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    LINC01539 long intergenic non-protein coding RNA 1539 [ Homo sapiens (human) ]

    Gene ID: 100505474, updated on 26-Oct-2024

    Summary

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    Official Symbol
    LINC01539provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1539provided by HGNC
    Primary source
    HGNC:HGNC:51307
    See related
    Ensembl:ENSG00000267712 AllianceGenome:HGNC:51307
    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
    LINC03069
    Expression
    Restricted expression toward testis (RPKM 8.1) See more
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    Genomic context

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    See LINC01539 in Genome Data Viewer
    Location:
    18q21.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (56083356..56137536, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (56286115..56340236, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (53750587..53804767, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3092 Neighboring gene long intergenic non-protein coding RNA 3069 Neighboring gene long intergenic non-protein coding RNA 1905 Neighboring gene small nucleolar RNA SNORA73 family Neighboring gene uncharacterized LOC105372132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13362 Neighboring gene NANOG hESC enhancer GRCh37_chr18:54019108-54019609 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:54080945-54081494 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:54087957-54088683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:54230563-54231064 Neighboring gene uncharacterized LOC105372135

    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. 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)

    General gene information

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    Markers

    Other Names

    • long intergenic non-protein coding RNA 3069

    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_040025.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AK057336, AK058169
      Related
      ENST00000587904.5

    2. NR_040026.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons, includes two alternate exons, and uses an alternate splice site, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC006305, AK057336
      Related
      ENST00000591974.5

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      56083356..56137536 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      56286115..56340236 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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