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SEMA3F semaphorin 3F [ Homo sapiens (human) ]

Gene ID: 6405, updated on 12-Oct-2019

Summary

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Official Symbol
SEMA3Fprovided by HGNC
Official Full Name
semaphorin 3Fprovided by HGNC
Primary source
HGNC:HGNC:10728
See related
Ensembl:ENSG00000001617 MIM:601124
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
SEMA4; SEMAK; SEMA-IV
Summary
This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Expression
Broad expression in skin (RPKM 21.7), esophagus (RPKM 16.4) and 19 other tissues See more
Orthologs
mouse all

Genomic context

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See SEMA3F in Genome Data Viewer
Location:
3p21.31
Exon count:
23
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (50155058..50189075)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50192562..50226508)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 6 Neighboring gene RBM5 antisense RNA 1 Neighboring gene RNA binding motif protein 5 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene basic proline-rich protein-like Neighboring gene G protein subunit alpha transducin 1 Neighboring gene solute carrier family 38 member 3

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
  • 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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Related articles in PubMed

  1. The crucial role of SEMA3F in suppressing the progression of oral squamous cell carcinoma. Liu Y, et al. Cell Mol Biol Lett, 2017. PMID 29299034, Free PMC Article
  2. Semaphorin 3F expression is reduced in pregnancy complicated by preeclampsia. An observational clinical study. Stallone G, et al. PLoS One, 2017. PMID 28350837, Free PMC Article
  3. Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer. Aversa R, et al. Int J Mol Sci, 2016 Jan 16. PMID 26784191, Free PMC Article
  4. Semaphorin-3F functions as a tumor suppressor in colorectal cancer due to regulation by DNA methylation. Gao X, et al. Int J Clin Exp Pathol, 2015. PMID 26722466, Free PMC Article
  5. The axon guidance molecule semaphorin 3F is a negative regulator of tumor progression and proliferation in ileal neuroendocrine tumors. Bollard J, et al. Oncotarget, 2015 Nov 3. PMID 26447612, Free PMC Article

See all (63) 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. SEMA3F plays a role as a tumor suppressor in Oral squamous cell carcinoma cell proliferation, migration and invasion.
    Title: The crucial role of SEMA3F in suppressing the progression of oral squamous cell carcinoma.
  2. in situ hybridization analysis revealed that Sema 3C and Sema 3F are expressed at the RNA level in the endometriosis affected peritoneum
    Title: Reduced Sympathetic Innervation in Endometriosis is Associated to Semaphorin 3C and 3F Expression.
  3. Semaphorin 3F placenta tissue expression was significantly reduced in preeclampsia. In addition, semaphorin 3F level at delivery was significantly lower in serum, amniotic fluid and venous umbilical blood of preeclamptic patients compared with normal pregnant women.
    Title: Semaphorin 3F expression is reduced in pregnancy complicated by preeclampsia. An observational clinical study.
  4. There is a positive association between the expression of AKAP12 and Semaphorin 3F in prostate cancer, suggesting that the activation of Semaphorin 3F by AKAP12 may be involved in prostate cancer progression and metastasis.
    Title: SSeCKS/AKAP12 induces repulsion between human prostate cancer and microvessel endothelial cells through the activation of Semaphorin 3F.
  5. Study demonstrates an anti-tumoral role of SEMA3F in ileal NETs. We thus suggest that SEMA3F and/or its cellular signaling pathway could represent a target for ileal NET therapy.
    Title: The axon guidance molecule semaphorin 3F is a negative regulator of tumor progression and proliferation in ileal neuroendocrine tumors.
  6. SEMA3F was downregulated in colorectal cancer tissues as compared to matched adjacent non-tumor tissues
    Title: Semaphorin-3F functions as a tumor suppressor in colorectal cancer due to regulation by DNA methylation.
  7. A new SEMA3F transcript is expressed in all breast cell lines and breast cancer biopsies, and is translated into a new semaphorin 3F isoform.
    Title: Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer.
  8. SEMA3F-NRP2 interactions inhibit intracellular PI-3K activity, mTORC2-dependent signaling, RhoA activity and cytoskeletal stress fiber formation.
    Title: Regulation of mTOR Signaling by Semaphorin 3F-Neuropilin 2 Interactions In Vitro and In Vivo.
  9. Data indicate that semaphorin 3F (SEMA3F) and its receptor neuropilin-2 (NRP2) are expressed in the thymus.
    Title: Semaphorin 3F and neuropilin-2 control the migration of human T-cell precursors.
  10. SEMA3F functions as a suppressor of colorectal cancer metastasis by down-regulating the ASCL2-CXCR4 signaling axis.
    Title: SEMA3F prevents metastasis of colorectal cancer by PI3K-AKT-dependent down-regulation of the ASCL2-CXCR4 axis.
Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from BioSystems

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  • 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...

