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    Sema6c sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [ Mus musculus (house mouse) ]

    Gene ID: 20360, updated on 23-May-2018
    Official Symbol
    Sema6cprovided by MGI
    Official Full Name
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Cprovided by MGI
    Primary source
    MGI:MGI:1338032
    See related
    Ensembl:ENSMUSG00000038777 Vega:OTTMUSG00000022286
    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
    Semay; mKIAA1869
    Expression
    Broad expression in whole brain E14.5 (RPKM 28.2), CNS E14 (RPKM 23.1) and 18 other tissues See more
    Orthologs
    See Sema6c in Genome Data Viewer
    Location:
    3; 3 F2.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 3 NC_000069.6 (95160420..95174050)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (94968296..94977238)

    Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene LysM, putative peptidoglycan-binding, domain containing 1 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2 Neighboring gene predicted gene 9169 Neighboring gene GA repeat binding protein, beta 2 Neighboring gene predicted gene, 16740 Neighboring gene myeloid/lymphoid or mixed-lineage leukemia; translocated to, 11 Neighboring gene CDC42 small effector 1

    • 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

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Axon guidance, organism-specific biosystem (from KEGG)
      Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, conserved biosystem (from KEGG)
      Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    semaphorin-6C
    Names
    Sema Y
    m-Sema Y
    semaphorin-Y

    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_001272024.1NP_001258953.1  semaphorin-6C isoform 1 precursor

      See identical proteins and their annotated locations for NP_001258953.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB013729, AC131769, AC140190, BC059007
      Consensus CDS
      CCDS71289.1
      UniProtKB/Swiss-Prot
      Q9WTM3
      UniProtKB/TrEMBL
      E9Q613
      Related
      ENSMUSP00000088333.1, OTTMUSP00000025221, ENSMUST00000090823.7, OTTMUST00000053081
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. NM_011351.2NP_035481.1  semaphorin-6C isoform 2 precursor

      See identical proteins and their annotated locations for NP_035481.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AB013729, AC140190, AK165085
      Consensus CDS
      CCDS17604.1
      UniProtKB/Swiss-Prot
      Q9WTM3
      Related
      ENSMUSP00000144039.1, ENSMUST00000202315.2
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. NR_073549.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon structure and an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC131769, AC140190, AK031131, AK165085
      Related
      ENSMUST00000204709.2, OTTMUST00000139842
    2. NR_073550.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate 5' exon structure and an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC131769, AC140190, AK031131, AK165085
      Related
      ENSMUST00000142449.8, OTTMUST00000053082
    3. NR_073551.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate 5' and 3' exon structure and an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC131769, AC140190, BC051979, BC059007

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000069.6 Reference GRCm38.p4 C57BL/6J

      Range
      95160420..95174050
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501205.1XP_006501268.1  semaphorin-6C isoform X2

      See identical proteins and their annotated locations for XP_006501268.1

      UniProtKB/Swiss-Prot
      Q9WTM3
      Related
      ENSMUSP00000088331.3, OTTMUSP00000025222, ENSMUST00000090821.9, OTTMUST00000053084
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. XM_006501192.3XP_006501255.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501255.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. XM_006501195.3XP_006501258.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501258.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. XM_006501193.3XP_006501256.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501256.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    5. XM_006501196.3XP_006501259.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501259.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    6. XM_006501194.3XP_006501257.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501257.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    7. XM_006501197.3XP_006501260.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501260.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    8. XM_006501198.3XP_006501261.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501261.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    9. XM_006501201.3XP_006501264.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501264.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    10. XM_006501202.3XP_006501265.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501265.1

      UniProtKB/TrEMBL
      E9Q613
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    11. XM_006501204.3XP_006501267.1  semaphorin-6C isoform X1

      See identical proteins and their annotated locations for XP_006501267.1

      UniProtKB/TrEMBL
      E9Q613
      Related
      ENSMUSP00000129081.2, OTTMUSP00000070593, ENSMUST00000168321.7, OTTMUST00000132396
      Conserved Domains (2) summary
      pfam01437
      Location:519571
      PSI; Plexin repeat
      cl15693
      Location:54518
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    12. XM_006501208.3XP_006501271.1  semaphorin-6C isoform X5

      See identical proteins and their annotated locations for XP_006501271.1

      Conserved Domains (2) summary
      pfam01437
      Location:372424
      PSI; Plexin repeat
      cl15693
      Location:1371
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    13. XM_006501209.3XP_006501272.1  semaphorin-6C isoform X5

      See identical proteins and their annotated locations for XP_006501272.1

      Conserved Domains (2) summary
      pfam01437
      Location:372424
      PSI; Plexin repeat
      cl15693
      Location:1371
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    14. XM_006501206.3XP_006501269.1  semaphorin-6C isoform X3

      Conserved Domains (2) summary
      pfam01437
      Location:479531
      PSI; Plexin repeat
      cl15693
      Location:39478
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    15. XM_006501207.3XP_006501270.1  semaphorin-6C isoform X4

      Conserved Domains (2) summary
      pfam01437
      Location:456508
      PSI; Plexin repeat
      cl15693
      Location:16455
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
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