP_001298026.1  semaphorin-6A isoform 2 precursor

      See identical proteins and their annotated locations for NP_001298026.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC121783, AC124466, AI606937, AK034123, AK082711, BC059238, BC062979
      Consensus CDS
      CCDS79642.1
      Related
      ENSMUSP00000075420.7, ENSMUST00000076043.13
      Conserved Domains (2) summary
      cd11266
      Location:48513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514544
      PSI; Plexin repeat
    2. NM_018744.2NP_061214.2  semaphorin-6A isoform 1 precursor

      See identical proteins and their annotated locations for NP_061214.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC124466, AI606937, AK042751, BC059238
      Consensus CDS
      CCDS37813.1
      UniProtKB/Swiss-Prot
      O35464, Q6P5A8, Q6PCN9, Q9EQ71
      Related
      ENSMUSP00000019791.8, ENSMUST00000019791.14
      Conserved Domains (2) summary
      cd11266
      Location:48513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514544
      PSI; Plexin repeat

    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_000084.7 Reference GRCm39 C57BL/6J

      Range
      47378321..47504267 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006525726.2XP_006525789.1  semaphorin-6A isoform X1

      See identical proteins and their annotated locations for XP_006525789.1

      UniProtKB/TrEMBL
      D3YWM8
      Related
      ENSMUSP00000120011.2, ENSMUST00000135790.8
      Conserved Domains (2) summary
      cd11266
      Location:48513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514546
      PSI; Plexin repeat
    2. XM_006525727.5XP_006525790.1  semaphorin-6A isoform X1

      See identical proteins and their annotated locations for XP_006525790.1

      UniProtKB/TrEMBL
      D3YWM8
      Conserved Domains (2) summary
      cd11266
      Location:48513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514546
      PSI; Plexin repeat