Efnb2 ephrin B2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Efnb2provided by RGD
Official Full Name: ephrin B2provided by RGD
Primary source: RGD:1309497
See related: Ensembl:ENSRNOG00000064362 AllianceGenome:RGD:1309497
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 ephrin receptor binding activity. Involved in cellular response to lipopolysaccharide and presynapse assembly. Is active in glutamatergic synapse. Is integral component of presynaptic membrane. Biomarker of irritable bowel syndrome. Orthologous to human EFNB2 (ephrin B2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 356.9), Heart (RPKM 94.0) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q12.5

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (87485215..87529224)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (80783389..80827420)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (86631151..86672050)

Chromosome 16 - NC_086034.1 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?

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.
EphrinB2-RhoA upregulation attenuates sympathetic hyperinnervation and decreases the incidence of ventricular arrhythmia after myocardial infarction.
Title: EphrinB2-RhoA upregulation attenuates sympathetic hyperinnervation and decreases the incidence of ventricular arrhythmia after myocardial infarction.
Increased Ephrin-B2 expression in pericytes contributes to retinal vascular death in rodents.
Title: Increased Ephrin-B2 expression in pericytes contributes to retinal vascular death in rodents.
This study shows that activation of ephrin B2 promotes angiogenesis, ameliorates ABETA accumulation and the secondary thalamic damage after cerebral infarction.
Title: EphrinB2 activation enhances angiogenesis, reduces amyloid-β deposits and secondary damage in thalamus at the early stage after cortical infarction in hypertensive rats.
These data indicate that ephrin-B2 plays a role in pituitary stem/progenitor cell niches by selective interaction with EphB3 in cis and EphB2 in trans.
Title: Cell type-specific localization of Ephs pairing with ephrin-B2 in the rat postnatal pituitary gland.
siRNA targeting ephrin-B2 significantly reduced both the number and the diameter of cell clusters induced by TGF-beta1 treatment of coculture of astrocytes and meningeal fibroblasts, and diminished the expression of aggrecan and versican in the coculture, and allowed for significantly longer extension of outgrowing spinal cord axons into astroglial-fibrotic scar as assessed on the microfluidic platform.
Title: RNAi-mediated ephrin-B2 silencing attenuates astroglial-fibrotic scar formation and improves spinal cord axon growth.
elevated GluA2 trafficking induced by activated EphB2/ephrinB2 reverse signaling likely contributes to Retinal Ganglion Cell apoptosis in Chronic Ocular Hypertension rats.
Title: GluA2 trafficking is involved in apoptosis of retinal ganglion cells induced by activation of EphB/EphrinB reverse signaling in a rat chronic ocular hypertension model.
These findings suggest the involvement of cell-cell EphA4 and ephrin-B2 signaling in establishing order in the developing inferior colliculus
Title: EphA4 and ephrin-B2 expression patterns during inferior colliculus projection shaping prior to experience.
Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1.
Title: Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1.
EphB-ephrinB interactions play an important role in NMDA-dependent, activity-dependent synaptic plasticity in the adult spinal cord, inducing the phosphorylation of the NR2B subunit via Src family kinases, thus contributing to chronic pain states.
Title: EphrinB2 induces tyrosine phosphorylation of NR2B via Src-family kinases during inflammatory hyperalgesia.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Efnb2 (e-PCR), detects polymorphism
- UniSTS:495877

Efnb2 (e-PCR), detects polymorphism
- UniSTS:496712

BE098957 (e-PCR)
- UniSTS:245332

RH143318 (e-PCR)
- UniSTS:232565

Efnb2 (e-PCR), detects polymorphism
- UniSTS:547743

Efnb2 (e-PCR), detects polymorphism
- UniSTS:266983

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 signaling receptor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell costimulation	ISO Inferred from Sequence Orthology more info
involved_in adherens junction organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in blood vessel morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in cell migration involved in sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in ephrin receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ephrin receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymph vessel development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nephric duct morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of aorta morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in presynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic neurotransmitter receptor internalization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within venous blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in Schaffer collateral - CA1 synapse	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
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 glutamatergic 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	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ephrin-B2

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_001107328.2 → NP_001100798.1 ephrin-B2

See identical proteins and their annotated locations for NP_001100798.1

Status: PROVISIONAL

Source sequence(s)

DQ011669

UniProtKB/TrEMBL

A0A8I5ZYG5, A6IWT6, B2B9A9

Related

ENSRNOP00000084601.1, ENSRNOT00000103879.1

Conserved Domains (1) summary

cd10426
Location:32 → 168

Ephrin-B_Ectodomain; Ectodomain of Ephrin B

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_086034.1 Reference GRCr8

Range

87485215..87529224

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039094605.2 → XP_038950533.1 ephrin-B2 isoform X1

UniProtKB/TrEMBL

A0A8I6AJ66

Related

ENSRNOP00000093640.1

Conserved Domains (1) summary

cl19115
Location:32 → 145

Cupredoxin; Cupredoxin superfamily