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EFNA4 ephrin A4 [ Homo sapiens (human) ]

Gene ID: 1945, updated on 5-Aug-2018

Summary

Official Symbol
EFNA4provided by HGNC
Official Full Name
ephrin A4provided by HGNC
Primary source
HGNC:HGNC:3224
See related
Ensembl:ENSG00000243364 MIM:601380; Vega:OTTHUMG00000035309
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
EFL4; EPLG4; LERK4
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 EFNA class ephrin. Three transcript variants that encode distinct proteins have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 7.7), colon (RPKM 6.4) and 23 other tissues See more
Orthologs

Genomic context

See EFNA4 in Genome Data Viewer
Location:
1q21.3
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (155063737..155069553)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (155036213..155042029)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene DC-STAMP domain containing 1 Neighboring gene DCST1 antisense RNA 1 Neighboring gene ADAM metallopeptidase domain 15 Neighboring gene ephrin A3 Neighboring gene ephrin A1

Genomic regions, transcripts, and products

Expression

  • Project title: 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • EPH-Ephrin signaling, organism-specific biosystem (from REACTOME)
    EPH-Ephrin signaling, organism-specific biosystemDuring the development process cell migration and adhesion are the main forces involved in morphing the cells into critical anatomical structures. The ability of a cell to migrate to its correct dest...
  • EPH-ephrin mediated repulsion of cells, organism-specific biosystem (from REACTOME)
    EPH-ephrin mediated repulsion of cells, organism-specific biosystemDespite high-affinity multimeric interaction between EPHs and ephrins (EFNs), the cellular response to EPH-EFN engagement is usually repulsion between the two cells and signal termination. These repu...
  • EPHA-mediated growth cone collapse, organism-specific biosystem (from REACTOME)
    EPHA-mediated growth cone collapse, organism-specific biosystemEPH/Ephrin signaling is coupled to Rho family GTPases such as Rac, Rho and Cdc42 that connect bidirectional receptor-ligand interactions to changes in the actin cytoskeleton (Noren & Pasquale 2004, G...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Rap1 signaling pathway, organism-specific biosystem (from KEGG)
    Rap1 signaling pathway, organism-specific biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Rap1 signaling pathway, conserved biosystem (from KEGG)
    Rap1 signaling pathway, conserved biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Ras signaling pathway, organism-specific biosystem (from KEGG)
    Ras signaling pathway, organism-specific biosystemThe Ras proteins are GTPases that function as molecular switches for signaling pathways regulating cell proliferation, survival, growth, migration, differentiation or cytoskeletal dynamism. Ras prote...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: EFNA3

Homology

Clone Names

  • FLJ57652, MGC125826

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ephrin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ephrin receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane-ephrin receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bone remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
ephrin receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ephrin receptor signaling pathway TAS
Traceable Author Statement
more info
 
osteoclast differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
intrinsic component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
ephrin-A4
Names
LERK-4
eph-related receptor tyrosine kinase ligand 4
ligand of eph-related kinase 4

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029561.1 RefSeqGene

    Range
    5001..10817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005227.2NP_005218.1  ephrin-A4 isoform a precursor

    See identical proteins and their annotated locations for NP_005218.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as ephrin-A4 (m), is the longest transcript and it encodes isoform a. Isoform a is a membrane-bound protein.
    Source sequence(s)
    AI459151, BE780161, BQ940212, CD671399
    Consensus CDS
    CCDS1089.1
    UniProtKB/Swiss-Prot
    P52798
    Related
    ENSP00000357394.3, OTTHUMP00000033237, ENST00000368409.7, OTTHUMT00000085421
    Conserved Domains (1) summary
    cd10425
    Location:27152
    Ephrin-A_Ectodomain; Ectodomain of Ephrin A
  2. NM_182689.1NP_872631.1  ephrin-A4 isoform b precursor

    See identical proteins and their annotated locations for NP_872631.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a downstream translation termination. It encodes isoform b which has a little longer and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AI459151, BE780161, BM740848, BQ940212
    Consensus CDS
    CCDS44237.1
    UniProtKB/Swiss-Prot
    P52798
    Related
    ENSP00000414378.2, OTTHUMP00000219769, ENST00000427683.2, OTTHUMT00000363904
    Conserved Domains (1) summary
    cd10425
    Location:27152
    Ephrin-A_Ectodomain; Ectodomain of Ephrin A
  3. NM_182690.2NP_872632.2  ephrin-A4 isoform c precursor

    See identical proteins and their annotated locations for NP_872632.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as ephrin-A4 (s), uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a downstream translation termination. It encodes isoform c which has a distinct and slightly shorter C-terminus compared to isoform a. Isoform c lacks a characteristic transmembrane domain and the GPI-signal sequence contained in isoform a. Isoform c is a secreted molecule.
    Source sequence(s)
    AJ006353, AL691442, BM740848
    Consensus CDS
    CCDS41407.1
    UniProtKB/Swiss-Prot
    P52798
    Related
    ENSP00000352789.4, OTTHUMP00000033238, ENST00000359751.8, OTTHUMT00000085422
    Conserved Domains (1) summary
    cd10425
    Location:27152
    Ephrin-A_Ectodomain; Ectodomain of Ephrin A

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    155063737..155069553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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