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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 2-Nov-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 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 (34) 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 neuropilin binding 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
    		  
    enables semaphorin receptor binding IEA
    Inferred from Electronic Annotation
    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
    		  
    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 
    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 dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    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 
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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