epha4a eph receptor A4a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: epha4aprovided by ZNC
Official Full Name: eph receptor A4aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001207-7
See related: Ensembl:ENSDARG00000054454 AllianceGenome:ZFIN:ZDB-GENE-001207-7
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ek2; rtk1; zek2; EphA4; apha3; cb246; epha3; sb:cb246; zgc:109882
Summary: Predicted to enable transmembrane receptor protein tyrosine kinase activity. Acts upstream of or within several processes, including brain development; optic vesicle morphogenesis; and regulation of nervous system development. Predicted to be located in early endosome and membrane. Predicted to be part of receptor complex. Predicted to be active in plasma membrane. Is expressed in several structures, including central nervous system; germ ring; mesoderm; neural keel; and neural tube. Orthologous to human EPHA4 (EPH receptor A4). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (40067815..40136024, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (40102169..40170934, complement)

Chromosome 2 - NC_007113.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The authors show that forward signaling of EphA4 is required for border sharpening and induction of boundary cells in the zebrafish hindbrain, which they find both require kinase-dependent signaling, with a lesser input of PDZ domain-dependent signaling.
Title: Actomyosin regulation by Eph receptor signaling couples boundary cell formation to border sharpness.
In myelinating co-cultures and in zebrafish, we find that the number of mature oligodendrocytes does not change as result of manipulating signaling through the ephrinA1-EphA4 system. However, in both systems, inhibition of EphA4 signaling leads to a higher number of myelin sheaths formed by each oligodendrocyte. In isolated oligodendrocyte cultures, activation of EphA4 reduced process extension.
Title: Ephrin-A1-EphA4 signaling negatively regulates myelination in the central nervous system.
Downregulation of EphA4a compromises actomyosin cables and cells with different rhombomeric identity intermingle, and the phenotype is rescued enhancing myosin II activity.
Title: Cell segregation in the vertebrate hindbrain relies on actomyosin cables located at the interhombomeric boundaries.
Data show that EfnB2a is required in developing hindbrain for normal cell affinity and that EphA4 and EfnB2a regulate cell affinity independently within their respective rhombomeres.
Title: EphA4 and EfnB2a maintain rhombomere coherence by independently regulating intercalation of progenitor cells in the zebrafish neural keel.
EphA4 is required for cell adhesion and rhombomere-boundary formation in the zebrafish.
Title: EphA4 is required for cell adhesion and rhombomere-boundary formation in the zebrafish.

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General gene information

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Markers

fi31g02.x1 (e-PCR)
- UniSTS:204544

zek2 (e-PCR)
- UniSTS:187057

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ephrin receptor activity	IEA Inferred from Electronic Annotation more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane receptor protein tyrosine kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell surface receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell surface receptor protein tyrosine kinase signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell-cell recognition	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of axon extension	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of collateral sprouting of intact axon in response to injury	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within optic vesicle morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within phosphorylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein phosphorylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of myelination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere boundary formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within rhombomere boundary formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somite development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in early endosome	IEA Inferred from Electronic Annotation more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation 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
part_of receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: ephrin type-A receptor 4a

Names: eph receptor A3; eph-like kinase 2; eph-like receptor tyrosine kinase 1; ephrin receptor EphA4; etID309926.2; tyrosine-protein kinase receptor ZEK2

NP_001005919.2

EC 2.7.10.1

NP_001352100.1

EC 2.7.10.1

XP_005171372.1

EC 2.7.10.1

XP_005171373.1

EC 2.7.10.1

XP_005171374.1

EC 2.7.10.1

XP_005171375.1

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_001005919.2 → NP_001005919.2 ephrin type-A receptor 4a isoform 2 precursor

Status: VALIDATED

Source sequence(s)

CU929371, FP236331

UniProtKB/TrEMBL

A0A8M2BIL4, Q5ZEW1

Related

ENSDARP00000143572.2, ENSDART00000176951.2

Conserved Domains (5) summary

cd09545
Location:914 → 984

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:618 → 884

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

pfam14575
Location:554 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
NM_001365171.1 → NP_001352100.1 ephrin type-A receptor 4a isoform 1 precursor

Status: VALIDATED

Source sequence(s)

CU929371, FP236331

UniProtKB/TrEMBL

A0A8M2BIL7, Q5ZEW1

Related

ENSDARP00000123962.2, ENSDART00000149895.4

Conserved Domains (5) summary

cd09545
Location:923 → 993

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:618 → 893

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

pfam14575
Location:554 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

40067815..40136024 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005171318.5 → XP_005171375.1 ephrin type-A receptor 4a isoform X4

UniProtKB/TrEMBL

A0A8M2BIL4, Q5ZEW1

Conserved Domains (5) summary

cd09545
Location:914 → 984

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:618 → 884

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

pfam14575
Location:554 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_005171317.5 → XP_005171374.1 ephrin type-A receptor 4a isoform X3

UniProtKB/TrEMBL

A0A8M2BIL7, Q5ZEW1

Related

ENSDARP00000089403.5, ENSDART00000098632.5

Conserved Domains (5) summary

cd09545
Location:923 → 993

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:618 → 893

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

pfam14575
Location:554 → 618

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_005171316.5 → XP_005171373.1 ephrin type-A receptor 4a isoform X2

UniProtKB/TrEMBL

A0A8M2BJ36, Q5ZEW1

Conserved Domains (7) summary

cd09545
Location:950 → 1020

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

smart00454
Location:951 → 1014

SAM; Sterile alpha motif

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:654 → 920

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

pfam07714
Location:659 → 916

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:554 → 654

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
XM_005171315.5 → XP_005171372.1 ephrin type-A receptor 4a isoform X1

UniProtKB/TrEMBL

A0A8M2BIM5, Q5ZEW1

Conserved Domains (7) summary

cd09545
Location:959 → 1029

SAM_EPH-A4; SAM domain of EPH-A4 subfamily of tyrosine kinase receptors

smart00454
Location:960 → 1023

SAM; Sterile alpha motif

cd10482
Location:33 → 206

EphR_LBD_A4; Ligand Binding Domain of Ephrin type-A Receptor 4

cd00063
Location:443 → 534

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:654 → 929

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

pfam07714
Location:659 → 925

Pkinase_Tyr; Protein tyrosine kinase

pfam14575
Location:554 → 654

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain