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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-Sep-2014
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; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Semay; mKIAA1869
See Sema6c in Epigenomics, MapViewer
Location:
3; 3 F2
Exon count:
22
Annotation release Status Assembly Chr Location
104 current GRCm38.p2 (GCF_000001635.22) 3 NC_000069.6 (95160420..95174050)

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 (trithorax homolog, Drosophila); translocated to, 11 Neighboring gene CDC42 small effector 1

  • 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
receptor activity IEA
Inferred from Electronic Annotation
more info
 
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 organismal development IEA
Inferred from Electronic Annotation
more info
 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
semaphorin-6C
Names
semaphorin-6C
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 proteins identical to 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/TrEMBL
    E9Q613
    UniProtKB/Swiss-Prot
    Q9WTM3
    Related
    ENSMUSP00000088333, OTTMUSP00000025221, ENSMUST00000090823, OTTMUST00000053081
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    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 proteins identical to 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
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:675719
    DUF4527; Protein of unknown function (DUF4527)
    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
  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
  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 104

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

Reference GRCm38.p2 C57BL/6J

Genomic

  1. NC_000069.6 

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

mRNA and Protein(s)

  1. XM_006501205.1XP_006501268.1  

    See proteins identical to XP_006501268.1

    UniProtKB/Swiss-Prot
    Q9WTM3
    Related
    ENSMUSP00000088331, OTTMUSP00000025222, ENSMUST00000090821, OTTMUST00000053084
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:675719
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. XM_006501192.1XP_006501255.1  

    See proteins identical to XP_006501255.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  3. XM_006501195.1XP_006501258.1  

    See proteins identical to XP_006501258.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_006501193.1XP_006501256.1  

    See proteins identical to XP_006501256.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. XM_006501196.1XP_006501259.1  

    See proteins identical to XP_006501259.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. XM_006501210.1XP_006501273.1  

    Conserved Domains (3) summary
    pfam01437
    Location:88109
    PSI; Plexin repeat
    pfam15030
    Location:276320
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:187
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  7. XM_006501194.1XP_006501257.1  

    See proteins identical to XP_006501257.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  8. XM_006501197.1XP_006501260.1  

    See proteins identical to XP_006501260.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  9. XM_006501198.1XP_006501261.1  

    See proteins identical to XP_006501261.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  10. XM_006501201.1XP_006501264.1  

    See proteins identical to XP_006501264.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  11. XM_006501202.1XP_006501265.1  

    See proteins identical to XP_006501265.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  12. XM_006501199.1XP_006501262.1  

    See proteins identical to XP_006501262.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  13. XM_006501200.1XP_006501263.1  

    See proteins identical to XP_006501263.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  14. XM_006501203.1XP_006501266.1  

    See proteins identical to XP_006501266.1

    UniProtKB/TrEMBL
    E9Q613
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  15. XM_006501204.1XP_006501267.1  

    See proteins identical to XP_006501267.1

    UniProtKB/TrEMBL
    E9Q613
    Related
    ENSMUSP00000102835, OTTMUSP00000025224, ENSMUST00000107217, OTTMUST00000053086
    Conserved Domains (4) summary
    smart00630
    Location:62472
    Sema; semaphorin domain
    pfam01437
    Location:519540
    PSI; Plexin repeat
    pfam15030
    Location:707751
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:54518
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  16. XM_006501208.1XP_006501271.1  

    See proteins identical to XP_006501271.1

    Conserved Domains (4) summary
    smart00630
    Location:38325
    Sema; semaphorin domain
    pfam01437
    Location:372393
    PSI; Plexin repeat
    pfam15030
    Location:560604
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:1371
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  17. XM_006501209.1XP_006501272.1  

    See proteins identical to XP_006501272.1

    Conserved Domains (4) summary
    smart00630
    Location:38325
    Sema; semaphorin domain
    pfam01437
    Location:372393
    PSI; Plexin repeat
    pfam15030
    Location:560604
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:1371
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  18. XM_006501206.1XP_006501269.1  

    Conserved Domains (4) summary
    smart00630
    Location:39432
    Sema; semaphorin domain
    pfam01437
    Location:479500
    PSI; Plexin repeat
    pfam15030
    Location:667711
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:39478
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  19. XM_006501207.1XP_006501270.1  

    Conserved Domains (4) summary
    smart00630
    Location:16409
    Sema; semaphorin domain
    pfam01437
    Location:456477
    PSI; Plexin repeat
    pfam15030
    Location:644688
    DUF4527; Protein of unknown function (DUF4527)
    cl15693
    Location:16455
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

Alternate Mm_Celera

Genomic

  1. AC_000025.1 

    Range
    96591498..96605128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)