U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SEMA4F ssemaphorin 4F [ Homo sapiens (human) ]

Gene ID: 10505, updated on 11-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
2p13.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74654247..74709713)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74662820..74718286)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics. Park YD, et al. Proteomics Clin Appl, 2008 Mar. PMID 21136834
  2. Cancer-related axonogenesis and neurogenesis in prostate cancer. Ayala GE, et al. Clin Cancer Res, 2008 Dec 1. PMID 19047084
  3. 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
  4. NF1 loss disrupts Schwann cell-axonal interactions: a novel role for semaphorin 4F. Parrinello S, et al. Genes Dev, 2008 Dec 1. PMID 19056885, Free PMC Article
  5. Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus: quantitative association analysis and positional candidate genes SEMA4F and OTX1. Francks C, et al. Psychiatr Genet, 2002 Mar. PMID 11901358

See all (32) citations in PubMed

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 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 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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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
    ENSP00000482238.1, ENST00000611975.4
    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_2023_10

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

    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

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