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

    Gene ID: 135250, updated on 8-Oct-2018

    Summary

    Official Symbol
    RAET1Eprovided by HGNC
    Official Full Name
    retinoic acid early transcript 1Eprovided by HGNC
    Primary source
    HGNC:HGNC:16793
    See related
    Ensembl:ENSG00000164520 Ensembl:ENSG00000285991 MIM:609243; Vega:OTTHUMG00000015796
    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

    Genomic context

    See RAET1E in Genome Data Viewer
    Location:
    6q25.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (149864399..149898353, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (150204511..150217195, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene protein-L-isoaspartate (D-aspartate) O-methyltransferase Neighboring gene uncharacterized LOC107986660 Neighboring gene LDL receptor related protein 11 Neighboring gene RAET1E antisense RNA 1 Neighboring gene chaperonin containing TCP1 subunit 7 pseudogene 1 Neighboring gene multimerin 2 pseudogene Neighboring gene retinoic acid early transcript 1F pseudogene

    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?

    Pathways from BioSystems

    • Adaptive Immune System, organism-specific biosystem (from REACTOME)
      Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
      Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
    • Natural killer cell mediated cytotoxicity, organism-specific biosystem (from KEGG)
      Natural killer cell mediated cytotoxicity, organism-specific biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...
    • Natural killer cell mediated cytotoxicity, conserved biosystem (from KEGG)
      Natural killer cell mediated cytotoxicity, conserved biosystemNatural killer (NK) cells are lymphocytes of the innate immune system that are involved in early defenses against both allogeneic (nonself) cells and autologous cells undergoing various forms of stre...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC125308, MGC125309

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    natural killer cell lectin-like receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    natural killer cell lectin-like receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    T cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    natural killer cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    natural killer cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    natural killer cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of natural killer cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of immune response TAS
    Traceable Author Statement
    more info
     
    susceptibility to natural killer cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    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)

    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_029833.1 RefSeqGene

      Range
      5001..17685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses alternate in-frame donor and acceptor splice sites at adjacent coding exons compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AY054974, AY069961, AY359075
      Consensus CDS
      CCDS59044.1
      UniProtKB/Swiss-Prot
      Q8TD07
      Related
      ENSP00000356332.3, OTTHUMP00000017403, ENST00000367363.3, OTTHUMT00000042658
      Conserved Domains (1) summary
      cl08246
      Location:26159
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    2. NM_001243327.1NP_001230256.1  retinoic acid early transcript 1E isoform 3 precursor

      See identical proteins and their annotated locations for NP_001230256.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs at the 3' end compared to variant 1. This results in a frame-shift and a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AY359075, EF489426
      Consensus CDS
      CCDS59042.1
      UniProtKB/Swiss-Prot
      Q8TD07
      Related
      ENSP00000432366.1, OTTHUMP00000229731, ENST00000529948.1, OTTHUMT00000384023
      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    3. NM_001243328.1NP_001230257.1  retinoic acid early transcript 1E isoform 4 precursor

      See identical proteins and their annotated locations for NP_001230257.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an additional 5' non-coding exon, and an alternate 3' terminal exon compared to variant 1. This results in a frame-shift and shorter isoform (4) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AY359075
      Consensus CDS
      CCDS59043.1
      UniProtKB/Swiss-Prot
      Q8TD07
      Related
      ENSP00000437067.1, OTTHUMP00000229728, ENST00000532335.5, OTTHUMT00000384020
      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    4. NM_139165.2NP_631904.1  retinoic acid early transcript 1E isoform 1 precursor

      See identical proteins and their annotated locations for NP_631904.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AY069961, AY359075
      Consensus CDS
      CCDS5221.1
      UniProtKB/Swiss-Prot
      Q8TD07
      Related
      ENSP00000349709.4, OTTHUMP00000017404, ENST00000357183.8, OTTHUMT00000042659
      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    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_000006.12 Reference GRCh38.p12 Primary Assembly

      Range
      149864399..149898353 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010286.1XP_016865775.1  retinoic acid early transcript 1E isoform X2

      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    2. XM_017010287.1XP_016865776.1  retinoic acid early transcript 1E isoform X2

      Related
      ENSP00000498179.1, ENST00000647612.1
      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    3. XM_017010285.1XP_016865774.1  retinoic acid early transcript 1E isoform X2

      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    4. XM_011535475.2XP_011533777.1  retinoic acid early transcript 1E isoform X1

      See identical proteins and their annotated locations for XP_011533777.1

      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    5. XM_011535476.2XP_011533778.1  retinoic acid early transcript 1E isoform X1

      See identical proteins and their annotated locations for XP_011533778.1

      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    6. XM_011535479.2XP_011533781.1  retinoic acid early transcript 1E isoform X4

      See identical proteins and their annotated locations for XP_011533781.1

      UniProtKB/Swiss-Prot
      Q8TD07
      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    7. XM_011535478.2XP_011533780.1  retinoic acid early transcript 1E isoform X3

      Conserved Domains (1) summary
      cl08246
      Location:30195
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    8. XM_017010288.1XP_016865777.1  retinoic acid early transcript 1E isoform X5

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