EPHA6 EPH receptor A6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EPHA6provided by HGNC
Official Full Name: EPH receptor A6provided by HGNC
Primary source: HGNC:HGNC:19296
See related: Ensembl:ENSG00000080224 MIM:600066; AllianceGenome:HGNC:19296
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: EHK2; EK12; EPA6; EHK-2; HEK12; PRO57066
Summary: Predicted to enable transmembrane-ephrin receptor activity. Predicted to be involved in axon guidance and ephrin receptor signaling pathway. Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 3q11.2

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (96814594..97761532)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (99518416..100468755)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (96533438..97480376)

Chromosome 3 - NC_000003.12 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?

our data imply that EPHA6 expression is beneficial for glioblastoma multiforme inhibition, particularly in combination with activation of BMP-2 signaling.These results suggest that EPHA6 expression or protein levels could be used as biomarkers for identification of subsets of glioblastoma multiforme patients who might benefit from BMP treatment.
Title: Tyrosine kinase Eph receptor A6 sensitizes glioma-initiating cells towards bone morphogenetic protein-induced apoptosis.
The EPHA6 rs4857055 C > T SNP is a novel candidate gene for hypertension in the Korean population.
Title: EPHA6 rs4857055 C > T polymorphism associates with hypertension through triglyceride and LDL particle size in the Korean population.
Gene-based analysis identified EPHA6 as the gene most significantly associated with paclitaxel-induced neuropathy...This first study sequencing EPHA genes revealed that low-frequency variants in EPHA6, EPHA5, and EPHA8 contribute to the susceptibility to paclitaxel-induced neuropathy
Title: Targeted Sequencing Reveals Low-Frequency Variants in EPHA Genes as Markers of Paclitaxel-Induced Peripheral Neuropathy.
EphA6 mRNA expression is higher in 112 CaP tumor samples compared with benign tissues from 58 benign prostate hyperplasia patients. Positive correlation was identified between EphA6 expression and vascular invasion, neural invasion, PSA level, and TNM staging in CaP cases.
Title: EphA6 promotes angiogenesis and prostate cancer metastasis and is associated with human prostate cancer progression.
Two predominant genes, ephrin type A receptor 6 (EPHA6) and folliculin (FLCN), with mutations exclusive to African American CRCs, are by genetic and biological criteria highly likely African American CRC driver genes.
Title: Novel recurrently mutated genes in African American colon cancers.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: A genome-wide study reveals copy number variants exclusive to childhood obesity cases.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
During development of the retinal vasculature, migration of ligand-bearing astrocytes is slowed along Eph-A6 expression gradient through repellent Eph-A6 - ephrin-A1 and -A4 signaling.
Title: Gradients of Eph-A6 expression in primate retina suggest roles in both vascular and axon guidance.
Observational study and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Identification of novel candidate genes for treatment response to risperidone and susceptibility for schizophrenia: integrated analysis among pharmacogenomics, mouse expression, and genetic case-control association approaches.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study identifies loci affecting blood copper, selenium and zinc. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Epha6 (e-PCR), detects polymorphism
- UniSTS:495884

SHGC-86254 (e-PCR)
- UniSTS:104484

SHGC-86263 (e-PCR)
- UniSTS:104493

RH118817 (e-PCR)
- UniSTS:138798

SHGC-12079 (e-PCR)
- UniSTS:40293

SHGC-86196 (e-PCR)
- UniSTS:104831

RH120914 (e-PCR)
- UniSTS:133773

SHGC-146553 (e-PCR)
- UniSTS:175288

SHGC-102341 (e-PCR)
- UniSTS:168901

SHGC-107627 (e-PCR)
- UniSTS:170453

NoName (e-PCR)
- UniSTS:486106

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables GPI-linked ephrin receptor activity	IEA Inferred from Electronic Annotation more info
enables boss receptor activity	IEA Inferred from Electronic Annotation more info
enables brain-derived neurotrophic factor receptor activity	IEA Inferred from Electronic Annotation more info
enables epidermal growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables fibroblast growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables hepatocyte growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXY142 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3Y41 kinase activity	IEA Inferred from Electronic Annotation more info
enables insulin receptor activity	IEA Inferred from Electronic Annotation more info
enables insulin-like growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables macrophage colony-stimulating factor receptor activity	IEA Inferred from Electronic Annotation more info
enables placental growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor alpha-receptor activity	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor beta-receptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine kinase collagen receptor activity	IEA Inferred from Electronic Annotation more info
enables stem cell factor receptor activity	IEA Inferred from Electronic Annotation more info
enables transmembrane-ephrin receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables vascular endothelial growth factor receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Kit signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain-derived neurotrophic factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in collagen-activated tyrosine kinase receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in ephrin receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in epidermal growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in fibroblast growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in hepatocyte growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin-like growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in macrophage colony-stimulating factor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in platelet-derived growth factor receptor-alpha signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in platelet-derived growth factor receptor-beta signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in vascular endothelial growth factor receptor-1 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in vascular endothelial growth factor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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-A receptor 6

