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    SEMA4F ssemaphorin 4F [ Homo sapiens (human) ]

    Gene ID: 10505, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SEMA4Fprovided by HGNC
    Official Full Name
    ssemaphorin 4Fprovided by HGNC
    Primary source
    HGNC:HGNC:10734
    See related
    Ensembl:ENSG00000135622 MIM:603706; AllianceGenome:HGNC:10734
    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]
    Expression
    Broad expression in brain (RPKM 2.1), testis (RPKM 1.1) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEMA4F in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74654247..74709713)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74662820..74718286)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74881374..74910968)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene meiosis 1 associated protein Neighboring gene TOR1B pseudogene 1 Neighboring gene TVP23B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11671 Neighboring gene uncharacterized LOC102724497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11672 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:74967320-74968519 Neighboring gene uncharacterized LOC102724482 Neighboring gene ribosomal protein S28 pseudogene 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:75017750-75017897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11674 Neighboring gene HK2 divergent transcript

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    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

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38268

    Gene Ontology Provided by GOA

    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 semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of axon extension IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    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
    		  
    involved_in retinal ganglion cell axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    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 postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-4F
    Names
    sema domain immunoglobulin domain transmembrane domain (TM) and short cytoplasmic domain (semaphorin) 4F
    sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F
    semaphorin M
    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_001271661.2 → NP_001258590.1  semaphorin-4F isoform 2 precursor

      See identical proteins and their annotated locations for NP_001258590.1

      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
      Consensus CDS
      CCDS62942.1
      UniProtKB/Swiss-Prot
      O95754
      Related
      ENSP00000342675.5, ENST00000339773.9
      Conserved Domains (3) summary
      pfam01437
      Location:357 → 408
      PSI; Plexin repeat
      cl11960
      Location:415 → 494
      Ig; Immunoglobulin domain
      cl15693
      Location:52 → 356
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001271662.2 → 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
      Consensus CDS
      CCDS74529.1
      UniProtKB/TrEMBL
      A0A087WYZ7
      Related
      ENSP00000407698.2, ENST00000434486.6
      Conserved Domains (3) summary
      cd11261
      Location:52 → 478
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:479 → 530
      PSI; Plexin repeat
      cl11960
      Location:537 → 616
      Ig; Immunoglobulin domain

    3. NM_004263.5 → NP_004254.2  semaphorin-4F isoform 1 precursor

      See identical proteins and their annotated locations for NP_004254.2

      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, Q542Y7, Q9NS35
      Related
      ENSP00000350547.2, ENST00000357877.7
      Conserved Domains (3) summary
      cd05872
      Location:570 → 649
      Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
      cd11261
      Location:52 → 511
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:512 → 563
      PSI; Plexin repeat

    RNA

    1. NR_073398.2 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_073399.2 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      74654247..74709713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442927.1 → XP_047298883.1  semaphorin-4F isoform X6

    2. XM_047442929.1 → XP_047298885.1  semaphorin-4F isoform X8

    3. XM_047442926.1 → XP_047298882.1  semaphorin-4F isoform X2

    4. XM_011532477.4 → XP_011530779.1  semaphorin-4F isoform X6

      Conserved Domains (2) summary
      cd11261
      Location:52 → 511
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:512 → 563
      PSI; Plexin repeat

    5. XM_011532476.4 → XP_011530778.1  semaphorin-4F isoform X5

      Conserved Domains (2) summary
      cd11261
      Location:52 → 511
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:512 → 563
      PSI; Plexin repeat

    6. XM_047442928.1 → XP_047298884.1  semaphorin-4F isoform X7

    7. XM_011532475.4 → XP_011530777.1  semaphorin-4F isoform X4

      Related
      ENSP00000520881.1, ENST00000850594.1
      Conserved Domains (3) summary
      cd11261
      Location:52 → 511
      Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
      pfam01437
      Location:512 → 563
      PSI; Plexin repeat
      cl11960
      Location:570 → 616
      Ig; Immunoglobulin domain

    8. XM_017003172.2 → XP_016858661.1  semaphorin-4F isoform X1

    9. XM_017003173.2 → XP_016858662.1  semaphorin-4F isoform X3

    RNA

    1. XR_007068742.1 RNA Sequence

    2. XR_001738589.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      74662820..74718286
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340192.1 → XP_054196167.1  semaphorin-4F isoform X6

    2. XM_054340195.1 → XP_054196170.1  semaphorin-4F isoform X8

    3. XM_054340193.1 → XP_054196168.1  semaphorin-4F isoform X6

    4. XM_054340191.1 → XP_054196166.1  semaphorin-4F isoform X5

    5. XM_054340194.1 → XP_054196169.1  semaphorin-4F isoform X7

    6. XM_054340190.1 → XP_054196165.1  semaphorin-4F isoform X4

    7. XM_054340188.1 → XP_054196163.1  semaphorin-4F isoform X1

    8. XM_054340189.1 → XP_054196164.1  semaphorin-4F isoform X3

    RNA

    1. XR_008486252.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95754.2 GenPept UniProtKB/Swiss-Prot:O95754

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