Sema3f sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema3fprovided by MGI
Official Full Name: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fprovided by MGI
Primary source: MGI:MGI:1096347
See related: Ensembl:ENSMUSG00000034684 AllianceGenome:MGI:1096347
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Sema4; Semak
Summary: Enables chemorepellent activity. Involved in several processes, including nervous system development; semaphorin-plexin signaling pathway; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including axon guidance; negative regulation of axon extension involved in axon guidance; and trunk neural crest cell migration. Located in extracellular space. Is active in glutamatergic synapse. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human SEMA3F (semaphorin 3F). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in lung adult (RPKM 77.6), limb E14.5 (RPKM 39.8) and 19 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 9 F1; 9 58.91 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (107558698..107587674, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (107681499..107710475, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
Title: Semaphorin 3F signaling actively retains neutrophils at sites of inflammation.
Results define a developmental function for NrCAM in Sema3F receptor signaling that limits dendritic spine density on cortical pyramidal neurons during adolescence.
Title: Temporal Regulation of Dendritic Spines Through NrCAM-Semaphorin3F Receptor Signaling in Developing Cortical Pyramidal Neurons.
Studies of interneuron cell-specific knockout of Sema 3F signaling suggest that deficient Sema 3F signaling may lead to neuroinflammation and oxidative stress.
Title: Deletion of Semaphorin 3F in Interneurons Is Associated with Decreased GABAergic Neurons, Autism-like Behavior, and Increased Oxidative Stress Cascades.
data suggest that Sema3f and Nrp2 are dispensable for the exclusion of vessels from the cap mesenchyme during kidney development.
Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney.
Sema3f is suppressed in outer nuclear layer in very low-density lipid-receptor deficient retina.
Title: Sema3f Protects Against Subretinal Neovascularization In Vivo.
Sema3F functions as an unconventional Sema3 that promotes extraembryonic angiogenesis by inhibiting the Myc-regulated synthesis of Thbs1 in visceral yolk sac epithelial cells.
Title: Sema3F (Semaphorin 3F) Selectively Drives an Extraembryonic Proangiogenic Program.
Nrp2 deficiency increased blood vessel permeability and decreased lymphatic vessel drainage during inflammation, highlighting the importance of the NRP2/SEMA3F pathway in the modulation of tissue swelling and resolution of postinflammatory edema.
Title: Inflammation and Lymphedema Are Exacerbated and Prolonged by Neuropilin 2 Deficiency.
Sema3F plays important roles in the development of neuronal circuitry underlying the regulation of some aspects of anxiety and fear responses.
Title: Comprehensive behavioral phenotyping of a new Semaphorin 3 F mutant mouse.
The authors demonstrate that expression of Semaphorin-3F in the outer hair cell region inhibits type I spiral ganglion neuron process extension by activating Neuropilin-2 receptors expressed on spiral ganglion neurons.
Title: Neuropilin-2/Semaphorin-3F-mediated repulsion promotes inner hair cell innervation by spiral ganglion neurons.
the embryonically developed wiring deficits in Sema3F mutants persist until adulthood
Title: A critical period for postnatal adaptive plasticity in a model of motor axon miswiring.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Gene trapped (1)
Targeted (9) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Gene Ontology Provided by MGI

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 chemorepellent activity	ISO Inferred from Sequence Orthology more info	PubMed
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of axon extension involved in axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info	PubMed
involved_in branchiomotor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in facial nerve structural organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative chemotaxis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of postsynapse organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynapse organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sympathetic ganglion development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sympathetic neuron projection extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sympathetic neuron projection guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in trigeminal nerve structural organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within trunk neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ventral trunk neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular space	HDA more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: semaphorin-3F

Names: semaphorin IV

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001311151.3 → NP_001298080.1 semaphorin-3F isoform 1 precursor

See identical proteins and their annotated locations for NP_001298080.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC152718, AC162905

Consensus CDS

CCDS81069.1

UniProtKB/Swiss-Prot

E9QNC5, O88632, O88633

Related

ENSMUSP00000141865.2, ENSMUST00000192727.6

Conserved Domains (3) 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)

smart00423
Location:547 → 584

PSI; domain found in Plexins, Semaphorins and Integrins
NM_001379496.2 → NP_001366425.1 semaphorin-3F isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC152718, AC162905

Conserved Domains (3) summary

cd11254
Location:48 → 517

Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

smart00423
Location:516 → 553

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:577 → 666

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
NM_001405023.1 → NP_001391952.1 semaphorin-3F isoform 4 precursor

Status: VALIDATED

Source sequence(s)

AC152718, AC162905
NM_001405024.1 → NP_001391953.1 semaphorin-3F isoform 5 precursor

Status: VALIDATED

Source sequence(s)

AC152718, AC162905
NM_001405025.2 → NP_001391954.1 semaphorin-3F isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC152718, AC162905

UniProtKB/Swiss-Prot

E9QNC5, O88632, O88633
NM_011349.4 → NP_035479.2 semaphorin-3F isoform 2 precursor

See identical proteins and their annotated locations for NP_035479.2

Status: VALIDATED

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)

AC152718, AC162905

Consensus CDS

CCDS23505.1

UniProtKB/Swiss-Prot

O88632

Related

ENSMUSP00000079400.4, ENSMUST00000080560.9

Conserved Domains (3) summary

cd11254
Location:48 → 517

Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

smart00423
Location:516 → 553

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:577 → 666

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

107558698..107587674 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017313230.2 → XP_017168719.1 semaphorin-3F isoform X4

Conserved Domains (3) summary

smart00423
Location:321 → 358

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:383 → 424

Ig; Immunoglobulin domain

cl15693
Location:1 → 322

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_017313229.3 → XP_017168718.1 semaphorin-3F isoform X4

Conserved Domains (3) summary

smart00423
Location:321 → 358

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:383 → 424

Ig; Immunoglobulin domain

cl15693
Location:1 → 322

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins