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RAET1E retinoic acid early transcript 1E [ Homo sapiens (human) ]

Gene ID: 135250, updated on 5-Mar-2024

Summary

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Official Symbol
RAET1Eprovided by HGNC
Official Full Name
retinoic acid early transcript 1Eprovided by HGNC
Primary source
HGNC:HGNC:16793
See related
Ensembl:ENSG00000164520 MIM:609243; AllianceGenome:HGNC:16793
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
RL-4; LETAL; ULBP4; N2DL-4; NKG2DL4; RAET1E2; bA350J20.7
Summary
This gene belong to the RAET1 family, which consists of major histocompatibility complex (MHC) class I-related genes located in a cluster on chromosome 6q24.2-q25.3. This and RAET1G protein differ from other RAET1 proteins in that they have type I membrane-spanning sequences at their C termini rather than glycosylphosphatidylinositol anchor sequences. This protein functions as a ligand for NKG2D receptor, which is expressed on the surface of several types of immune cells, and is involved in innate and adaptive immune responses. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2011]
Expression
Biased expression in esophagus (RPKM 7.0) and skin (RPKM 2.7) See more
Orthologs
all
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Genomic context

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Location:
6q25.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (149883179..149898113, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (151082513..151097456, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (150204315..150219249, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RAET1E-LRP11 readthrough Neighboring gene LDL receptor related protein 11 Neighboring gene uncharacterized LOC124901427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:150185306-150185806 Neighboring gene RAET1E antisense RNA 1 Neighboring gene chaperonin containing TCP1 subunit 7 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9442 Neighboring gene multimerin 2 pseudogene Neighboring gene retinoic acid early transcript 1F (pseudogene)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Raet1e Polymorphisms Are Associated with Increased Risk of Developing Premature Coronary Artery Disease and with Some Cardiometabolic Parameters: The GEA Mexican Study. Posadas-Sánchez R, et al. Mediators Inflamm, 2018. PMID 30662365, Free PMC Article
  2. Decreased expression of the NKG2D ligand ULBP4 may be an indicator of poor prognosis in patients with nasopharyngeal carcinoma. Xu Y, et al. Oncotarget, 2017 Jun 27. PMID 28159927, Free PMC Article
  3. Increasing polymorphism of the RAET1E/ULBP4 gene in humans. Pearson H, et al. HLA, 2016 Jan. PMID 26814419
  4. Characterization of 5' promoter and exon 1-3 polymorphism of the RAET1E gene. Cox ST, et al. Hum Immunol, 2016 Jan. PMID 26519211
  5. Ovarian carcinoma expresses the NKG2D ligand Letal and promotes the survival and expansion of CD28- antitumor T cells. Conejo-Garcia JR, et al. Cancer Res, 2004 Mar 15. PMID 15026360

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The NKG2D ligand ULBP4 is not expressed by human monocytes.
    Title: The NKG2D ligand ULBP4 is not expressed by human monocytes.
  2. Transcriptomic analysis of micropapillary high grade T1 urothelial bladder cancer.
    Title: Transcriptomic analysis of micropapillary high grade T1 urothelial bladder cancer.
  3. An association of the raet1e polymorphisms with an increased risk of developing premature CAD and with cardiometabolic parameters has been shown for the first time.
    Title: Raet1e Polymorphisms Are Associated with Increased Risk of Developing Premature Coronary Artery Disease and with Some Cardiometabolic Parameters: The GEA Mexican Study.
  4. decreased expression levels of ULBP4 in NPC tissues as compared to that in normal NP epithelial tissues. In addition, low ULBP4 expression correlated with poor OS, DFS, DMFS, and may prove to be a novel prognostic factor.
    Title: Decreased expression of the NKG2D ligand ULBP4 may be an indicator of poor prognosis in patients with nasopharyngeal carcinoma.
  5. Blocking the interaction of NKG2D with its ligands deleted the sensitizing effects of HCQ. In addition, we showed that HCQ did not affect the synthesis or degradation of ULBP4, but induced the translocation of ULBP4 from the cytoplasm to the cell membrane
    Title: Hydroxychloroquine sensitizes chronic myeloid leukemia cells to Vγ9Vδ2 T cell-mediated lysis independent of autophagy.
  6. 5 of the 7 promoter polymorphisms of the RAET1E gene may disrupt transcription factor binding
    Title: Characterization of 5' promoter and exon 1-3 polymorphism of the RAET1E gene.
  7. RAET1E promoter polymorphism has increased to nine types, and there are now 12 alleles determined by the coding exons, including one null.
    Title: Increasing polymorphism of the RAET1E/ULBP4 gene in humans.
  8. genetic polymorphism among the ethnic groups
    Title: Single nucleotide polymorphism analysis of the NKG2D ligand cluster on the long arm of chromosome 6: Extensive polymorphisms and evidence of diversity between human populations.
  9. Patients whose tumors had high expression of RAET1E, ULBP1 and ULBP3 surviving a median of 11, 14 and 11 months, respectively, compared with disease-specific survival of 29, 30 and 25 months in patients whose tumors showed no expression of these ligands
    Title: ULBP2 and RAET1E NKG2D ligands are independent predictors of poor prognosis in ovarian cancer patients.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough RAET1E-LRP11

