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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 11-Apr-2024

Summary

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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 AllianceGenome:MGI:1340055
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
human all
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Genomic context

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See Sema4f in Genome Data Viewer
Location:
6 C3; 6 35.94 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (82888865..82916724, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (82911884..82939769, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2310069B03 gene Neighboring gene STARR-seq mESC enhancer starr_16453 Neighboring gene karyopherin alpha 7 (importin alpha 8) pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:82864066-82864219 Neighboring gene STARR-seq mESC enhancer starr_16454 Neighboring gene 60S ribosomal protein L34 pseudogene Neighboring gene meiosis 1 associated protein Neighboring gene STARR-positive B cell enhancer ABC_E4835 Neighboring gene STARR-positive B cell enhancer ABC_E2194 Neighboring gene predicted gene, 53290

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Transcriptional profiling of the injured sciatic nerve of mice carrying the Wld(S) mutant gene: identification of genes involved in neuroprotection, neuroinflammation, and nerve regeneration. Barrette B, et al. Brain Behav Immun, 2010 Nov. PMID 20688153
  2. Expression of Semaphorin 4F in neurons and brain oligodendrocytes and the regulation of oligodendrocyte precursor migration in the optic nerve. Armendáriz BG, et al. Mol Cell Neurosci, 2012 Jan. PMID 21945643
  3. Semaphorin4F interacts with the synapse-associated protein SAP90/PSD-95. Schultze W, et al. J Neurochem, 2001 Aug. PMID 11483650
  4. Cloning, expression, and genetic mapping of Sema W, a member of the semaphorin family. Encinas JA, et al. Proc Natl Acad Sci U S A, 1999 Mar 2. PMID 10051670, Free PMC Article
  5. An antagonistic interaction between PlexinB2 and Rnd3 controls RhoA activity and cortical neuron migration. Azzarelli R, et al. Nat Commun, 2014 Feb 27. PMID 24572910, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Sema4F expressed by oligodendrocyte precursor cells contributes to the outward migration and differentiation of these cells in the optic nerve.
    Title: Expression of Semaphorin 4F in neurons and brain oligodendrocytes and the regulation of oligodendrocyte precursor migration in the optic nerve.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of axon extension ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
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 negative regulation of axon extension ISO
Inferred from Sequence Orthology
more info
 PubMed 
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
  
acts_upstream_of_or_within retinal ganglion cell axon guidance ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic density membrane ISO
Inferred from Sequence Orthology
more info
  
located_in postsynaptic membrane ISO
Inferred from Sequence Orthology
more info
  
located_in synapse ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
semaphorin-4F
Names
semaphorin-W

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_001308374.2 → NP_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. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AC158652
    Conserved Domains (3) summary
    smart00423
    Location:282 → 333
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:340 → 419
    Ig; Immunoglobulin domain
    cl15693
    Location:1 → 281
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  2. NM_001410310.1 → NP_001397239.1  semaphorin-4F isoform c

    Status: REVIEWED

    Source sequence(s)
    AC158652

  3. NM_011350.5 → NP_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
    Consensus CDS
    CCDS20264.1
    UniProtKB/Swiss-Prot
    Q505G0, Q9R1Y1, Q9Z123
    UniProtKB/TrEMBL
    Q810B2
    Related
    ENSMUSP00000000641.10, ENSMUST00000000641.15
    Conserved Domains (3) summary
    cd11261
    Location:58 → 517
    Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
    pfam01437
    Location:518 → 569
    PSI; Plexin repeat
    cl11960
    Location:576 → 655
    Ig; Immunoglobulin domain

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_000072.7 Reference GRCm39 C57BL/6J

    Range
    82888865..82916724 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011241265.3 → XP_011239567.1  semaphorin-4F isoform X1

    See identical proteins and their annotated locations for XP_011239567.1

    Conserved Domains (3) summary
    smart00423
    Location:282 → 333
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:340 → 419
    Ig; Immunoglobulin domain
    cl15693
    Location:1 → 281
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

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.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Z123.2 GenPept UniProtKB/Swiss-Prot:Q9Z123

Gene LinkOut

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