U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

EFNB2 ephrin B2 [ Homo sapiens (human) ]

Gene ID: 1948, updated on 19-Sep-2024

Summary

Official Symbol
EFNB2provided by HGNC
Official Full Name
ephrin B2provided by HGNC
Primary source
HGNC:HGNC:3227
See related
Ensembl:ENSG00000125266 MIM:600527; AllianceGenome:HGNC:3227
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HTKL; EPLG5; Htk-L; LERK5; ephrin-B2
Summary
This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. This gene encodes an EFNB class ephrin which binds to the EPHB4 and EPHA3 receptors. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lung (RPKM 8.5), colon (RPKM 7.4) and 23 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See EFNB2 in Genome Data Viewer
Location:
13q33.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (106489745..106535662, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (105710156..105756072, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (107142093..107188010, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr13:107093146-107093647 Neighboring gene ribosomal protein L35 pseudogene 7 Neighboring gene uncharacterized LOC105370346 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:107124121-107125320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:107125598-107126285 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:107131600-107132799 Neighboring gene uncharacterized LOC124903247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:107144828-107145328 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:107145476-107146675 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:107178953-107179606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7982 Neighboring gene arginine and glutamate rich 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:107219841-107220751 Neighboring gene ARGLU1 divergent transcript

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC126226, MGC126227, MGC126228

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ephrin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ephrin receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables virus receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in T cell costimulation IEA
Inferred from Electronic Annotation
more info
 
involved_in adherens junction organization IEA
Inferred from Electronic Annotation
more info
 
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
involved_in animal organ morphogenesis IEA
Inferred from Electronic Annotation
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
 
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell migration involved in sprouting angiogenesis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
involved_in ephrin receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in ephrin receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in keratinocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in lymph vessel development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of keratinocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of neuron projection development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nephric duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of aorta morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cardiac muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of postsynaptic neurotransmitter receptor internalization IEA
Inferred from Electronic Annotation
more info
 
involved_in symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
 
involved_in venous blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
 
located_in adherens junction IEA
Inferred from Electronic Annotation
more info
 
located_in focal adhesion HDA PubMed 
is_active_in glutamatergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in presynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
ephrin-B2
Names
HTK ligand
eph-related receptor tyrosine kinase ligand 5
ligand of eph-related kinase 5

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001372056.1NP_001358985.1  ephrin-B2 isoform 2 precursor

    Status: REVIEWED

    Source sequence(s)
    AL138689, KF455823
    Conserved Domains (1) summary
    cl19115
    Location:29142
    Cupredoxin; Cupredoxin superfamily
  2. NM_001372057.1NP_001358986.1  ephrin-B2 isoform 3 precursor

    Status: REVIEWED

    Source sequence(s)
    AL138689, KF455823
    Conserved Domains (1) summary
    cd10426
    Location:29165
    Ephrin-B_Ectodomain; Ectodomain of Ephrin B
  3. NM_001372058.1NP_001358987.1  ephrin-B2 isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL138689
    Conserved Domains (1) summary
    cl19115
    Location:29136
    Cupredoxin; Cupredoxin superfamily
  4. NM_004093.4NP_004084.1  ephrin-B2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_004084.1

    Status: REVIEWED

    Source sequence(s)
    AL138689, KF455823
    Consensus CDS
    CCDS9507.1
    UniProtKB/Swiss-Prot
    P52799, Q5JV56
    Related
    ENSP00000493716.1, ENST00000646441.1
    Conserved Domains (1) summary
    cd10426
    Location:29165
    Ephrin-B_Ectodomain; Ectodomain of Ephrin B

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    106489745..106535662 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020406.3XP_016875895.1  ephrin-B2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    105710156..105756072 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374150.1XP_054230125.1  ephrin-B2 isoform X1