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

Gene ID: 20359, updated on 12-May-2024

Summary

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 located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space. Predicted to be integral component of 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, Apr 2022]
Expression
Broad expression in frontal lobe adult (RPKM 19.8), cortex adult (RPKM 18.3) and 24 other tissues See more
Orthologs
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Genomic context

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

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

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in central nervous system development ISO
Inferred from Sequence Orthology
more info
 
involved_in hippocampus development 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
 
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
 
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
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

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_001130456.1NP_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:708875
    PHA03269; envelope glycoprotein C; Provisional
    cd11267
    Location:58526
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    smart00423
    Location:527573
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. NM_013662.2NP_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:708875
    PHA03269; envelope glycoprotein C; Provisional
    cd11267
    Location:58526
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    smart00423
    Location:527573
    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_006523930.5XP_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:708875
    PHA03269; envelope glycoprotein C; Provisional
    cd11267
    Location:58526
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    smart00423
    Location:527573
    PSI; domain found in Plexins, Semaphorins and Integrins