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    LINC01108 long intergenic non-protein coding RNA 1108 [ Homo sapiens (human) ]

    Gene ID: 102216342, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LINC01108provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1108provided by HGNC
    Primary source
    HGNC:HGNC:49234
    See related
    Ensembl:ENSG00000226673 AllianceGenome:HGNC:49234
    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
    LncRNA-ES1
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    Location:
    6p23
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (14280127..14285454, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (14152651..14157970, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14280358..14285685, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 133 pseudogene Neighboring gene MPRA-validated peak5669 silencer Neighboring gene uncharacterized LOC105374940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24049 Neighboring gene MPRA-validated peak5670 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14235700-14236200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14236201-14236701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24050 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14265410-14265941 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14270712-14271911 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:14273182-14274095 Neighboring gene uncharacterized LOC124901266 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14297089-14297757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14298956-14299481 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:14301988-14302627 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14302628-14303268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14330461-14330962 Neighboring gene Sharpr-MPRA regulatory region 8710 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14381289-14381830 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14381831-14382374 Neighboring gene uncharacterized LOC105374943

    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. Long non-coding RNA ENST01108 promotes carcinogenesis of glioma by acting as a molecular sponge to modulate miR-489. Xu D, et al. Biomed Pharmacother, 2018 Apr. PMID 29421578
    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. Intergenic variants may predispose to major depression disorder through regulation of long non-coding RNA expression. Ye N, et al. Gene, 2017 Feb 15. PMID 27940106
    4. VIRMA mediates preferential m(6)A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Yue Y, et al. Cell Discov, 2018. PMID 29507755, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Other Names

    • lncrna embryonic stem cell 1

    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_108096.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL353152

    2. NR_108097.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AL353152
      Related
      ENST00000427276.1

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      14280127..14285454 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      14152651..14157970 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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