EFNA1 ephrin A1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EFNA1provided by HGNC
Official Full Name: ephrin A1provided by HGNC
Primary source: HGNC:HGNC:3221
See related: Ensembl:ENSG00000169242 MIM:191164; AllianceGenome:HGNC:3221
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: B61; EFL1; GMAN; ECKLG; EPLG1; LERK1; LERK-1; TNFAIP4
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 which binds to the EPHA2, EPHA4, EPHA5, EPHA6, and EPHA7 receptors. Two transcript variants that encode different isoforms were identified through sequence analysis. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 65.2), lung (RPKM 54.9) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q22

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (155127876..155134899)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (154267224..154274255)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (155100352..155107375)

Chromosome 1 - NC_000001.11 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?

Increased Serum EphrinA1 Is Associated with Parenchymal Hematoma after Ischemic Stroke.
Title: Increased Serum EphrinA1 Is Associated with Parenchymal Hematoma after Ischemic Stroke.
Role of EFNA1 SNP (rs12904) in Tumorigenesis and Metastasis of Colorectal Cancer: A Bioinformatic Analysis and HRM SNP Genotyping Verification.
Title: Role of EFNA1 SNP (rs12904) in Tumorigenesis and Metastasis of Colorectal Cancer: A Bioinformatic Analysis and HRM SNP Genotyping Verification.
Association of Epidermal Growth Factor 61A>G, Survivin -31G>C, and EFNA1 -1732G>A Polymorphisms with Susceptibility to Colorectal Cancer.
Title: Association of Epidermal Growth Factor 61A>G, Survivin -31G>C, and EFNA1 -1732G>A Polymorphisms with Susceptibility to Colorectal Cancer.
An integrated analysis of single-cell and bulk transcriptomics reveals EFNA1 as a novel prognostic biomarker for cervical cancer.
Title: An integrated analysis of single-cell and bulk transcriptomics reveals EFNA1 as a novel prognostic biomarker for cervical cancer.
Plasma Ephrin-A1 level in a cohort of diabetic retinopathy patients.
Title: Plasma Ephrin-A1 level in a cohort of diabetic retinopathy patients.
EFNA1 is a potential key gene that correlates with immune infiltration in low-grade glioma.
Title: EFNA1 is a potential key gene that correlates with immune infiltration in low-grade glioma.
Role of EFNA1 in tumorigenesis and prospects for cancer therapy.
Title: Role of EFNA1 in tumorigenesis and prospects for cancer therapy.
C1GALT1 is associated with poor survival and promotes soluble Ephrin A1-mediated cell migration through activation of EPHA2 in gastric cancer.
Title: C1GALT1 is associated with poor survival and promotes soluble Ephrin A1-mediated cell migration through activation of EPHA2 in gastric cancer.
The lncRNA referred to as GMAN is part of the EFNA1 locus.
Title: Long Noncoding RNA GMAN, Up-regulated in Gastric Cancer Tissues, Is Associated With Metastasis in Patients and Promotes Translation of Ephrin A1 by Competitively Binding GMAN-AS.
A case-control study revealed no significant association between the rs12904 polymorphism in the 3'-untranslated region of ephrin A1 ligand and the risk of sporadic colorectal cancer in Iranian population.
Title: rs12904 polymorphism in the 3'-untranslated region of ephrin A1 ligand and the risk of sporadic colorectal cancer in the Iranian population.

Submit: New GeneRIF Correction See all GeneRIFs (50)

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 influencing concentrations of liver enzymes in plasma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. 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

STS-W60696 (e-PCR)
- UniSTS:66185

EFNA1_321 (e-PCR)
- UniSTS:277186

Efna1 (e-PCR), detects polymorphism
- UniSTS:495859

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 signaling receptor binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in aortic valve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in endocardial cushion to mesenchymal transition involved in heart valve formation	ISS Inferred from Sequence or Structural Similarity more info
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 ephrin receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mitral valve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of dendritic spine morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of proteolysis involved in protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of thymocyte apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in notochord formation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of amyloid-beta formation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein phosphorylation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of protein tyrosine kinase activity	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein stabilization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of axonogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of blood vessel endothelial cell migration	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell adhesion mediated by integrin	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of peptidyl-tyrosine phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in substrate adhesion-dependent cell spreading	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	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	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ephrin-A1

Names: TNF alpha-induced protein 4; eph-related receptor tyrosine kinase ligand 1; epididymis secretory sperm binding protein; gastric cancer metastasis associated long noncoding RNA; immediate early response protein B61; ligand of eph-related kinase 1; tumor necrosis factor, alpha-induced protein 4

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_004428.3 → NP_004419.2 ephrin-A1 isoform a precursor

See identical proteins and their annotated locations for NP_004419.2

Status: REVIEWED

Description

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

Source sequence(s)

AK057845, AL833641, AW274944, M57730

Consensus CDS

CCDS1091.1

UniProtKB/Swiss-Prot

D3DV86, P20827, Q5SR60, Q5SR61, Q6I9T9, Q8N578

UniProtKB/TrEMBL

A0A384ME06, B2R7U1

Related

ENSP00000357392.3, ENST00000368407.8

Conserved Domains (1) summary

cd10425
Location:19 → 148

Ephrin-A_Ectodomain; Ectodomain of Ephrin A
NM_182685.2 → NP_872626.1 ephrin-A1 isoform b precursor

See identical proteins and their annotated locations for NP_872626.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment, compared to variant 1. The resulting protein (isoform b) is shorter when compared to isoform a.

Source sequence(s)

AK057845, AL833641, AW274944

Consensus CDS

CCDS1092.1

UniProtKB/TrEMBL

A8K0M4

Related

ENSP00000357391.2, ENST00000368406.2

Conserved Domains (1) summary

cd10425
Location:19 → 142

Ephrin-A_Ectodomain; Ectodomain of Ephrin A