Sema3e semaphorin 3E [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Sema3eprovided by RGD
Full Name: semaphorin 3Eprovided by RGD
Primary source: RGD:1310973
See related: Ensembl:ENSRNOG00000006631 AllianceGenome:RGD:1310973
Gene type: protein coding
RefSeq status: PROVISIONAL
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 and semaphorin receptor binding activity. Predicted to be involved in several processes, including angiogenesis; generation of neurons; and neural crest cell migration. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Human ortholog(s) of this gene implicated in CHARGE syndrome. Orthologous to human SEMA3E (semaphorin 3E). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 371.4), Brain (RPKM 70.3) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q12

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (21252686..21510449, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (20297534..20555287, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (17314745..17594659, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Study found that depletion of Sema3E/PlexinD1 signaling with lentivirus-mediated PlexinD1-specific-shRNA improves tissue survival and functional outcome following stroke. Sema3E/PlexinD1 inhibition not only increases cortical perfusion but also ameliorates blood-brain barrier damage.
Title: Sema3E/PlexinD1 inhibition is a therapeutic strategy for improving cerebral perfusion and restoring functional loss after stroke in aged rats.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in branching involved in blood vessel morphogenesis	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 negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	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
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in synapse organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor 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-3E

Names: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E

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_001106579.1 → NP_001100049.1 semaphorin-3E precursor

See identical proteins and their annotated locations for NP_001100049.1

Status: PROVISIONAL

Source sequence(s)

CH474020

UniProtKB/TrEMBL

A6K5F8, D3Z8E2

Related

ENSRNOP00000008936.5, ENSRNOT00000008936.6

Conserved Domains (3) summary

cd05871
Location:585 → 675

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

cd11253
Location:49 → 519

Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)

smart00423
Location:518 → 566

PSI; domain found in Plexins, Semaphorins and Integrins

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

21252686..21510449 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017592522.3 → XP_017448011.1 semaphorin-3E isoform X1

UniProtKB/TrEMBL

A6K5F8, D3Z8E2

Conserved Domains (3) summary

cd05871
Location:585 → 675

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

cd11253
Location:49 → 519

Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)

smart00423
Location:518 → 566

PSI; domain found in Plexins, Semaphorins and Integrins
XM_039107252.2 → XP_038963180.1 semaphorin-3E isoform X2

Conserved Domains (4) summary

cd11253
Location:49 → 519

Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)

smart00423
Location:518 → 566

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:585 → 590

Ig; Ig strand A [structural motif]

cl11960
Location:585 → 625

Ig; Immunoglobulin domain