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Aliases for HLA-E Gene

Aliases for HLA-E Gene

  • Major Histocompatibility Complex, Class I, E 2 3 5
  • MHC Class I Antigen E 3 4
  • HLA-6.2 3 4
  • HLA Class I Histocompatibility Antigen, Alpha Chain E 3
  • MHC Class Ib Antigen 3
  • HLAE 4
  • QA1 3

External Ids for HLA-E Gene

Previous GeneCards Identifiers for HLA-E Gene

  • GC06P030513
  • GC06P030228
  • GC06P030563
  • GC06P030565
  • GC06P030457
  • GC06P030257
  • GC06P030491
  • GC06P030635
  • GC06P030657
  • GC06P030764
  • GC06P030896

Summaries for HLA-E Gene

Entrez Gene Summary for HLA-E Gene

  • HLA-E belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. HLA-E binds a restricted subset of peptides derived from the leader peptides of other class I molecules. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLA-E Gene

HLA-E (Major Histocompatibility Complex, Class I, E) is a Protein Coding gene. Diseases associated with HLA-E include Hematopoietic Stem Cell Transplantation. Among its related pathways are Allograft rejection and PI3K-Akt signaling pathway. GO annotations related to this gene include receptor binding and MHC class I protein binding. An important paralog of this gene is HLA-A.

UniProtKB/Swiss-Prot for HLA-E Gene

  • Preferably binds to a peptide derived from the signal sequence of most HLA-A, -B, -C and -G molecules.

Gene Wiki entry for HLA-E Gene

Additional gene information for HLA-E Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HLA-E Gene

Genomics for HLA-E Gene

Regulatory Elements for HLA-E Gene

Enhancers for HLA-E Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H030678 1.9 FANTOM5 ENCODE dbSUPER 20.1 +195.9 195920 13.5 MLX DMAP1 YBX1 YY1 SLC30A9 ZNF416 ZNF143 SP3 NFYC MEF2D PPP1R10 MDC1 IER3 NRM TRIM39 RPL7P4 DHX16 ABCF1 HLA-E PPP1R18
GH06H030777 2.1 FANTOM5 Ensembl ENCODE dbSUPER 15.2 +293.0 292960 10.1 MLX ZFP64 DMAP1 YY1 SLC30A9 SP3 NFYC PPARGC1A MEF2D SSRP1 IER3 VARS2 PPP1R10 MDC1 DDX39B GTF2H4 ENSG00000233892 LY6G5B ETF1P1 TRIM39
GH06H030792 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.1 +304.5 304450 2.1 ELF3 TBL1XR1 ZBTB40 RARA RFX5 ZNF207 ATF7 RUNX3 IKZF2 SMARCA5 IER3 VARS2 FLOT1 LINC00243 DDR1 DDR1-AS1 GTF2H4 HCG20 DPCR1 HLA-E
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HLA-E on UCSC Golden Path with GeneCards custom track

Promoters for HLA-E Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195399 394 1601 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766 ZNF207

Genomic Locations for HLA-E Gene

Genomic Locations for HLA-E Gene
4,800 bases
Plus strand

Genomic View for HLA-E Gene

Genes around HLA-E on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HLA-E Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HLA-E Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for HLA-E Gene

  • Protein details for HLA-E Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    HLA class I histocompatibility antigen, alpha chain E
    Protein Accession:
    Secondary Accessions:
    • Q30169
    • Q9BT83
    • Q9GIY7
    • Q9GIY8

    Protein attributes for HLA-E Gene

    358 amino acids
    Molecular mass:
    40157 Da
    Quaternary structure:
    • Heterodimer of an alpha chain and a beta chain (beta-2-microglobulin).

    Three dimensional structures from OCA and Proteopedia for HLA-E Gene

neXtProt entry for HLA-E Gene

Post-translational modifications for HLA-E Gene

  • Ubiquitination at posLast=142142, isoforms=167, isoforms=191, and isoforms=343
  • Glycosylation at posLast=107107
  • Modification sites at PhosphoSitePlus

Other Protein References for HLA-E Gene

No data available for DME Specific Peptides for HLA-E Gene

Domains & Families for HLA-E Gene

Gene Families for HLA-E Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the MHC class I family.
  • Belongs to the MHC class I family.
genes like me logo Genes that share domains with HLA-E: view

Function for HLA-E Gene

Molecular function for HLA-E Gene

GENATLAS Biochemistry:
HLA class Ib,44kDa,6.2kb HindIII fragment,TAP and tapasin dependent,localized at the cell surface,harboring structural features conferring tight peptide binding specificity,correlating with the binding of an MHC class I leader peptide (see MHC1)
UniProtKB/Swiss-Prot Function:
Preferably binds to a peptide derived from the signal sequence of most HLA-A, -B, -C and -G molecules.

Phenotypes From GWAS Catalog for HLA-E Gene

Gene Ontology (GO) - Molecular Function for HLA-E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding IPI 18448674
GO:0030881 beta-2-microglobulin binding IMP 12411439
GO:0042288 MHC class I protein binding IDA 9754572
GO:0042605 peptide antigen binding IMP 12411439
GO:0042608 T cell receptor binding IDA 16474394
genes like me logo Genes that share ontologies with HLA-E: view
genes like me logo Genes that share phenotypes with HLA-E: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HLA-E Gene

Localization for HLA-E Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLA-E Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HLA-E gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
golgi apparatus 5
endosome 4
cytosol 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HLA-E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IDA 9754572
GO:0012507 ER to Golgi transport vesicle membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with HLA-E: view

