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    LINC00458 long intergenic non-protein coding RNA 458 [ Homo sapiens (human) ]

    Gene ID: 100507428, updated on 9-Jan-2024

    Summary

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    Official Symbol
    LINC00458provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 458provided by HGNC
    Primary source
    HGNC:HGNC:42807
    See related
    Ensembl:ENSG00000234787 AllianceGenome:HGNC:42807
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ES3; LncRNA-ES3
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LINC00458 in Genome Data Viewer
    Location:
    13q14.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (54124324..54132871, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (53339874..53348422, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (54698459..54707006, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370210 Neighboring gene Sharpr-MPRA regulatory region 6127 Neighboring gene long intergenic non-protein coding RNA 558 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:54515475-54516322 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:54701582-54702142 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:54706077-54706772 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:54706773-54707468 Neighboring gene NANOG hESC enhancer GRCh37_chr13:54759857-54760516 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:54841135-54841836 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:54842539-54843240 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:54841837-54842538 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:54843241-54843942 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:54880943-54881512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:54930851-54931492 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:54947288-54947939 Neighboring gene microRNA 1297 Neighboring gene NANOG hESC enhancer GRCh37_chr13:54957696-54958238 Neighboring gene ribosomal protein L13a pseudogene 25

    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. Upregulation of pluripotent long noncoding RNA ES3 in HER2-positive breast cancer. Keshavarz M, et al. J Cell Biochem, 2019 Oct. PMID 31211468
    2. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. Ng SY, et al. EMBO J, 2012 Feb 1. PMID 22193719, Free PMC Article
    3. GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association. Rentería ME, et al. Twin Res Hum Genet, 2013 Aug. PMID 23725790

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes.
      Title: Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association.
    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

    General gene information

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    Other Names

    • lncRNA embryonic stem cell 3

    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_108062.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL356052, BC018008, CX163049, CX163203
      Related
      ENST00000427299.6

    2. NR_108063.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and its 3' terminal exon extends past a splice site used in variant 1, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AL356052, BC017942, CX163049
      Related
      ENST00000451744.1

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      54124324..54132871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      53339874..53348422 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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