Ephb2 Eph receptor B2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ephb2provided by RGD
Full Name: Eph receptor B2provided by RGD
Primary source: RGD:1564232
See related: Ensembl:ENSRNOG00000012531 AllianceGenome:RGD:1564232
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: RGD1564232
Summary: Predicted to enable several functions, including amyloid-beta binding activity; identical protein binding activity; and transmembrane signaling receptor activity. Involved in several processes, including cell junction assembly; positive regulation of nervous system development; and regulation of gene expression. Located in Golgi apparatus; cell surface; and dendritic spine. Is active in glutamatergic synapse. Used to study irritable bowel syndrome and ulcerative colitis. Biomarker of irritable bowel syndrome and middle cerebral artery infarction. Human ortholog(s) of this gene implicated in blood platelet disease. Orthologous to human EPHB2 (EPH receptor B2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 50.5), Kidney (RPKM 28.4) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (154179065..154360459, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (148889574..149077027, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (155024478..155143539, complement)

Chromosome 5 - NC_086023.1 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?

Overexpression of EphB2 in the basolateral amygdala is crucial for inducing visceral pain sensitization in rats subjected to water avoidance stress.
Title: Overexpression of EphB2 in the basolateral amygdala is crucial for inducing visceral pain sensitization in rats subjected to water avoidance stress.
EphB2 knockdown decreases the formation of astroglial-fibrotic scars to promote nerve regeneration after spinal cord injury in rats.
Title: EphB2 knockdown decreases the formation of astroglial-fibrotic scars to promote nerve regeneration after spinal cord injury in rats.
The ephrin receptor EphB2 regulates the connectivity and activity of enteric neurons.
Title: The ephrin receptor EphB2 regulates the connectivity and activity of enteric neurons.
Extracellular vesicles derived from EphB2-overexpressing bone marrow mesenchymal stem cells ameliorate DSS-induced colitis by modulating immune balance.
Title: Extracellular vesicles derived from EphB2-overexpressing bone marrow mesenchymal stem cells ameliorate DSS-induced colitis by modulating immune balance.
Study identified a RhoA guanine nucleotide exchange factor, Ephexin5, which negatively regulates excitatory synapse development until EphrinB binding to the EphB receptor triggers Ephexin5 phosphorylation, ubiquitination, and degradation.
Title: EphB-mediated degradation of the RhoA GEF Ephexin5 relieves a developmental brake on excitatory synapse formation.
EphB2 regulates the actions of filopodia through a combination of precise subcellular localization and induction of specific intracellular signals within filopodia. Simple differences in the kinetics of EphB kinase signaling at the tips of filopodia mediate the choice between retraction and synaptogenesis.
Title: Filopodia Conduct Target Selection in Cortical Neurons Using Differences in Signal Kinetics of a Single Kinase.
Results show that EphB2 acts downstream of Ascl1, its direct target, in regulating tangential migration.
Title: Ascl1 promotes tangential migration and confines migratory routes by induction of Ephb2 in the telencephalon.
Overexpression of EphB2 also rescued the ADDLs-induced depletion of the expression of EphB2 and GluN2B-containing NMDA receptors trafficking in cultured hippocampal neurons.
Title: Overexpression of EphB2 in hippocampus rescues impaired NMDA receptors trafficking and cognitive dysfunction in Alzheimer model.
we revealed that stimulation with the extracellular domain of EphB2 to activate Eph/ephrin reverse signalling induced axonal retraction in hippocampal neurons.
Title: Eph/ephrin reverse signalling induces axonal retraction through RhoA/ROCK pathway.
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.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Ephb2 (e-PCR), detects polymorphism
- UniSTS:495888