Pathways & Interactions for HLA-E Gene

genes like me logo Genes that share pathways with HLA-E: view

Interacting Proteins for HLA-E Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
Selected Interacting proteins: ENSP00000365817 P13747-HLAE_HUMAN for HLA-E Gene via STRING IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for HLA-E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001916 positive regulation of T cell mediated cytotoxicity IDA 25631937
GO:0002250 adaptive immune response IDA 25631937
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I IEA,TAS --
GO:0002476 antigen processing and presentation of endogenous peptide antigen via MHC class Ib IDA 9754572
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS --
genes like me logo Genes that share ontologies with HLA-E: view

No data available for SIGNOR curated interactions for HLA-E Gene

Drugs & Compounds for HLA-E Gene

(6) Drugs for HLA-E Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adalimumab Approved Pharma 512
Certolizumab pegol Approved Pharma 130
Etanercept Approved, Investigational Pharma 408
Infliximab Approved Pharma 399
Methotrexate Approved Pharma Folate antagonist,inhibits DFHR 1576
genes like me logo Genes that share compounds with HLA-E: view

Transcripts for HLA-E Gene

Unigene Clusters for HLA-E Gene

Major histocompatibility complex, class I, E:
Representative Sequences:

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for HLA-E Gene

No ASD Table

Relevant External Links for HLA-E Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HLA-E Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HLA-E Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HLA-E Gene

This gene is overexpressed in Whole Blood (x12.7).

Protein differential expression in normal tissues from HIPED for HLA-E Gene

This gene is overexpressed in Skin (26.3) and Peripheral blood mononuclear cells (23.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HLA-E Gene

Protein tissue co-expression partners for HLA-E Gene

- Elite partner

SOURCE GeneReport for Unigene cluster for HLA-E Gene:


Evidence on tissue expression from TISSUES for HLA-E Gene

  • Blood(4.9)
  • Pancreas(4.8)
  • Lung(4.7)
  • Nervous system(4.7)
  • Intestine(4.4)
  • Spleen(4.2)
  • Skin(3.7)
  • Kidney(3.5)
  • Stomach(3.3)
  • Heart(3)
  • Liver(3)
  • Lymph node(2.6)
  • Muscle(2.5)
  • Bone(2.1)
genes like me logo Genes that share expression patterns with HLA-E: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HLA-E Gene

Orthologs for HLA-E Gene

This gene was present in the common ancestor of human and mouse.

Orthologs for HLA-E Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PATR-E 33 34
  • 98.67 (n)
(Mus musculus)
Mammalia H2-T23 33
  • 79.5 (n)
H2-T-ps 16
(Rattus norvegicus)
Mammalia RT1-S3 33
  • 77.97 (n)
Species where no ortholog for HLA-E was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HLA-E Gene

Gene Tree for HLA-E (if available)
Gene Tree for HLA-E (if available)

Paralogs for HLA-E Gene

Paralogs for HLA-E Gene

genes like me logo Genes that share paralogs with HLA-E: view

Variants for HLA-E Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HLA-E Gene

The following alleles of E-1 are known: E*01:01, E*01:02, E*01:03 and E*01:04. The sequence shown is that of E*01:01.

Sequence variations from dbSNP and Humsavar for HLA-E Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000413681 -- 30,489,388(+) CCTTC(A/T)TCCTG upstream-variant-2KB
rs1001937932 -- 30,492,442(+) GTAAG(G/T)GCGGG intron-variant, reference, missense
rs1002392425 -- 30,488,364(+) CAAGC(A/C)ATTCT upstream-variant-2KB
rs1003808081 -- 30,489,870(+) GCGGG(C/G)GCCGT reference, missense
rs1003909041 -- 30,490,398(+) TCTCC(A/G)AGCAA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for HLA-E Gene

Variant ID Type Subtype PubMed ID
nsv970103 CNV duplication 23825009
nsv601481 CNV loss 21841781
nsv601264 CNV loss 21841781
nsv5242 CNV insertion 18451855
nsv1144137 CNV deletion 24896259
nsv1122126 CNV deletion 24896259
nsv1074389 CNV deletion 25765185
esv3411275 CNV duplication 20981092
esv2731791 CNV deletion 23290073

Variation tolerance for HLA-E Gene

Residual Variation Intolerance Score: 63.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.79; 33.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HLA-E Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

Disorders for HLA-E Gene

MalaCards: The human disease database

(1) MalaCards diseases for HLA-E Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
hematopoietic stem cell transplantation
- elite association - COSMIC cancer census association via MalaCards
Search HLA-E in MalaCards View complete list of genes associated with diseases

Relevant External Links for HLA-E

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with HLA-E: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HLA-E Gene

Publications for HLA-E Gene

  1. Ethnic variability in human leukocyte antigen-E haplotypes. (PMID: 19140831) Antoun A … Briggs D (Tissue antigens 2009) 3 22 45 60
  2. HLA-E gene polymorphism associated with susceptibility to Kawasaki disease and formation of coronary artery aneurysms. (PMID: 19180512) Lin YJ … Tsai FJ (Arthritis and rheumatism 2009) 3 22 45 60
  3. HLA-E*0101 and HLA-G*010101 reduce the risk of Behcet's disease. (PMID: 17257316) Park KS … Lee ES (Tissue antigens 2007) 3 22 45 60
  4. HLA-E*0101 allele in homozygous state favors severe bacterial infections in sickle cell anemia. (PMID: 17961774) Tamouza R … Charron D (Human immunology 2007) 3 22 45 60
  5. Genetic variants in nonclassical major histocompatibility complex class I human leukocyte antigen (HLA)-E and HLA-G molecules are associated with susceptibility to heterosexual acquisition of HIV-1. (PMID: 16362895) Lajoie J … Roger M (The Journal of infectious diseases 2006) 3 22 45 60

Products for HLA-E Gene

Sources for HLA-E Gene

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