Names: EPH homology kinase 2; EPH-like kinase 12; ephrin receptor EphA6

NP_001073917.2

EC 2.7.10.1

NP_001265229.1

EC 2.7.10.1

NP_001265230.1

EC 2.7.10.1

NP_775926.1

EC 2.7.10.1

XP_006713655.1

EC 2.7.10.1

XP_011511007.1

EC 2.7.10.1

XP_011511008.1

EC 2.7.10.1

XP_011511009.1

EC 2.7.10.1

XP_016861699.1

EC 2.7.10.1

XP_016861700.1

EC 2.7.10.1

XP_016861701.1

EC 2.7.10.1

XP_016861702.1

EC 2.7.10.1

XP_016861703.1

EC 2.7.10.1

XP_016861704.2

EC 2.7.10.1

XP_016861705.2

EC 2.7.10.1

XP_016861706.1

EC 2.7.10.1

XP_016861707.1

EC 2.7.10.1

XP_016861708.1

EC 2.7.10.1

XP_047303964.1

EC 2.7.10.1

XP_047303965.1

EC 2.7.10.1

XP_054202245.1

EC 2.7.10.1

XP_054202246.1

EC 2.7.10.1

XP_054202247.1

EC 2.7.10.1

XP_054202248.1

EC 2.7.10.1

XP_054202249.1

EC 2.7.10.1

XP_054202250.1

EC 2.7.10.1

XP_054202251.1

EC 2.7.10.1

XP_054202252.1

EC 2.7.10.1

XP_054202253.1

EC 2.7.10.1

XP_054202254.1

EC 2.7.10.1

XP_054202255.1

EC 2.7.10.1

XP_054202256.1

EC 2.7.10.1

XP_054202257.1

EC 2.7.10.1

XP_054202258.1

EC 2.7.10.1

XP_054202259.1

EC 2.7.10.1

XP_054202260.1

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_001080448.3 → NP_001073917.2 ephrin type-A receptor 6 isoform a

See identical proteins and their annotated locations for NP_001073917.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC107482, AC110491, AC117439, AC117470, AC119745, AC130510, AC135369, BM676895, DA385338

Consensus CDS

CCDS46876.1

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33

UniProtKB/TrEMBL

A0A0B4J1T8

Related

ENSP00000374323.5, ENST00000389672.10

Conserved Domains (8) summary

cd09547
Location:1055 → 1118

SAM_EPH-A6; SAM domain of EPH-A6 subfamily of tyrosine kinase receptors

smart00454
Location:1052 → 1119

SAM; Sterile alpha motif

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6

cd00063
Location:537 → 628

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 ...

cd05066
Location:720 → 1028

PTKc_EphR_A; Catalytic domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors

pfam00041
Location:427 → 521

fn3; Fibronectin type III domain

pfam07714
Location:725 → 1024

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:648 → 720

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
NM_001278300.2 → NP_001265229.1 ephrin type-A receptor 6 isoform c

See identical proteins and their annotated locations for NP_001265229.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains multiple differences at the 5' and 3' ends, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (c) is shorter and has distinct N- and C- termini, compared to isoform a.

Source sequence(s)

AC117439, AC117470, AL133666, BC067287, DC398430

Consensus CDS

CCDS63697.1

UniProtKB/Swiss-Prot

Q9UF33

Related

ENSP00000421711.1, ENST00000514100.5

Conserved Domains (3) summary

pfam07714
Location:117 → 320

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:40 → 112

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:112 → 320

PKc_like; Protein Kinases, catalytic domain
NM_001278301.2 → NP_001265230.1 ephrin type-A receptor 6 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks multiple 3' exons, and includes an alternate 3' exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (d) is shorter and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AC119745, AY358738, DA385338

UniProtKB/TrEMBL

H0Y9V0

Related

ENSP00000425132.1, ENST00000506569.1

Conserved Domains (1) summary

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6
NM_173655.4 → NP_775926.1 ephrin type-A receptor 6 isoform b

See identical proteins and their annotated locations for NP_775926.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains multiple differences at the 5' and 3' ends, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (b) is shorter and has distinct N- and C- termini, compared to isoform a.

