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Sema4f sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain [ Mus musculus (house mouse) ]

Gene ID: 20355, updated on 7-Aug-2018

Summary

Official Symbol
Sema4fprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domainprovided by MGI
Primary source
MGI:MGI:1340055
See related
Ensembl:ENSMUSG00000000627 Vega:OTTMUSG00000021185
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Sema W
Summary
This gene encodes a member of semaphorin family of membrane-bound and secreted proteins that are involved in guiding axonal growth. The encoded protein is a transmembrane protein localized to the glutamatergic synapses via its association with a synapse-associated scaffolding protein. In oligodendrocyte precursor cells, the encoded protein contributes to the outward migration and differentiation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2015]
Expression
Biased expression in cerebellum adult (RPKM 9.8), CNS E18 (RPKM 7.9) and 10 other tissues See more
Orthologs

Genomic context

See Sema4f in Genome Data Viewer
Location:
6 C3; 6 35.94 cM
Exon count:
15
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 6 NC_000072.6 (82911884..82939769, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (82861879..82889744, complement)

Chromosome 6 - NC_000072.6Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2310069B03 gene Neighboring gene karyopherin alpha 7 (importin alpha 8) pseudogene Neighboring gene 60S ribosomal protein L34 pseudogene Neighboring gene meiosis 1 associated protein Neighboring gene predicted gene, 32644

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

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
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 ISO
Inferred from Sequence Orthology
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 
retinal ganglion cell axon guidance ISO
Inferred from Sequence Orthology
more info
PubMed 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane ISO
Inferred from Sequence Orthology
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
postsynaptic membrane ISO
Inferred from Sequence Orthology
more info
 
synapse ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
semaphorin-4F
Names
semaphorin-W

NCBI Reference Sequences (RefSeq)

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_001308374.1NP_001295303.1  semaphorin-4F isoform c

    See identical proteins and their annotated locations for NP_001295303.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC158652, BC057048
    Conserved Domains (3) summary
    pfam01437
    Location:282333
    PSI; Plexin repeat
    cl11960
    Location:340419
    Ig; Immunoglobulin domain
    cl15693
    Location:1281
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. NM_011350.4NP_035480.3  semaphorin-4F isoform a precursor

    See identical proteins and their annotated locations for NP_035480.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC158652, BC094567
    Consensus CDS
    CCDS20264.1
    UniProtKB/Swiss-Prot
    Q9Z123
    Related
    ENSMUSP00000000641.9, OTTMUSP00000023388, ENSMUST00000000641.14, OTTMUST00000050182
    Conserved Domains (3) summary
    cd11261
    Location:58517
    Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
    pfam01437
    Location:518569
    PSI; Plexin repeat
    cl11960
    Location:576655
    Ig; Immunoglobulin domain

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_000072.6 Reference GRCm38.p4 C57BL/6J

    Range
    82911884..82939769 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011241264.1XP_011239566.1  semaphorin-4F isoform X1

    See identical proteins and their annotated locations for XP_011239566.1

    Conserved Domains (3) summary
    pfam01437
    Location:282333
    PSI; Plexin repeat
    cl11960
    Location:340419
    Ig; Immunoglobulin domain
    cl15693
    Location:1281
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. XM_011241265.2XP_011239567.1  semaphorin-4F isoform X1

    See identical proteins and their annotated locations for XP_011239567.1

    Conserved Domains (3) summary
    pfam01437
    Location:282333
    PSI; Plexin repeat
    cl11960
    Location:340419
    Ig; Immunoglobulin domain
    cl15693
    Location:1281
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

Reference GRCm38.p4 129X1/SvJ

Genomic

  1. NT_039372.2 Reference GRCm38.p4 129X1/SvJ

    Range
    177642..205549 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001113481.1: Suppressed sequence

    Description
    NM_001113481.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
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