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 GOA

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
chemorepellent activity IDA
Inferred from Direct Assay
more info
 PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Process Evidence Code Pubs
axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
axon guidance IDA
Inferred from Direct Assay
more info
 PubMed 
branchiomotor neuron axon guidance IEA
Inferred from Electronic Annotation
more info
  
facial nerve structural organization IEA
Inferred from Electronic Annotation
more info
  
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nerve development ISS
Inferred from Sequence or Structural Similarity
more info
  
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
neural crest cell migration involved in autonomic nervous system development IEA
Inferred from Electronic Annotation
more info
  
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
regulation of postsynapse organization IEA
Inferred from Electronic Annotation
more info
  
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
semaphorin-plexin signaling pathway involved in axon guidance IEA
Inferred from Electronic Annotation
more info
  
semaphorin-plexin signaling pathway involved in neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
sympathetic ganglion development ISS
Inferred from Sequence or Structural Similarity
more info
  
sympathetic neuron projection extension ISS
Inferred from Sequence or Structural Similarity
more info
  
sympathetic neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
trigeminal nerve structural organization IEA
Inferred from Electronic Annotation
more info
  
ventral trunk neural crest cell migration IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

General protein information

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Preferred Names
semaphorin-3F
Names
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3F
semaphorin III/F
semaphorin IV

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_001318798.2 → NP_001305727.1  semaphorin-3F isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the 5' coding region and initiates translation at a downstream start site, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
    Source sequence(s)
    AB209259, AC000063, BQ949723, CB240860
    Consensus CDS
    CCDS82780.1
    UniProtKB/TrEMBL
    C9JPG5, Q59G50
    Related
    ENSP00000388931.1, ENST00000413852.5
    Conserved Domains (4) summary
    cd05871
    Location:510 → 598
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:1 → 449
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:513 → 597
    IG_like; Immunoglobulin like
    smart00423
    Location:448 → 485
    PSI; domain found in Plexins, Semaphorins and Integrins

  2. NM_001318800.1 → NP_001305729.1  semaphorin-3F isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
    Source sequence(s)
    AB209259, AC000063, AC104450, CB240860, U38276
    Consensus CDS
    CCDS82779.1
    UniProtKB/Swiss-Prot
    Q13275
    UniProtKB/TrEMBL
    Q59G50
    Related
    ENSP00000409859.1, ENST00000434342.5
    Conserved Domains (4) summary
    cd05871
    Location:578 → 666
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48 → 517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:581 → 665
    IG_like; Immunoglobulin like
    smart00423
    Location:516 → 553
    PSI; domain found in Plexins, Semaphorins and Integrins

  3. NM_004186.5 → NP_004177.3  semaphorin-3F isoform 1 precursor

    See identical proteins and their annotated locations for NP_004177.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA378582, AC104450, BC042914, BF058597, CB240860
    Consensus CDS
    CCDS2811.1
    UniProtKB/Swiss-Prot
    Q13275
    Related
    ENSP00000002829.3, ENST00000002829.8
    Conserved Domains (4) summary
    cd05871
    Location:609 → 697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48 → 548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:612 → 696
    IG_like; Immunoglobulin like
    smart00423
    Location:547 → 584
    PSI; domain found in Plexins, Semaphorins and Integrins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    50155058..50189075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533998.2 → XP_011532300.1  semaphorin-3F isoform X1

    See identical proteins and their annotated locations for XP_011532300.1

    UniProtKB/Swiss-Prot
    Q13275
    Conserved Domains (4) summary
    cd05871
    Location:609 → 697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48 → 548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:612 → 696
    IG_like; Immunoglobulin like
    smart00423
    Location:547 → 584
    PSI; domain found in Plexins, Semaphorins and Integrins

  2. XM_005265382.4 → XP_005265439.1  semaphorin-3F isoform X2

    See identical proteins and their annotated locations for XP_005265439.1

    UniProtKB/Swiss-Prot
    Q13275
    Conserved Domains (4) summary
    cd05871
    Location:578 → 666
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48 → 517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:581 → 665
    IG_like; Immunoglobulin like
    smart00423
    Location:516 → 553
    PSI; domain found in Plexins, Semaphorins and Integrins

  3. XM_011534000.2 → XP_011532302.1  semaphorin-3F isoform X4

    Conserved Domains (1) summary
    cl15693
    Location:48 → 485
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  4. XM_006713290.3 → XP_006713353.1  semaphorin-3F isoform X5

    Conserved Domains (1) summary
    cl15693
    Location:48 → 479
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  5. XM_005265381.4 → XP_005265438.1  semaphorin-3F isoform X1

    See identical proteins and their annotated locations for XP_005265438.1

    UniProtKB/Swiss-Prot
    Q13275
    Conserved Domains (4) summary
    cd05871
    Location:609 → 697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48 → 548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00410
    Location:612 → 696
    IG_like; Immunoglobulin like
    smart00423
    Location:547 → 584
    PSI; domain found in Plexins, Semaphorins and Integrins

  6. XM_006713289.3 → XP_006713352.1  semaphorin-3F isoform X3

    Conserved Domains (4) summary
    cd05871
    Location:412 → 500
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00410
    Location:415 → 499
    IG_like; Immunoglobulin like
    smart00423
    Location:350 → 387
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:17 → 351
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RNA

  1. XR_940487.2 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13275.2 GenPept UniProtKB/Swiss-Prot:Q13275

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