Sema3a semaphorin 3A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema3aprovided by RGD
Official Full Name: semaphorin 3Aprovided by RGD
Primary source: RGD:3657
See related: EnsemblRapid:ENSRNOG00000023337 AllianceGenome:RGD:3657
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in negative regulation of axon extension. Acts upstream of or within axon guidance. Located in axon and dendrite. 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: Biased expression in Lung (RPKM 34.4), Brain (RPKM 32.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q12

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (22239418..22709907, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (21282398..21754834, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (18170375..18545190, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sema3A ameliorates the pathological progression of osteoarthritis by modulating mitochondrial damage in chondrocytes.
Title: Sema3A ameliorates the pathological progression of osteoarthritis by modulating mitochondrial damage in chondrocytes.
Pure platelet-rich plasma promotes semaphorin-3A expression: a novel insight to ameliorate intervertebral disk degeneration in vitro.
Title: Pure platelet-rich plasma promotes semaphorin-3A expression: a novel insight to ameliorate intervertebral disk degeneration in vitro.
Sema3A inactivates the ERK/JNK signalling pathways to alleviate inflammation and oxidative stress in lipopolysaccharide-stimulated rat endothelial cells and lung tissues.
Title: Sema3A inactivates the ERK/JNK signalling pathways to alleviate inflammation and oxidative stress in lipopolysaccharide-stimulated rat endothelial cells and lung tissues.
Semaphorin 3A promotes the osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells in inflammatory environments by suppressing the Wnt/beta-catenin signaling pathway.
Title: Semaphorin 3A promotes the osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells in inflammatory environments by suppressing the Wnt/β-catenin signaling pathway.
Neuropilin-1 receptor in the rapid and selective estrogen-induced neurovascular remodeling of rat uterus.
Title: Neuropilin-1 receptor in the rapid and selective estrogen-induced neurovascular remodeling of rat uterus.
miR-30b overexpression and Sema3A siRNA could statistically significantly promote the growth of axons while inhibiting the growth of dendrites from retinal ganglion cells.
Title: MicroRNA-30b regulates the polarity of retinal ganglion cells by inhibiting semaphorin-3A.
Study found that agonist activity directed at the alpha2 but not the alpha1 subunit of the GABAA receptor is required to inhibit the collapse response to Sema3A in dissociated cortical neurons.
Title: Anesthetics disrupt growth cone guidance cue sensing through actions on the GABA(A) α2 receptor mediated by the immature chloride gradient.
markedly suppressed in annulus fibrosis tissues of an intervertebral disc degeneration model
Title: Potential involvement of semaphorin 3A in maintaining intervertebral disc tissue homeostasis.
Stimulation with oxygen glucose deprivation induces neuronal expression of VEGF165 and regulates the migration of vascular endothelial cells, thereby enhancing their participation in angiogenesis, which may involve Sema3A.
Title: Roles of Sema3A and VEGF165 in cortical neurons and vascular endothelial cells during oxygen glucose deprivation stimulation.
Sema3A is a target of miR-145-5p in the adipose-derived stem cells.Sema3a role in the osteogenesis and adipogenesis.
Title: miR-145-5p suppresses osteogenic differentiation of adipose-derived stem cells by targeting semaphorin 3A.

Submit: New GeneRIF Correction See all GeneRIFs (55)

General gene information

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Markers

RH69031 (e-PCR)
- UniSTS:62231

D4Mgh1 (e-PCR)
- UniSTS:239901

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemorepellent activity	ISO Inferred from Sequence Orthology more info
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables neuropilin binding	ISO Inferred from Sequence Orthology 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
enables semaphorin receptor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of axon extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axonal fasciculation	ISO Inferred from Sequence Orthology more info
involved_in axonogenesis involved in innervation	ISO Inferred from Sequence Orthology more info
involved_in basal dendrite arborization	ISO Inferred from Sequence Orthology more info
involved_in branchiomotor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendrite morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching	ISO Inferred from Sequence Orthology more info
acts_upstream_of epithelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in facial nerve structural organization	ISO Inferred from Sequence Orthology more info
involved_in facioacoustic ganglion development	ISO Inferred from Sequence Orthology more info
involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus	ISO Inferred from Sequence Orthology more info
involved_in maintenance of synapse structure	ISO Inferred from Sequence Orthology more info
involved_in motor neuron axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of axon extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of epithelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in nerve development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell migration involved in sympathetic nervous system development	ISO Inferred from Sequence Orthology more info
involved_in neuron migration	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron migration	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in regulation of plasma membrane bounded cell projection organization	IEA Inferred from Electronic Annotation more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in sympathetic ganglion development	ISO Inferred from Sequence Orthology more info
involved_in sympathetic neuron projection extension	ISO Inferred from Sequence Orthology more info
involved_in sympathetic neuron projection guidance	ISO Inferred from Sequence Orthology more info
involved_in synaptic target recognition	ISO Inferred from Sequence Orthology more info
involved_in trigeminal ganglion development	ISO Inferred from Sequence Orthology more info
involved_in trigeminal nerve structural organization	ISO Inferred from Sequence Orthology more info
involved_in ventral trunk neural crest cell migration	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
is_active_in cerebellar climbing fiber to Purkinje cell synapse	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	TAS Traceable Author Statement more info	PubMed
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology 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-3A

Names: sema III; sema domain, immunoglobulin domain (Ig), short basic domain, sec; sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A; semaphorin III

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_017310.2 → NP_059006.1 semaphorin-3A precursor

See identical proteins and their annotated locations for NP_059006.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q63548

UniProtKB/TrEMBL

A0A8L2QL58, A6K213

Related

ENSRNOP00000036472.3, ENSRNOT00000034692.5

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

22239418..22709907 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008762702.3 → XP_008760924.1 semaphorin-3A isoform X1

See identical proteins and their annotated locations for XP_008760924.1

UniProtKB/Swiss-Prot

Q63548

UniProtKB/TrEMBL

A0A8L2QL58, A6K213

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_063285863.1 → XP_063141933.1 semaphorin-3A isoform X1

UniProtKB/Swiss-Prot

Q63548

UniProtKB/TrEMBL

A6K213
XM_006235990.5 → XP_006236052.1 semaphorin-3A isoform X1

See identical proteins and their annotated locations for XP_006236052.1

UniProtKB/Swiss-Prot

Q63548

UniProtKB/TrEMBL

A0A8L2QL58, A6K213

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