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Aliases for SEMA3F Gene

Aliases for SEMA3F Gene

  • Semaphorin 3F 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3F 2 3
  • Semaphorin IV 3 4
  • Sema IV 2 4
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, 3F 3
  • Semaphorin III/F 3
  • Semaphorin-3F 3
  • Sema III/F 4
  • SEMA-IV 3
  • SEMA4 3
  • SEMAK 3

External Ids for SEMA3F Gene

Previous GeneCards Identifiers for SEMA3F Gene

  • GC03M049760
  • GC03M049931
  • GC03P050046
  • GC03P050151

Summaries for SEMA3F Gene

Entrez Gene Summary for SEMA3F Gene

  • 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]

GeneCards Summary for SEMA3F Gene

SEMA3F (Semaphorin 3F) is a Protein Coding gene. Diseases associated with SEMA3F include Wallerian Degeneration and Brachial Plexus Lesion. Among its related pathways are Axon guidance. Gene Ontology (GO) annotations related to this gene include receptor activity and chemorepellent activity. An important paralog of this gene is SEMA3C.

UniProtKB/Swiss-Prot for SEMA3F Gene

  • May play a role in cell motility and cell adhesion.

Gene Wiki entry for SEMA3F Gene

Additional gene information for SEMA3F Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA3F Gene

Genomics for SEMA3F Gene

GeneHancer (GH) Regulatory Elements for SEMA3F Gene

Promoters and enhancers for SEMA3F Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I050154 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 560.5 +8.8 8764 18.7 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 SLC30A9 FOS SEMA3F RBM6 RBM5 MON1A GNAI2 HYAL3 CYB561D2 CCDC36 MAPKAPK3 KLHDC8B
GH03I050234 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.7 +90.2 90211 21.2 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF207 GNAI2 HYAL3 RBM5 SEMA3F-AS1 RBM6 HYAL1 CYB561D2 RHOA-IT1 AMT HEMK1
GH03I050201 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.7 +49.0 49045 4.8 HDGF FOXA2 ARID4B DMAP1 ZNF48 YY1 ATF7 RXRA SP5 NFYC SLC38A3 RBM6 GNAI2 SEMA3B SEMA3B-AS1 LSMEM2 CYB561D2 HYAL3 SEMA3F SEMA3F-AS1
GH03I050192 Enhancer 1.2 Ensembl ENCODE 12.1 +39.4 39377 4.3 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 FOS HYAL3 RBM6 GNAI2 SEMA3F SEMA3F-AS1 SEMA3B SEMA3B-AS1 LSMEM2 HYAL1 IFRD2
GH03I050188 Enhancer 1 Ensembl ENCODE 12.5 +34.4 34408 1.2 RB1 ARID4B ZNF48 RAD21 RFX5 ARID2 EGR1 ZNF143 RCOR1 CREM GC03P050187 GC03P050190 GNAI2 SEMA3F SEMA3F-AS1 SEMA3B SEMA3B-AS1 LSMEM2 IFRD2 HYAL3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SEMA3F on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA3F gene promoter:

Genomic Locations for SEMA3F Gene

Genomic Locations for SEMA3F Gene
34,031 bases
Plus strand

Genomic View for SEMA3F Gene

Genes around SEMA3F on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3F Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA3F Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3F Gene

Proteins for SEMA3F Gene

  • Protein details for SEMA3F Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • C9JQ85
    • Q13274
    • Q13372
    • Q15704
    • Q6GTR4

    Protein attributes for SEMA3F Gene

    785 amino acids
    Molecular mass:
    88381 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SEMA3F Gene


neXtProt entry for SEMA3F Gene

Post-translational modifications for SEMA3F Gene

  • Glycosylation at posLast=5353 and posLast=126126
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA3F Gene

Domains & Families for SEMA3F Gene

Gene Families for SEMA3F Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SEMA3F Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the semaphorin family.
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3F: view

Function for SEMA3F Gene

Molecular function for SEMA3F Gene

GENATLAS Biochemistry:
semaphorin 3F,secreted,expressed in mammary gland,kidney,fetal brain,lung,repellent of the nerve growth cone guidance
UniProtKB/Swiss-Prot Function:
May play a role in cell motility and cell adhesion.

Phenotypes From GWAS Catalog for SEMA3F Gene

Gene Ontology (GO) - Molecular Function for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0038191 neuropilin binding IBA --
GO:0045499 chemorepellent activity IDA 15814794
genes like me logo Genes that share ontologies with SEMA3F: view
genes like me logo Genes that share phenotypes with SEMA3F: view

Animal Models for SEMA3F Gene

MGI Knock Outs for SEMA3F:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA3F

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA3F Gene

Localization for SEMA3F Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3F Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEMA3F gene
Compartment Confidence
extracellular 4
plasma membrane 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA,TAS --
genes like me logo Genes that share ontologies with SEMA3F: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SEMA3F Gene

Pathways & Interactions for SEMA3F Gene

SuperPathways for SEMA3F Gene

SuperPathway Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA3F: view

Pathways by source for SEMA3F Gene

1 KEGG pathway for SEMA3F Gene

SIGNOR curated interactions for SEMA3F Gene


Gene Ontology (GO) - Biological Process for SEMA3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007411 axon guidance IDA 15814794
GO:0021612 facial nerve structural organization IEA --
GO:0021637 trigeminal nerve structural organization IEA --
GO:0021675 nerve development ISS --
GO:0021785 branchiomotor neuron axon guidance IEA --
genes like me logo Genes that share ontologies with SEMA3F: view

Drugs & Compounds for SEMA3F Gene

(1) Additional Compounds for SEMA3F Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SEMA3F: view

Transcripts for SEMA3F Gene

Unigene Clusters for SEMA3F Gene

Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3F Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - - - - -
SP3: - -
SP4: - - -
SP5: - -

Relevant External Links for SEMA3F Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA3F Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA3F Gene

mRNA differential expression in normal tissues according to GTEx for SEMA3F Gene

This gene is overexpressed in Esophagus - Mucosa (x5.4).

Protein differential expression in normal tissues from HIPED for SEMA3F Gene

This gene is overexpressed in Vitreous humor (26.2), Plasma (19.0), and Amniocyte (14.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SEMA3F Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA3F Gene:


SOURCE GeneReport for Unigene cluster for SEMA3F Gene:


mRNA Expression by UniProt/SwissProt for SEMA3F Gene:

Tissue specificity: Expressed abundantly but differentially in a variety of neural and nonneural tissues. There is high expression in mammary gland, kidney, fetal brain, and lung and lower expression in heart and liver.

Evidence on tissue expression from TISSUES for SEMA3F Gene

  • Nervous system(4.5)
  • Kidney(2.4)
  • Lung(2)
genes like me logo Genes that share expression patterns with SEMA3F: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3F Gene

Orthologs for SEMA3F Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA3F Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA3F 33 34
  • 98.77 (n)
(Canis familiaris)
Mammalia SEMA3F 33 34
  • 90.96 (n)
(Rattus norvegicus)
Mammalia Sema3f 33
  • 89.04 (n)
(Mus musculus)
Mammalia Sema3f 33 16 34
  • 88.95 (n)
(Bos Taurus)
Mammalia SEMA3F 33 34
  • 88.87 (n)
(Monodelphis domestica)
Mammalia SEMA3F 34
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia SEMA3F 34
  • 78 (a)
(Gallus gallus)
Aves SEMA3F 33 34
  • 78.27 (n)
(Anolis carolinensis)
Reptilia SEMA3F 34
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3f 33
  • 73.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68870 33
(Danio rerio)
Actinopterygii sema3fa 34
  • 68 (a)
sema3fb 33 34
  • 67.4 (n)
sema3gb 34
  • 61 (a)
sema3ga 34
  • 60 (a)
Species where no ortholog for SEMA3F was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SEMA3F Gene

Gene Tree for SEMA3F (if available)
Gene Tree for SEMA3F (if available)

Paralogs for SEMA3F Gene

Variants for SEMA3F Gene

Sequence variations from dbSNP and Humsavar for SEMA3F Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000019306 -- 50,189,463(+) A/G downstream_transcript_variant
rs1000079164 -- 50,189,206(+) T/G downstream_transcript_variant
rs1000136800 -- 50,162,940(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000167279 -- 50,170,545(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000195766 -- 50,171,598(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA3F Gene

Variant ID Type Subtype PubMed ID
dgv2524n106 CNV deletion 24896259
dgv602n27 CNV loss 19166990
dgv8316n54 CNV loss 21841781
esv2759148 CNV loss 17122850
nsv1072687 CNV deletion 25765185
nsv470561 CNV loss 18288195
nsv515986 CNV loss 19592680
nsv523560 CNV loss 19592680
nsv523662 CNV loss 19592680
nsv834690 CNV loss 17160897
nsv834692 CNV loss 17160897
nsv954855 CNV deletion 24416366

Variation tolerance for SEMA3F Gene

Residual Variation Intolerance Score: 8.74% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.22; 62.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA3F Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3F Gene

Disorders for SEMA3F Gene

MalaCards: The human disease database

(3) MalaCards diseases for SEMA3F Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
wallerian degeneration
  • wallerian degeneration of the pyramidal tract
brachial plexus lesion
  • brachial plexus lesions
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA3F

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEMA3F: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA3F Gene

Publications for SEMA3F Gene

  1. Isolation of the human semaphorin III/F gene (SEMA3F) at chromosome 3p21, a region deleted in lung cancer. (PMID: 8786119) Xiang RH … Naylor SL (Genomics 1996) 2 3 4 22 58
  2. Distinct 3p21.3 deletions in lung cancer and identification of a new human semaphorin. (PMID: 8649831) Roche J … Drabkin H (Oncogene 1996) 2 3 4 58
  3. Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns. (PMID: 8633026) Sekido Y … Minna JD (Proceedings of the National Academy of Sciences of the United States of America 1996) 3 4 22 58
  4. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 44 58
  5. Hormonal regulation and distinct functions of semaphorin-3B and semaphorin-3F in ovarian cancer. (PMID: 20124444) Joseph D … Syed V (Molecular cancer therapeutics 2010) 3 22 58

Products for SEMA3F Gene

Sources for SEMA3F Gene

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