EPHB6 EPH receptor B6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EPHB6provided by HGNC
Official Full Name: EPH receptor B6provided by HGNC
Primary source: HGNC:HGNC:3396
See related: Ensembl:ENSG00000106123 MIM:602757; AllianceGenome:HGNC:3396
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: HEP
Summary: This gene encodes a member of a family of transmembrane proteins that function as receptors for ephrin-B family proteins. Unlike other members of this family, the encoded protein does not contain a functional kinase domain. Activity of this protein can influence cell adhesion and migration. Expression of this gene is downregulated during tumor progression, suggesting that the protein may suppress tumor invasion and metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression: Biased expression in skin (RPKM 52.0), brain (RPKM 17.5) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q34

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (142855076..142871093)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (144210901..144226909)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (142552838..142568847)

Chromosome 7 - NC_000007.14 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EphB6 deficiency in intestinal neurons promotes tumor growth in colorectal cancer by neurotransmitter GABA signaling.
Title: EphB6 deficiency in intestinal neurons promotes tumor growth in colorectal cancer by neurotransmitter GABA signaling.
Structure of the EphB6 receptor ectodomain.
Title: Structure of the EphB6 receptor ectodomain.
DNA methylation maintains the CLDN1-EPHB6-SLUG axis to enhance chemotherapeutic efficacy and inhibit lung cancer progression.
Title: DNA methylation maintains the CLDN1-EPHB6-SLUG axis to enhance chemotherapeutic efficacy and inhibit lung cancer progression.
Cataloguing the dead: breathing new life into pseudokinase research.
Title: Cataloguing the dead: breathing new life into pseudokinase research.
The gut microbiota regulates autism-like behavior by mediating vitamin B6 homeostasis in EphB6-deficient mice.
Title: The gut microbiota regulates autism-like behavior by mediating vitamin B(6) homeostasis in EphB6-deficient mice.
This study demonstrated that EPHB6-mutated cells acquire cell adhesion-mediated drug resistance (CAM-DR) in association with CDH11 expression and RhoA/focal adhesion kinase (FAK) activation. Targeted inhibition of EPHA2 or CDH11 reversed the acquired paclitaxel resistance, suggesting its potential clinical utility.
Title: EPHB6 mutation induces cell adhesion-mediated paclitaxel resistance via EPHA2 and CDH11 expression.
LncRNA DGCR5 regulates the non-small cell lung cancer cell growth, migration, and invasion through regulating miR-211-5p/EPHB6 axis.
Title: LncRNA DGCR5 regulates the non-small cell lung cancer cell growth, migration, and invasion through regulating miR-211-5p/EPHB6 axis.
Analysis of the association of EPHB6, EFNB1 and EFNB3 variants with hypertension risks in males with hypogonadism.
Title: Analysis of the association of EPHB6, EFNB1 and EFNB3 variants with hypertension risks in males with hypogonadism.
observations highlight a novel role for EphB6 in reducing drug resistance of T-ALL and suggest that doxorubicin treatment should produce better results if personalised based on EphB6 levels
Title: The EphB6 receptor is overexpressed in pediatric T cell acute lymphoblastic leukemia and increases its sensitivity to doxorubicin treatment.
It may be beneficial to enhance EPHB6 action concurrent with applying a conventional DNA-damaging treatment.
Title: EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	The amplified luminescent proximity homogeneous assay (AlphaScreen) identifies the interaction of HIV-1 Gag with EPHB6	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH71266 (e-PCR)
- UniSTS:7964

IB201 (e-PCR)
- UniSTS:27963

SHGC-52550 (e-PCR)
- UniSTS:38280

RH120388 (e-PCR)
- UniSTS:132531

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ephrin receptor activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor activity	TAS Traceable Author Statement more info	PubMed
enables transmembrane-ephrin receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in ephrin receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein phosphorylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: ephrin type-B receptor 6

Names: human kinase-defective Eph-family receptor protein; tyrosine-protein kinase-defective receptor EPH-6

NP_001267723.2

EC 2.7.10.1

NP_001267724.2

EC 2.7.10.1

NP_004436.4

EC 2.7.10.1

XP_011514181.1

EC 2.7.10.1

XP_011514182.1

EC 2.7.10.1

XP_011514183.1

EC 2.7.10.1

XP_011514184.1

EC 2.7.10.1

XP_024302443.1

EC 2.7.10.1

XP_047275939.1

EC 2.7.10.1

XP_047275940.1

EC 2.7.10.1

XP_054184674.1

EC 2.7.10.1

XP_054184675.1

EC 2.7.10.1

XP_054184676.1

EC 2.7.10.1

XP_054184677.1

EC 2.7.10.1

XP_054184678.1

EC 2.7.10.1

XP_054184679.1

EC 2.7.10.1

XP_054213437.1

EC 2.7.10.1

XP_054213438.1

EC 2.7.10.1

XP_054213439.1

EC 2.7.10.1

XP_054213440.1

EC 2.7.10.1

XP_054213441.1

EC 2.7.10.1

XP_054213442.1

EC 2.7.10.1

XP_054213443.1

EC 2.7.10.1

XP_054213444.1

EC 2.7.10.1

XP_054213445.1

EC 2.7.10.1

XP_054213446.1

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_001280794.3 → NP_001267723.2 ephrin type-B receptor 6 isoform b

See identical proteins and their annotated locations for NP_001267723.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks an exon in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform (b).

Source sequence(s)

AC245427

Consensus CDS

CCDS75672.1

UniProtKB/TrEMBL

A0A0G2JNC5

Conserved Domains (7) summary

smart00454
Location:654 → 714

SAM; Sterile alpha motif

cd00063
Location:196 → 287

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07699
Location:12 → 53

GCC2_GCC3; GCC2 and GCC3

pfam07714
Location:378 → 623

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:320 → 373

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl15755
Location:653 → 721

SAM_superfamily; SAM (Sterile alpha motif )

cl21453
Location:373 → 627

PKc_like; Protein Kinases, catalytic domain
NM_001280795.2 → NP_001267724.2 ephrin type-B receptor 6 isoform b

See identical proteins and their annotated locations for NP_001267724.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, lacks an exon in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform (b).

Source sequence(s)

AL832533, BC047892, BC056159, BC110606, BX410199

Consensus CDS

CCDS75672.1

UniProtKB/TrEMBL

A0A0G2JNC5

Conserved Domains (7) summary

smart00454
Location:654 → 714

SAM; Sterile alpha motif

cd00063
Location:196 → 287

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07699
Location:12 → 53

GCC2_GCC3; GCC2 and GCC3

pfam07714
Location:378 → 623

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:320 → 373

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl15755
Location:653 → 721

SAM_superfamily; SAM (Sterile alpha motif )

cl21453
Location:373 → 627

PKc_like; Protein Kinases, catalytic domain
NM_004445.6 → NP_004436.4 ephrin type-B receptor 6 isoform a precursor

See identical proteins and their annotated locations for NP_004436.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC245427, AL532843, BC110607, BX419816, CN283345, CN283348

Consensus CDS

CCDS5873.2

UniProtKB/TrEMBL

F8WCM8

Related

ENSP00000498670.1, ENST00000652003.1

Conserved Domains (7) summary

cd09555
Location:946 → 1014

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:371 → 472

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:490 → 572

fn3; Fibronectin type III domain

pfam07699
Location:305 → 346

Ephrin_rec_like; Putative ephrin-receptor like

pfam14575
Location:613 → 665

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:666 → 920

PKc_like; Protein Kinases, catalytic domain

RNA

NR_104001.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) includes an additional 5' exon and contains multiple differences in the internal exon structure, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AL832533, BC047892, BC051028

Related

ENST00000611578.4

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

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

142855076..142871093

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011515879.2 → XP_011514181.1 ephrin type-B receptor 6 isoform X1

See identical proteins and their annotated locations for XP_011514181.1

UniProtKB/TrEMBL

F8WCM8

Conserved Domains (7) summary

cd09555
Location:946 → 1014

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:371 → 472

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:490 → 572

fn3; Fibronectin type III domain

pfam07699
Location:305 → 346

Ephrin_rec_like; Putative ephrin-receptor like

pfam14575
Location:613 → 665

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:666 → 920

PKc_like; Protein Kinases, catalytic domain
XM_047419983.1 → XP_047275939.1 ephrin type-B receptor 6 isoform X2
XM_047419984.1 → XP_047275940.1 ephrin type-B receptor 6 isoform X3
XM_011515880.2 → XP_011514182.1 ephrin type-B receptor 6 isoform X1

See identical proteins and their annotated locations for XP_011514182.1

UniProtKB/TrEMBL

F8WCM8

Conserved Domains (7) summary

cd09555
Location:946 → 1014

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:371 → 472

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:490 → 572

fn3; Fibronectin type III domain

pfam07699
Location:305 → 346

Ephrin_rec_like; Putative ephrin-receptor like

pfam14575
Location:613 → 665

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:666 → 920

PKc_like; Protein Kinases, catalytic domain
XM_011515881.4 → XP_011514183.1 ephrin type-B receptor 6 isoform X2

Conserved Domains (8) summary

cd09555
Location:945 → 1013

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

smart00454
Location:946 → 1006

SAM; Sterile alpha motif

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:489 → 580

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07699
Location:305 → 346

GCC2_GCC3; GCC2 and GCC3

pfam07714
Location:671 → 915

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:613 → 666

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:666 → 919

PKc_like; Protein Kinases, catalytic domain
XM_011515882.3 → XP_011514184.1 ephrin type-B receptor 6 isoform X3

Conserved Domains (8) summary

cd09555
Location:915 → 983

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

smart00454
Location:916 → 976

SAM; Sterile alpha motif

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:371 → 472

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07699
Location:305 → 346

GCC2_GCC3; GCC2 and GCC3

pfam07714
Location:640 → 885

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:582 → 635

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:635 → 889

PKc_like; Protein Kinases, catalytic domain
XM_024446675.2 → XP_024302443.1 ephrin type-B receptor 6 isoform X4

Conserved Domains (7) summary

cd09555
Location:914 → 982

SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors

cd10475
Location:33 → 232

EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6

cd00063
Location:489 → 549

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:372 → 472

fn3; Fibronectin type III domain

pfam07699
Location:305 → 346

Ephrin_rec_like; Putative ephrin-receptor like

pfam14575
Location:582 → 634

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:635 → 888

PKc_like; Protein Kinases, catalytic domain

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187562.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

878132..894136

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054328699.1 → XP_054184674.1 ephrin type-B receptor 6 isoform X1

UniProtKB/TrEMBL

A0A0G2JNH7
XM_054328700.1 → XP_054184675.1 ephrin type-B receptor 6 isoform X1

UniProtKB/TrEMBL

A0A0G2JNH7
XM_054328702.1 → XP_054184677.1 ephrin type-B receptor 6 isoform X2
XM_054328703.1 → XP_054184678.1 ephrin type-B receptor 6 isoform X3
XM_054328701.1 → XP_054184676.1 ephrin type-B receptor 6 isoform X1

UniProtKB/TrEMBL

A0A0G2JNH7
XM_054328704.1 → XP_054184679.1 ephrin type-B receptor 6 isoform X3