MARC_17495-17496:1030378704:1 (e-PCR)
- UniSTS:268320

UNH1020 (e-PCR)
- UniSTS:265293

D5Rat41 (e-PCR), detects polymorphism
- UniSTS:118910

D5Uwm43 (e-PCR)
- UniSTS:239999

RH131438 (e-PCR)
- UniSTS:214721

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables amyloid-beta binding	ISO Inferred from Sequence Orthology more info
enables axon guidance receptor activity	ISO Inferred from Sequence Orthology more info
enables ephrin receptor activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein tyrosine kinase activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info
enables transmembrane-ephrin receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane-ephrin receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in B cell activation	ISO Inferred from Sequence Orthology more info
involved_in angiogenesis	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
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axonal fasciculation	ISO Inferred from Sequence Orthology more info
acts_upstream_of axonogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell surface receptor protein tyrosine kinase signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amyloid-beta	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within central nervous system projection neuron axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in commissural neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in corpus callosum development	ISO Inferred from Sequence Orthology more info
involved_in dendritic spine development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendritic spine morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in dendritic spine morphogenesis	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	ISO Inferred from Sequence Orthology more info
involved_in hindbrain tangential cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within learning	ISO Inferred from Sequence Orthology more info
involved_in learning or memory	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of Ras protein signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cytokine production involved in inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in neuron projection retraction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within optic nerve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of B cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendritic spine morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of immunoglobulin production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of long-term neuronal synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of long-term synaptic potentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein localization to cell surface	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein localization to plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in postsynaptic membrane assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in postsynaptic membrane assembly	IEP Inferred from Expression Pattern more info	PubMed
involved_in postsynaptic membrane assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein phosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of T-helper 17 type immune response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_positive_effect regulation of autophagosome assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of behavioral fear response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of blood coagulation	ISO Inferred from Sequence Orthology more info
involved_in regulation of body fluid levels	ISO Inferred from Sequence Orthology more info
involved_in regulation of filopodium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of neuronal synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in regulation of receptor signaling pathway via JAK-STAT	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal ganglion cell axon guidance	ISO Inferred from Sequence Orthology more info
involved_in roof of mouth development	ISO Inferred from Sequence Orthology more info
involved_in tight junction assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in urogenital system development	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated intercellular transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	IDA Inferred from Direct Assay more info	PubMed
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 hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	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
located_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ephrin type-B receptor 2

Names: ephrin type-B receptor 2-like

NP_001120791.2

EC 2.7.10.1

XP_038965983.1

EC 2.7.10.1

XP_038965984.1

EC 2.7.10.1

XP_038965985.1

EC 2.7.10.1

XP_038965986.1

EC 2.7.10.1

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_001127319.4 → NP_001120791.2 ephrin type-B receptor 2 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

B2B9B0

Related

ENSRNOP00000070517.2, ENSRNOT00000089574.2

Conserved Domains (5) summary

cd05065
Location:616 → 884

PTKc_EphR_B; Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors

cd09552
Location:910 → 980

SAM_EPH-B2; SAM domain of EPH-B2 subfamily of tyrosine kinase receptors

cd10477
Location:19 → 196

EphR_LBD_B2; Ligand Binding Domain of Ephrin type-B Receptor 2

pfam00041
Location:437 → 520

fn3; Fibronectin type III domain

pfam14575
Location:567 → 617

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

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_086023.1 Reference GRCr8

Range

154179065..154360459 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039110058.2 → XP_038965986.1 ephrin type-B receptor 2 isoform X4

UniProtKB/TrEMBL

B2B9B0

Conserved Domains (5) summary

cd05065
Location:586 → 854

PTKc_EphR_B; Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors

cd09552
Location:880 → 950

SAM_EPH-B2; SAM domain of EPH-B2 subfamily of tyrosine kinase receptors

cd10477
Location:19 → 196

EphR_LBD_B2; Ligand Binding Domain of Ephrin type-B Receptor 2

pfam00041
Location:326 → 421

fn3; Fibronectin type III domain

pfam14575
Location:534 → 587

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_039110055.2 → XP_038965983.1 ephrin type-B receptor 2 isoform X1

UniProtKB/TrEMBL

B2B9B0

Conserved Domains (5) summary

cd05065
Location:618 → 886

PTKc_EphR_B; Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors

cd09552
Location:912 → 982

SAM_EPH-B2; SAM domain of EPH-B2 subfamily of tyrosine kinase receptors

cd10477
Location:19 → 196

EphR_LBD_B2; Ligand Binding Domain of Ephrin type-B Receptor 2

pfam00041
Location:437 → 521

fn3; Fibronectin type III domain

pfam14575
Location:566 → 619

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_039110057.2 → XP_038965985.1 ephrin type-B receptor 2 isoform X3

UniProtKB/TrEMBL

B2B9B0

Conserved Domains (5) summary

cd05065
Location:617 → 885

PTKc_EphR_B; Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors

cd09552
Location:911 → 981

SAM_EPH-B2; SAM domain of EPH-B2 subfamily of tyrosine kinase receptors

cd10477
Location:19 → 196

EphR_LBD_B2; Ligand Binding Domain of Ephrin type-B Receptor 2

pfam00041
Location:437 → 520

fn3; Fibronectin type III domain

pfam14575
Location:565 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_039110056.2 → XP_038965984.1 ephrin type-B receptor 2 isoform X2

UniProtKB/TrEMBL

B2B9B0, F1MAJ0

Related

ENSRNOP00000016983.7

Conserved Domains (5) summary

cd05065
Location:617 → 885

PTKc_EphR_B; Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors

cd09552
Location:911 → 981

SAM_EPH-B2; SAM domain of EPH-B2 subfamily of tyrosine kinase receptors

cd10477
Location:19 → 196

EphR_LBD_B2; Ligand Binding Domain of Ephrin type-B Receptor 2

pfam00041
Location:437 → 521

fn3; Fibronectin type III domain

pfam14575
Location:568 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain