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

    Gene ID: 135250, updated on 10-Dec-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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    See RAET1E in Genome Data Viewer
    Location:
    6q25.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (149883179..149898113, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (151082513..151097456, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Characterization of 5' promoter and exon 1-3 polymorphism of the RAET1E gene. Cox ST, et al. Hum Immunol, 2016 Jan. PMID 26519211
    2. 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
    3. Increasing polymorphism of the RAET1E/ULBP4 gene in humans. Pearson H, et al. HLA, 2016 Jan. PMID 26814419
    4. 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
    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 (29) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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