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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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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

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