Readthrough gene: RAET1E-LRP11, Included gene: LRP11

Homology

Clone Names

  • MGC125308, MGC125309

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables natural killer cell lectin-like receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space 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
  

General protein information

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Preferred Names
retinoic acid early transcript 1E
Names
NKG2D ligand 4
RAE-1-like transcript 4
UL16-binding protein 4
lymphocyte effector toxicity activation ligand

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.

Genomic

  1. NG_029833.2 RefSeqGene

    Range
    5000..19934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243325.2 → NP_001230254.1  retinoic acid early transcript 1E isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL355312
    Consensus CDS
    CCDS59044.1
    UniProtKB/TrEMBL
    Q3ZAR2
    Related
    ENSP00000356332.3, ENST00000367363.3
    Conserved Domains (1) summary
    cl08246
    Location:26 → 159
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  2. NM_001243327.2 → NP_001230256.1  retinoic acid early transcript 1E isoform 3 precursor

    See identical proteins and their annotated locations for NP_001230256.1

    Status: REVIEWED

    Source sequence(s)
    AL355312
    Consensus CDS
    CCDS59042.1
    UniProtKB/TrEMBL
    A0A0G3VSE5
    Related
    ENSP00000432366.1, ENST00000529948.1
    Conserved Domains (1) summary
    cl08246
    Location:30 → 195
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  3. NM_001243328.3 → NP_001230257.1  retinoic acid early transcript 1E isoform 4 precursor

    See identical proteins and their annotated locations for NP_001230257.1

    Status: REVIEWED

    Source sequence(s)
    AL355312
    Consensus CDS
    CCDS59043.1
    UniProtKB/TrEMBL
    A0A0G3VSE5
    Related
    ENSP00000437067.1, ENST00000532335.5
    Conserved Domains (1) summary
    cl08246
    Location:30 → 195
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  4. NM_001394056.1 → NP_001380985.1  retinoic acid early transcript 1E isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AL355312
    UniProtKB/TrEMBL
    A0A2P1NST7
    Conserved Domains (1) summary
    cl08246
    Location:30 → 195
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  5. NM_001394057.1 → NP_001380986.1  retinoic acid early transcript 1E isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AL355312
    Consensus CDS
    CCDS5221.1
    UniProtKB/Swiss-Prot
    A6YF59, Q5VYB7, Q5VYB8, Q8TD07, Q8TEZ2, Q96L41
    UniProtKB/TrEMBL
    Q3ZAR2
    Related
    ENSP00000349709.4, ENST00000357183.9
    Conserved Domains (1) summary
    cl08246
    Location:30 → 195
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  6. NM_139165.3 → NP_631904.1  retinoic acid early transcript 1E isoform 1 precursor

    See identical proteins and their annotated locations for NP_631904.1

    Status: REVIEWED

    Source sequence(s)
    AL355312
    Consensus CDS
    CCDS5221.1
    UniProtKB/Swiss-Prot
    A6YF59, Q5VYB7, Q5VYB8, Q8TD07, Q8TEZ2, Q96L41
    UniProtKB/TrEMBL
    Q3ZAR2
    Conserved Domains (1) summary
    cl08246
    Location:30 → 195
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    149883179..149898113 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    151082513..151097456 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TD07.1 GenPept UniProtKB/Swiss-Prot:Q8TD07

Gene LinkOut

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