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Efnb2 ephrin B2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 306636, updated on 8-Dec-2022

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
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Genomic context

See Efnb2 in Genome Data Viewer
Location:
16q12.5
Exon count:
5
Annotation release Status Assembly Chr Location
108 current 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_051351.1Genomic Context describing neighboring genes Neighboring gene similar to zinc finger protein, subfamily 1A, 5 Neighboring gene arginine and glutamate rich 1 Neighboring gene sushi domain containing 3, pseudogene 1 Neighboring gene uncharacterized LOC103694011

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ephrin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in blood vessel morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 positive regulation of neuron death 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 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
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 

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)

  1. NM_001107328.2NP_001100798.1  ephrin-B2

    See identical proteins and their annotated locations for NP_001100798.1

    Status: PROVISIONAL

    Source sequence(s)
    DQ011669
    UniProtKB/TrEMBL
    B2B9A9
    Related
    ENSRNOP00000084601.1, ENSRNOT00000103879.1
    Conserved Domains (1) summary
    cd10426
    Location:32168
    Ephrin-B_Ectodomain; Ectodomain of Ephrin B

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051351.1 Reference mRatBN7.2 Primary Assembly

    Range
    80783389..80827420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A8I6AJ66
    Related
    ENSRNOP00000093640.1, ENSRNOT00000093850.1
    Conserved Domains (1) summary
    cl19115
    Location:32145
    Cupredoxin; Cupredoxin superfamily