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    LINC02542 long intergenic non-protein coding RNA 2542 [ Homo sapiens (human) ]

    Gene ID: 102724168, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LINC02542provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2542provided by HGNC
    Primary source
    HGNC:HGNC:53576
    See related
    AllianceGenome:HGNC:53576
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Biased expression in salivary gland (RPKM 1.6), gall bladder (RPKM 0.5) and 12 other tissues See more
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    Genomic context

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    See LINC02542 in Genome Data Viewer
    Location:
    6q14.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (81843781..82101765, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (83053185..83311151, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (82553498..82811482, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377873 Neighboring gene small nucleolar RNA SNORA70 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24775 Neighboring gene long intergenic non-protein coding RNA 1526 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:82647366-82648565 Neighboring gene MPRA-validated peak5921 silencer Neighboring gene Sharpr-MPRA regulatory region 11142 Neighboring gene uncharacterized LOC107986617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24776 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:82853903-82855102 Neighboring gene inhibitor of Bruton tyrosine kinase Neighboring gene MPRA-validated peak5922 silencer Neighboring gene RNA, U6 small nuclear 130, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:82949825-82950342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17353 Neighboring gene single stranded DNA binding protein 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 1235

    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. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    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

    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_149134.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355294, DB182239

    2. NR_149135.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355294, AL360157, DA443454

    3. NR_149136.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355294, AL360157

    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
      81843781..82101765 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      83053185..83311151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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