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    RTEL1-TNFRSF6B RTEL1-TNFRSF6B readthrough (NMD candidate) [ Homo sapiens (human) ]

    Gene ID: 100533107, updated on 17-Sep-2024

    Summary

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    Official Symbol
    RTEL1-TNFRSF6Bprovided by HGNC
    Official Full Name
    RTEL1-TNFRSF6B readthrough (NMD candidate)provided by HGNC
    Primary source
    HGNC:HGNC:44095
    See related
    Ensembl:ENSG00000026036 AllianceGenome:HGNC:44095
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This locus represents naturally occurring read-through transcription between the neighboring RTEL1 (regulator of telomere elongation helicase 1) and TNFRSF6B (tumor necrosis factor receptor superfamily, member 6b, decoy) genes on chromosome 20. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in testis (RPKM 5.8), appendix (RPKM 5.5) and 25 other tissues See more
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    Genomic context

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    See RTEL1-TNFRSF6B in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63657810..63698698)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65471931..65519004)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62289163..62330051)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62269990-62270750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62285437-62286115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18241 Neighboring gene stathmin 3 Neighboring gene uncharacterized LOC124904954 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ARF related protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene zinc finger CCCH-type and G-patch domain containing Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62368201-62369118 Neighboring gene LIME1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13186 Neighboring gene ZBTB46 antisense RNA 2 Neighboring gene SLC2A4 regulator Neighboring gene Lck interacting transmembrane adaptor 1 Neighboring gene zinc finger and BTB domain containing 46

    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 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. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Wrensch M, et al. Nat Genet, 2009 Aug. PMID 19578366, Free PMC Article
    2. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Walsh KM, et al. Nat Genet, 2014 Jul. PMID 24908248, Free PMC Article
    3. Genome-wide association study of glioma and meta-analysis. Rajaraman P, et al. Hum Genet, 2012 Dec. PMID 22886559, Free PMC Article
    4. Overexpression of M68/DcR3 in human gastrointestinal tract tumors independent of gene amplification and its location in a four-gene cluster. Bai C, et al. Proc Natl Acad Sci U S A, 2000 Feb 1. PMID 10655513, Free PMC Article
    5. Genome-wide association study identifies five susceptibility loci for glioma. Shete S, et al. Nat Genet, 2009 Aug. PMID 19578367, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Chromosome 7p11.2 (EGFR) variation influences glioma risk.
    EBI GWAS Catalog
    Genome-wide association scan of dental caries in the permanent dentition.
    EBI GWAS Catalog
    Genome-wide association study identifies five susceptibility loci for glioma.
    EBI GWAS Catalog
    Genome-wide association study of glioma and meta-analysis.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog
    Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility.
    EBI GWAS Catalog
    Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk.
    EBI GWAS Catalog

    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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    Other Names

    • RTEL1-TNFRSF6B readthrough (non-protein coding)

    Clone Names

    • FLJ00362, KIAA1088, DKFZp434O0510

    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.

    RNA

    1. NR_037882.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AB029011, AL121845, AL353715
      Related
      ENST00000492259.6

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      63657810..63698698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65471931..65519004
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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