Efnb1 ephrin B1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Efnb1provided by RGD
Official Full Name: ephrin B1provided by RGD
Primary source: RGD:2540
See related: EnsemblRapid:ENSRNOG00000006877 AllianceGenome:RGD:2540
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
Also known as: EFL-3; LERK2
Summary: Predicted to enable ephrin receptor binding activity. Involved in presynapse assembly. Located in synapse. Is active in glutamatergic synapse and presynaptic membrane. Human ortholog(s) of this gene implicated in craniofrontonasal syndrome and dysostosis. Orthologous to human EFNB1 (ephrin B1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 200.7), Kidney (RPKM 147.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq22

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (68297529..68310335)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (64257351..64270158)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (68891227..68904034)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Peripheral EphrinB1/EphB1 signalling attenuates muscle hyperalgesia in MPS patients and a rat model of taut band-associated persistent muscle pain.
Title: Peripheral EphrinB1/EphB1 signalling attenuates muscle hyperalgesia in MPS patients and a rat model of taut band-associated persistent muscle pain.
Through interactions with nephrin, ephrin-B1 maintains the structure and barrier function of the slit diaphragm. Moreover, phosphorylation of ephrin-B1 and, consequently, JNK are involved in the development of podocyte injury.
Title: Nephrin-Binding Ephrin-B1 at the Slit Diaphragm Controls Podocyte Function through the JNK Pathway.
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.
The EphB2 and ephrin-B1 are possibly involved in epithelial boundary formation at the squamocolumnar junction.
Title: Complementary expression and repulsive signaling suggest that EphB2 and ephrin-B1 are possibly involved in epithelial boundary formation at the squamocolumnar junction in the rodent stomach.
identified expression of EphrinB1 in prostatic mesenchyme and suggest that the EphrinB signalling system acts as a regulator of prostate growth. EphrinB-EphB signalling may function as an autocrine regulator of mesenchyme
Title: Identification of EphrinB1 expression in prostatic mesenchyme and a role for EphB-EphrinB signalling in prostate development.
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.
EphrinB1-EphB receptor signaling plays a critical role is induction and maintenance of neuropathic pain by regulating neural excitability and synaptic plasticity in the dorsal root ganglion and the spinal dorsal horn.
Title: EphrinB-EphB receptor signaling contributes to neuropathic pain by regulating neural excitability and spinal synaptic plasticity in rats.
These findings indicate that ephrinB-EphB receptor activation and redistribution in DRG and DH neurons after nerve injury could contribute to neuropathic pain. This study may also provide a new mechanism underlying DR-induced analgesia in clinic.
Title: Upregulation and redistribution of ephrinB and EphB receptor in dorsal root ganglion and spinal dorsal horn neurons after peripheral nerve injury and dorsal rhizotomy.
Dual labeled immunofluorescence showed ephrin-B1 colocalized with the slit diaphragm proteins nephrin and CD2-associated protein.
Title: Ephrin-B1 localizes at the slit diaphragm of the glomerular podocyte.
Stimulation of the ephrin-B reverse signaling pathway induces a phenotype characterized by upregulation of repair-related genes, which may partially be mediated by ERK1/2 pathways.
Title: Ephrin-B reverse signaling induces expression of wound healing associated genes in IEC-6 intestinal epithelial cells.

Submit: New GeneRIF Correction See all GeneRIFs (11)

General gene information

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Markers

Efnb1 (e-PCR), detects polymorphism
- UniSTS:495876

AA964352 (e-PCR)
- UniSTS:248424

EFNB1_609 (e-PCR)
- UniSTS:277189

Efnb1 (e-PCR), detects polymorphism
- UniSTS:506876

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	IEA Inferred from Electronic Annotation more info
enables ephrin receptor binding	ISO Inferred from Sequence Orthology more info
enables ephrin receptor binding	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in T cell costimulation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell costimulation	ISO Inferred from Sequence Orthology more info
involved_in T cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	TAS Traceable Author Statement more info	PubMed
involved_in embryonic pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic pattern specification	ISO Inferred from Sequence Orthology more info
involved_in ephrin receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ephrin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in ephrin receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural crest cell migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural crest cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of T cell 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 autophagosome assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_positive_effect regulation of autophagosome assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cell surface	IEA Inferred from Electronic Annotation more info
is_active_in cell surface	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
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
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	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	IEA Inferred from Electronic Annotation more info
located_in plasma 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
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ephrin-B1

Names: ELK ligand; ELK-L; EPH-related receptor tyrosine kinase ligand 2; LERK-2

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.