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SEMA3F semaphorin 3F [ Homo sapiens (human) ]

Gene ID: 6405, updated on 11-Apr-2024

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; AllianceGenome:HGNC:10728
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
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Genomic context

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See SEMA3F in Genome Data Viewer
Location:
3p21.31
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50155058..50189075)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50184392..50218408)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50192491..50226508)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977213-49977735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977736-49978257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14379 Neighboring gene RNA binding motif protein 6 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50050258-50050926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50119658-50120158 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:50120996-50121560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126209-50126800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126801-50127391 Neighboring gene MPRA-validated peak4650 silencer Neighboring gene RBM5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50157731-50158609 Neighboring gene RNA binding motif protein 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50158610-50159487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50160473-50160973 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50162997-50163986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50170449-50170950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50172709-50173300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50177671-50178232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50178233-50178794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50188081-50188752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14381 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14380 Neighboring gene Sharpr-MPRA regulatory region 10077 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:50207171-50207381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50207797-50208770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50230799-50231315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231316-50231832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231833-50232348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50232401-50232932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50246621-50247149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50250030-50250839 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257474-50257974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257975-50258475 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. Reverse effect of Semaphorin-3F on rituximab resistance in diffuse large B-cell lymphoma via the Hippo pathway. Li Q, et al. Chin Med J (Engl), 2023 Jun 20. PMID 37114652, Free PMC Article
  2. Semaphorin3F Drives Dendritic Spine Pruning Through Rho-GTPase Signaling. Duncan BW, et al. Mol Neurobiol, 2021 Aug. PMID 33856648, Free PMC Article
  3. Semaphorin 3F Serves as a Tumor Suppressor in Esophageal Squamous Cell Carcinoma and is Associated With Lymph Node Metastasis in Disease Progression. Xie Z, et al. Technol Cancer Res Treat, 2020 Jan-Dec. PMID 32441221, Free PMC Article
  4. Endothelial Semaphorin 3F Maintains Endothelial Barrier Function and Inhibits Monocyte Migration. Zhang H, et al. Int J Mol Sci, 2020 Feb 21. PMID 32098168, Free PMC Article
  5. SEMA3F Promotes Liver Hepatocellular Carcinoma Metastasis by Activating Focal Adhesion Pathway. Ye K, et al. DNA Cell Biol, 2020 Mar. PMID 31968181

See all (75) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Reverse effect of Semaphorin-3F on rituximab resistance in diffuse large B-cell lymphoma via the Hippo pathway.
    Title: Reverse effect of Semaphorin-3F on rituximab resistance in diffuse large B-cell lymphoma via the Hippo pathway.
  2. Semaphorin3F Drives Dendritic Spine Pruning Through Rho-GTPase Signaling.
    Title: Semaphorin3F Drives Dendritic Spine Pruning Through Rho-GTPase Signaling.
  3. Semaphorin 3fa Controls Ocular Vascularization From the Embryo Through to the Adult.
    Title: Semaphorin 3fa Controls Ocular Vascularization From the Embryo Through to the Adult.
  4. Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
    Title: Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
  5. Semaphorin 3F Serves as a Tumor Suppressor in Esophageal Squamous Cell Carcinoma and is Associated With Lymph Node Metastasis in Disease Progression.
    Title: Semaphorin 3F Serves as a Tumor Suppressor in Esophageal Squamous Cell Carcinoma and is Associated With Lymph Node Metastasis in Disease Progression.
  6. Endothelial Semaphorin 3F Maintains Endothelial Barrier Function and Inhibits Monocyte Migration.
    Title: Endothelial Semaphorin 3F Maintains Endothelial Barrier Function and Inhibits Monocyte Migration.
  7. The level of SEMA3F was significantly higher in normal prostate tissues compared with that in prostate cancer cells.
    Title: Clinical relevance of semaphorin-3F in patients with prostate cancer.
  8. SEMA3F was significantly upregulated in hepatocellular carcinoma tissue and was associated with poor survival. SEMA3F promoted hepatocellular carcinoma metastasis by activating focal adhesion pathway.
    Title: SEMA3F Promotes Liver Hepatocellular Carcinoma Metastasis by Activating Focal Adhesion Pathway.
  9. SEMA 3F is recommended as an important therapeutic agent for the prevention of pathological angiogenesis. SEMA 3F may offer an effective and efficient anti-angiogenic intervention that can be administered at a lower dose alternative to typical VEGF blocking agents.
    Title: Inhibitory effects of Semaphorin 3F as an alternative candidate to anti-VEGF monoclonal antibody on angiogenesis.
  10. Familial chronic megacolon appears to be associated with SEMA3F, which is associated with genes impacting enteric nerve or pacemaker function.
    Title: Familial chronic megacolon presenting in childhood or adulthood: Seeking the presumed gene association.
Submit: New GeneRIF Correction See all GeneRIFs (48)

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

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

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_001318800.2 → 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/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
    C9JQ85, Q13274, Q13275, Q13372, Q15704, Q6GTR4
    UniProtKB/TrEMBL
    Q59G50
    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: 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_000003.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_005265438.1

    UniProtKB/Swiss-Prot
    C9JQ85, Q13274, Q13275, Q13372, Q15704, Q6GTR4
    UniProtKB/TrEMBL
    Q59G50
    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_011533998.3 → XP_011532300.1  semaphorin-3F isoform X1

    See identical proteins and their annotated locations for XP_011532300.1

    UniProtKB/Swiss-Prot
    C9JQ85, Q13274, Q13275, Q13372, Q15704, Q6GTR4
    UniProtKB/TrEMBL
    Q59G50
    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

  3. XM_047448700.1 → XP_047304656.1  semaphorin-3F isoform X2

  4. XM_005265382.5 → XP_005265439.1  semaphorin-3F isoform X2

    See identical proteins and their annotated locations for XP_005265439.1

    UniProtKB/TrEMBL
    Q59G50
    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

  5. XM_047448701.1 → XP_047304657.1  semaphorin-3F isoform X4

  6. XM_011534000.3 → XP_011532302.1  semaphorin-3F isoform X5

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

  7. XM_006713290.4 → XP_006713353.1  semaphorin-3F isoform X6

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

  8. XM_047448699.1 → XP_047304655.1  semaphorin-3F isoform X1

    UniProtKB/Swiss-Prot
    C9JQ85, Q13274, Q13275, Q13372, Q15704, Q6GTR4

  9. XM_006713289.4 → 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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50184392..50218408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347506.1 → XP_054203481.1  semaphorin-3F isoform X1

  2. XM_054347509.1 → XP_054203484.1  semaphorin-3F isoform X2

  3. XM_054347508.1 → XP_054203483.1  semaphorin-3F isoform X2

  4. XM_054347511.1 → XP_054203486.1  semaphorin-3F isoform X4

  5. XM_054347512.1 → XP_054203487.1  semaphorin-3F isoform X5

  6. XM_054347513.1 → XP_054203488.1  semaphorin-3F isoform X6

  7. XM_054347505.1 → XP_054203480.1  semaphorin-3F isoform X1

  8. XM_054347507.1 → XP_054203482.1  semaphorin-3F isoform X1

  9. XM_054347510.1 → XP_054203485.1  semaphorin-3F isoform X3

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

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