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    SEMA4F sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F [ Homo sapiens (human) ]

    Gene ID: 10505, updated on 15-May-2013
    Official Symbol
    SEMA4Fprovided by HGNC
    Official Full Name
    sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Fprovided by HGNC
    Primary source
    HGNC:10734
    See related
    Ensembl:ENSG00000135622; HPRD:04748; MIM:603706; Vega:OTTHUMG00000129952
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    S4F; SEMAM; SEMAW; M-SEMA; PRO2353; m-Sema-M
    Summary
    This gene encodes a transmembrane class IV semaphorin family protein, which plays a role in neural development. This gene may be involved in neurogenesis in prostate cancer, the development of neurofibromas, and breast cancer tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
    Location :
    2p13.1
    Sequence :
    Chromosome: 2; NC_000002.11 (74881393..74909185)
    See SEMA4F in Epigenomics, MapViewer

    Chromosome 2 - NC_000002.11Genomic Context describing neighboring genes Neighboring gene meiosis 1 associated protein Neighboring gene torsin family 1, member B (torsin B) pseudogene Neighboring gene trans-golgi network vesicle protein 23 homolog B (S. cerevisiae) pseudogene 2 Neighboring gene ribosomal protein S28 pseudogene 5 Neighboring gene hexokinase 2

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. Genetic variants on chromosome 1q41 influence ocular axial length and high myopia. Fan Q, et al. PLoS Genet, 2012. PMID 22685421.
    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. Semaphorin-plexin signalling genes associated with human breast tumourigenesis. Gabrovska PN, et al. Gene, 2011 Dec 10. PMID 21925246.
    4. Comprehensive gene and microRNA expression profiling reveals the crucial role of hsa-let-7i and its target genes in colorectal cancer metastasis. Zhang P, et al. Mol Biol Rep, 2012 Feb. PMID 21625861.
    5. Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics. Park YD, et al. Proteomics Clin Appl, 2008 Mar. PMID 21136834.

    See all (21) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. data seems to indicate that SEMA4F is involved in tumour progression in breast cancer
      Title: Semaphorin-plexin signalling genes associated with human breast tumourigenesis.
    2. Sema4F levels were strongly reduced in a panel of human neurofibromas, confirming the relevance of these findings to the human disease.
      Title: NF1 loss disrupts Schwann cell-axonal interactions: a novel role for semaphorin 4F.
    3. Fine mapping of the chromosome 2p12-16 dyslexia susceptibility candidate gene
      Title: Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus: quantitative association analysis and positional candidate genes SEMA4F and OTX1.
    Submit: New GeneRIF Correction

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    O95754 P78352 DLG4    HPRD  PubMed  
    O95754 O60462 NRP2    HPRD  PubMed  
    • 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...

    Markers

    Genotypes

    Homology

    Clone Names

    • FLJ38268

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    axon guidance TAS
    Traceable Author Statement
    more info
    		 PubMed 
    cell-cell signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    negative regulation of axon extension IEA
    Inferred from Electronic Annotation
    more info
    		  
    nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    retinal ganglion cell axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    integral to plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    Preferred Names
    semaphorin-4F
    Names
    semaphorin-4F
    semaphorin M
    semaphorin-M
    semaphorin-W

    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_001271661.1 → NP_001258590.1  semaphorin-4F isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks several internal exons, resulting in the loss of an in-frame segment in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC007387, BC018361, CK905501, DC306380
      UniProtKB/Swiss-Prot
      O95754
      Conserved Domains (4) summary
      smart00630
      Location:120 – 332
      Blast Score: 524
      Sema; semaphorin domain
      pfam01437
      Location:357 – 408
      Blast Score: 109
      PSI; Plexin repeat
      cl15693
      Location:120 – 356
      Blast Score: 1258
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
      cl11960
      Location:415 – 494
      Blast Score: 259
      Ig; Immunoglobulin domain

    2. NM_001271662.1 → NP_001258591.1  semaphorin-4F isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AC007387, AK308166, AL136552, CK905501, DC306380
      UniProtKB/Swiss-Prot
      O95754
      Conserved Domains (4) summary
      cd05872
      Location:537 – 616
      Blast Score: 263
      Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
      smart00630
      Location:65 – 454
      Blast Score: 853
      Sema; semaphorin domain
      cd11261
      Location:52 – 478
      Blast Score: 2221
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:479 – 530
      Blast Score: 111
      PSI; Plexin repeat

    3. NM_004263.4 → NP_004254.2  semaphorin-4F isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC007387, AL136552, CK905501, DC306380
      Consensus CDS
      CCDS1955.1
      UniProtKB/Swiss-Prot
      O95754
      Related
      ENSP00000350547, OTTHUMP00000160410, ENST00000357877, OTTHUMT00000252214
      Conserved Domains (4) summary
      cd05872
      Location:570 – 649
      Blast Score: 263
      Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
      smart00630
      Location:65 – 487
      Blast Score: 958
      Sema; semaphorin domain
      cd11261
      Location:52 – 511
      Blast Score: 2460
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:512 – 563
      Blast Score: 110
      PSI; Plexin repeat

    RNA

    1. NR_073398.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC007387, AK312728, CK905501, DC306380

    2. NR_073399.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB021292, AC007387, AL136552, CK905501, DC306380

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000002.11 Reference GRCh37.p10 Primary Assembly

      Range
      74881393..74909185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000134.1 Alternate HuRef

      Range
      74618851..74646636
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018913.1 Alternate CHM1_1.0

      Range
      74752615..74780407
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01075609.1 (14340..37634) None
    genomic ABBA01075610.1 None
    genomic AC007387.4 (7324..36389) None
    genomic AMYH01010454.1 (529942..557734) None
    genomic CH471053.2 EAW99605.1
      EAW99606.1
      EAW99607.1
      EAW99608.1
    genomic CS051179.1 CAI72085.1
    mRNA AB021292.1 None
    mRNA AB022317.1 BAA75631.1
    mRNA AF053369.1 AAF80660.1
    mRNA AK075384.1 BAC11584.1
    mRNA AK095587.1 None
    mRNA AK291023.1 BAF83712.1
    mRNA AK304358.1 BAH14167.1
    mRNA AK308166.1 None
    mRNA AK312728.1 None
    mRNA AL136552.1 CAB66487.1
    mRNA BC018361.1 AAH18361.1
    mRNA BC038411.1 AAH38411.1
    mRNA CK905501.1 None
    mRNA DC306380.1 None
    other-genetic AM393735.1 CAL38610.1
    other-genetic DQ895677.2 ABM86603.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95754.2 GenPept UniProtKB/Swiss-Prot:O95754

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous

      Supplemental Content

      Table of contents

      Related information

      • Order cDNA clone
        Order cDNA clone
      • BioAssay
        Related PubChem BioAssays
      • BioProjects
        BioProjects related to a gene
      • BioSystems
        BioSystems
      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
      • GEO Profiles
        Related GEO
      • HomoloGene
        Links between HomoloGene and Gene are provided by the HomoloGene group when a gene is included in a HomoloGene record.
      • Map Viewer
        These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
      • Nucleotide
        Link to related Nucleotide entry
      • OMIM
        Links between OMIM and Gene are calculated by Gene based on MIM numbers included in the summary and phenotype sections of the Gene record.
      • Probe
        Related Probe entry
      • Protein
        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
      • SNP: Genotype
        Gene Genotype Report
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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