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; 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: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (50155058..50189075)
RS_2023_03	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_000003.12 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?

Semaphorin3F Drives Dendritic Spine Pruning Through Rho-GTPase Signaling.
Title: Semaphorin3F Drives Dendritic Spine Pruning Through Rho-GTPase Signaling.
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.
Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
Title: Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
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.
Endothelial Semaphorin 3F Maintains Endothelial Barrier Function and Inhibits Monocyte Migration.
Title: Endothelial Semaphorin 3F Maintains Endothelial Barrier Function and Inhibits Monocyte Migration.
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.

Submit: New GeneRIF Correction See all GeneRIFs (47)

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: 293 organisms have orthologs with human gene SEMA3F
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables chemorepellent activity	IDA Inferred from Direct Assay more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

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	PubMed
acts_upstream_of_or_within axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in branchiomotor neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in facial nerve structural organization	IEA Inferred from Electronic Annotation more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of axon extension involved in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
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	PubMed
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	PubMed
involved_in semaphorin-plexin signaling pathway involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway involved in neuron projection guidance	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	IEA Inferred from Electronic Annotation more info
involved_in ventral trunk neural crest cell migration	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular space	TAS Traceable Author Statement more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation 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)

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, Q6GTR4

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_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

50155058..50189075

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

See identical proteins and their annotated locations for XP_005265438.1

UniProtKB/Swiss-Prot

Q13275, Q6GTR4

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_011533998.3 → XP_011532300.1 semaphorin-3F isoform X1

See identical proteins and their annotated locations for XP_011532300.1

UniProtKB/Swiss-Prot

Q13275, Q6GTR4

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_047448700.1 → XP_047304656.1 semaphorin-3F isoform X2
XM_005265382.5 → 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_047448701.1 → XP_047304657.1 semaphorin-3F isoform X4
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
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
XM_047448699.1 → XP_047304655.1 semaphorin-3F isoform X1

UniProtKB/Swiss-Prot

Q6GTR4
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