SEMA3F semaphorin 3F [Homo sapiens (human)] - Gene

Summary

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

Location:: 3p21.31

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
109.20200815	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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (42)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC22669P18 (e-PCR)
- UniSTS:272130

SHGC-76759 (e-PCR)
- UniSTS:40064

SEMA3F_2436 (e-PCR)
- UniSTS:280988

D3S3178 (e-PCR)
- UniSTS:153503

D3S4505 (e-PCR)
- UniSTS:474579

D3S4506 (e-PCR)
- UniSTS:474580

D3S4511 (e-PCR)
- UniSTS:474585

D3S4512 (e-PCR)
- UniSTS:474586

D3S4513 (e-PCR)
- UniSTS:474587

D3S4515 (e-PCR)
- UniSTS:474589

D3S4516 (e-PCR)
- UniSTS:474590

D3S4519 (e-PCR)
- UniSTS:474593

D3S4520 (e-PCR)
- UniSTS:474594

D3S4521 (e-PCR)
- UniSTS:474595

SGC31666 (e-PCR)
- UniSTS:52710

Homology

Homologs of the SEMA3F gene: The SEMA3F gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 207 organisms have orthologs with human gene SEMA3F
Orthologs

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)

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
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/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
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 Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p13 Primary Assembly

Range

50155058..50189075

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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