Efnb3 ephrin B3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Efnb3provided by RGD
Official Full Name: ephrin B3provided by RGD
Primary source: RGD:2541
See related: EnsemblRapid:ENSRNOG00000010320 AllianceGenome:RGD:2541
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
Also known as: ELK-L3
Summary: Predicted to enable ephrin receptor binding activity. Involved in positive regulation of presynapse assembly and positive regulation of synaptic transmission. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human EFNB3 (ephrin B3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 127.7), Brain (RPKM 47.9) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q24

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (54773282..54780727, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (54274506..54281951, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (56161431..56168819, complement)

Chromosome 10 - NC_086028.1 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 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?

In silico prediction of interaction between Nipah virus attachment glycoprotein and host cell receptors Ephrin-B2 and Ephrin-B3 in domestic and peridomestic mammals.
Title: In silico prediction of interaction between Nipah virus attachment glycoprotein and host cell receptors Ephrin-B2 and Ephrin-B3 in domestic and peridomestic mammals.
Study found up-regulated expression of ephrinB3/EphB3 in intractable temporal lobe epilepsy patients and experimental temporal lobe epilepsy rats, which suggested that ephrinB3/EphB3 might be involved in the pathogenesis of temporal lobe epilepsy
Title: Up-regulated ephrinB3/EphB3 expression in intractable temporal lobe epilepsy patients and pilocarpine induced experimental epilepsy rat model.
Findings suggest that EphrinB3 may be a relevant target for promoting remyelination in demyelinating disease
Title: Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination.
ephrin-B3 specifies the synaptic localization of PSD-95 and likely links the synaptic stability of PSD-95 to changes in neuronal activity
Title: Anchoring and synaptic stability of PSD-95 is driven by ephrin-B3.
ephrinB3 silencing contributes to axonal growth regeneration and improves recovery from spinal cord injury (SCI).
Title: Silencing ephrinB3 improves functional recovery following spinal cord injury.
Axonal growth was inhibited in cells from the lateral thalamus exposed to ephrin B3 but not from the medial thalamus, suggesting that ephrin-B3 contributes to regional specificity by suppressing axonal growth of lateral thalamic neurons.
Title: Ephrin-B3-EphA4 interactions regulate the growth of specific thalamocortical axon populations in vitro.
Novel mechanism for independent modulation of shaft synapses through ephrinB3 reverse signaling. (EphrinB3)
Title: Postsynaptic ephrinB3 promotes shaft glutamatergic synapse formation.

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General gene information

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Markers

Efnb3 (e-PCR), detects polymorphism
- UniSTS:495878

Efnb3 (e-PCR), detects polymorphism
- UniSTS:266984

Efnb3 (e-PCR), detects polymorphism
- UniSTS:506877

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ephrin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables ephrin receptor binding	ISO Inferred from Sequence Orthology more info
enables ephrin receptor binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell costimulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult walking behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axon choice point recognition	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in ephrin receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ephrin receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in ephrin receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynaptic membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ephrin-B3

Names: ephrin ligand B3

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_001100980.4 → NP_001094450.2 ephrin-B3 precursor

See identical proteins and their annotated locations for NP_001094450.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6HFR3, G3V7D4

Related

ENSRNOP00000013956.3, ENSRNOT00000013955.8

Conserved Domains (1) summary

cl19115
Location:29 → 168

Cupredoxin; Cupredoxin superfamily

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_086028.1 Reference GRCr8

Range

54773282..54780727 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086314.1 → XP_038942242.1 ephrin-B3 isoform X1

Conserved Domains (1) summary

cl19115
Location:29 → 168

Cupredoxin; Cupredoxin superfamily
XM_039086315.2 → XP_038942243.1 ephrin-B3 isoform X2