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

Gene ID: 20358, updated on 23-Nov-2021

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
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; AI851735; Sema6A-1; A730020P05Rik
Expression
Broad expression in limb E14.5 (RPKM 13.8), lung adult (RPKM 13.8) and 23 other tissues See more
Orthologs
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Genomic context

See Sema6a in Genome Data Viewer
Location:
18; 18 C
Exon count:
21
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (47404908..47528522, 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 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)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
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 differentiation IEA
Inferred from Electronic Annotation
more info
 
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 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
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 axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
acts_upstream_of_or_within 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
PubMed 
involved_in neuron migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
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
    UniProtKB/Swiss-Prot
    O35464
    UniProtKB/TrEMBL
    Q8BUT0
    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
    UniProtKB/TrEMBL
    Q8BXZ7
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
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