Sema3a sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema3aprovided by MGI
Official Full Name: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Aprovided by MGI
Primary source: MGI:MGI:107558
See related: Ensembl:ENSMUSG00000028883 AllianceGenome:MGI:107558
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: SemD; SEMA1; Semad; coll-1; Hsema-I
Summary: Enables chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in several processes, including nervous system development; positive regulation of male gonad development; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including dichotomous subdivision of terminal units involved in salivary gland branching; negative regulation of axon extension involved in axon guidance; and neuron projection development. Located in extracellular space. Is active in cerebellar climbing fiber to Purkinje cell synapse. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; metanephros; and sensory organ. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in limb E14.5 (RPKM 3.0), bladder adult (RPKM 3.0) and 16 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 A1; 5 4.31 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (13174789..13653453)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (13124822..13603485)

Chromosome 5 - NC_000071.7 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: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of semaphorin 3A on chondrogenic differentiation.
Title: The role of semaphorin 3A on chondrogenic differentiation.
PIEZO1 Promotes Odontoblast-Mediated Reactionary Dentinogenesis via SEMA3A.
Title: PIEZO1 Promotes Odontoblast-Mediated Reactionary Dentinogenesis via SEMA3A.
Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
Title: Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC.
Expression of semaphorin-3A in the joint and role in osteoarthritis.
Title: Expression of semaphorin-3A in the joint and role in osteoarthritis.
Nerve growth factor (Ngf) gene-driven semaphorin 3a (Sema3a) expression exacerbates thoracic aortic aneurysm dissection in mice.
Title: Nerve growth factor (Ngf) gene-driven semaphorin 3a (Sema3a) expression exacerbates thoracic aortic aneurysm dissection in mice.
Reduced expression of semaphorin 3A in osteoclasts causes lymphatic expansion in a Gorham-Stout disease (GSD) mouse model.
Title: Reduced expression of semaphorin 3A in osteoclasts causes lymphatic expansion in a Gorham-Stout disease (GSD) mouse model.
Sema3A Modified PDLSCs Exhibited Enhanced Osteogenic Capabilities and Stimulated Differentiation of Pre-Osteoblasts.
Title: Sema3A Modified PDLSCs Exhibited Enhanced Osteogenic Capabilities and Stimulated Differentiation of Pre-Osteoblasts.
miR-196b-5p Regulates Osteoblast and Osteoclast Differentiation and Bone Homeostasis by Targeting SEMA3A.
Title: miR-196b-5p Regulates Osteoblast and Osteoclast Differentiation and Bone Homeostasis by Targeting SEMA3A.
Semaphorin3A Exacerbates Cardiac Microvascular Rarefaction in Pressure Overload-Induced Heart Disease.
Title: Semaphorin3A Exacerbates Cardiac Microvascular Rarefaction in Pressure Overload-Induced Heart Disease.
Sema3A alleviates viral myocarditis by modulating SIRT1 to regulate cardiomyocyte mitophagy.
Title: Sema3A alleviates viral myocarditis by modulating SIRT1 to regulate cardiomyocyte mitophagy.

Submit: New GeneRIF Correction See all GeneRIFs (144)

Variation

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Alleles

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

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (5)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Sema3a (e-PCR), detects polymorphism
- UniSTS:507212

UniSTS:224589 (e-PCR)
- UniSTS:224589

Sema3a (e-PCR), detects polymorphism
- UniSTS:526942

Sema3a (e-PCR), detects polymorphism
- UniSTS:166290

Sema3a (e-PCR), detects polymorphism
- UniSTS:548025

NoName (e-PCR)
- UniSTS:224729

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 neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of axon extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of axon extension	IGI Inferred from Genetic Interaction more info	PubMed
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
acts_upstream_of_or_within axon guidance	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axonal fasciculation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonogenesis involved in innervation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in basal dendrite arborization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in branchiomotor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dendrite morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of epithelial cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in facial nerve structural organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in facioacoustic ganglion development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of synapse structure	IDA Inferred from Direct Assay more info	PubMed
involved_in maintenance of synapse structure	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motor neuron axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in motor neuron axon guidance	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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of axon extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of axon extension	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of axon extension	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within negative regulation of epithelial cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IGI Inferred from Genetic Interaction 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 neural crest cell migration involved in sympathetic nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in olfactory bulb development	ISO Inferred from Sequence Orthology more info
involved_in olfactory bulb development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of male gonad development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron migration	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of axon extension involved in axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of heart rate	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within semaphorin-plexin signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
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 synaptic target recognition	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic target recognition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in trigeminal ganglion development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in trigeminal nerve structural organization	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
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISO Inferred from Sequence Orthology more info
is_active_in cerebellar climbing fiber to Purkinje cell synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in cerebellar climbing fiber to Purkinje cell synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
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

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Preferred Names: semaphorin-3A

Names: collapsin-1; sema D; sema III; semaphorin III; semaphorin-D

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_001243072.1 → NP_001230001.1 semaphorin-3A precursor

See identical proteins and their annotated locations for NP_001230001.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC022368, BC090844

Consensus CDS

CCDS19092.1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Related

ENSMUSP00000092621.5, ENSMUST00000095012.11

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
NM_001243073.1 → NP_001230002.1 semaphorin-3A precursor

See identical proteins and their annotated locations for NP_001230002.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC022368, AK140817

Consensus CDS

CCDS19092.1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Related

ENSMUSP00000128153.3, ENSMUST00000137798.10

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
NM_009152.4 → NP_033178.2 semaphorin-3A precursor

See identical proteins and their annotated locations for NP_033178.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC022368, AC121125, BC057588

Consensus CDS

CCDS19092.1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Related

ENSMUSP00000030714.9, ENSMUST00000030714.9

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

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_000071.7 Reference GRCm39 C57BL/6J

Range

13174789..13653453

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006503557.5 → XP_006503620.2 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_011240665.4 → XP_011238967.2 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_036164936.1 → XP_036020829.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_036164937.1 → XP_036020830.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_006503559.3 → XP_006503622.2 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_036164935.1 → XP_036020828.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_006503558.5 → XP_006503621.2 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

E9QK85, O08665, Q5BL08, Q62180, Q62215

UniProtKB/TrEMBL

A0A803Z7F8

Conserved Domains (3) summary

cd11249
Location:26 → 518

Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

smart00423
Location:516 → 552

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:580 → 671

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