Source sequence(s)

AL133666, DC398430

Consensus CDS

CCDS54616.1

UniProtKB/Swiss-Prot

Q9UF33

Related

ENSP00000423950.1, ENST00000502694.1

Conserved Domains (3) summary

pfam07714
Location:117 → 321

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:40 → 112

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl21453
Location:112 → 320

PKc_like; Protein Kinases, catalytic domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

96814594..97761532

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017006211.2 → XP_016861700.1 ephrin type-A receptor 6 isoform X4

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33

Conserved Domains (8) summary

cd09547
Location:943 → 1006

SAM_EPH-A6; SAM domain of EPH-A6 subfamily of tyrosine kinase receptors

smart00454
Location:940 → 1007

SAM; Sterile alpha motif

cd00063
Location:409 → 516

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 ...

cd05066
Location:608 → 916

PTKc_EphR_A; Catalytic domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors

pfam00041
Location:299 → 393

fn3; Fibronectin type III domain

pfam07714
Location:613 → 912

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:536 → 608

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl02704
Location:23 → 172

EphR_LBD; Ligand Binding Domain of Ephrin Receptors
XM_006713592.4 → XP_006713655.1 ephrin type-A receptor 6 isoform X1

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33

Conserved Domains (8) summary

cd09547
Location:1071 → 1134

SAM_EPH-A6; SAM domain of EPH-A6 subfamily of tyrosine kinase receptors

smart00454
Location:1068 → 1135

SAM; Sterile alpha motif

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6

cd00063
Location:537 → 644

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 ...

cd05066
Location:736 → 1044

PTKc_EphR_A; Catalytic domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors

pfam00041
Location:427 → 521

fn3; Fibronectin type III domain

pfam07714
Location:741 → 1040

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:664 → 736

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_017006210.2 → XP_016861699.1 ephrin type-A receptor 6 isoform X2

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33
XM_047448008.1 → XP_047303964.1 ephrin type-A receptor 6 isoform X3
XM_017006214.2 → XP_016861703.1 ephrin type-A receptor 6 isoform X7
XM_017006219.2 → XP_016861708.1 ephrin type-A receptor 6 isoform X11

UniProtKB/TrEMBL

E7EU71

Related

ENSP00000420598.2, ENST00000470610.6
XM_011512705.3 → XP_011511007.1 ephrin type-A receptor 6 isoform X13

Conserved Domains (1) summary

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6
XM_011512706.3 → XP_011511008.1 ephrin type-A receptor 6 isoform X14

UniProtKB/TrEMBL

H0Y9V0

Conserved Domains (1) summary

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6
XM_011512707.3 → XP_011511009.1 ephrin type-A receptor 6 isoform X15

UniProtKB/TrEMBL

H0Y9V0

Conserved Domains (1) summary

cd10484
Location:128 → 300

EphR_LBD_A6; Ligand Binding Domain of Ephrin type-A Receptor 6
XM_017006212.1 → XP_016861701.1 ephrin type-A receptor 6 isoform X5

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33
XM_017006213.2 → XP_016861702.1 ephrin type-A receptor 6 isoform X6

UniProtKB/Swiss-Prot

D6RAL5, Q9UF33

Conserved Domains (8) summary

cd09547
Location:915 → 978

SAM_EPH-A6; SAM domain of EPH-A6 subfamily of tyrosine kinase receptors

smart00454
Location:912 → 979

SAM; Sterile alpha motif

cd00063
Location:381 → 488

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 ...

cd05066
Location:580 → 888

PTKc_EphR_A; Catalytic domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors

pfam00041
Location:271 → 365

fn3; Fibronectin type III domain

pfam07714
Location:585 → 884

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:508 → 580

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cl02704
Location:1 → 144

EphR_LBD; Ligand Binding Domain of Ephrin Receptors
XM_017006218.1 → XP_016861707.1 ephrin type-A receptor 6 isoform X10
XM_017006217.2 → XP_016861706.1 ephrin type-A receptor 6 isoform X9
XM_017006215.2 → XP_016861704.2 ephrin type-A receptor 6 isoform X8
XM_017006216.2 → XP_016861705.2 ephrin type-A receptor 6 isoform X8
XM_047448009.1 → XP_047303965.1 ephrin type-A receptor 6 isoform X12