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    LINC00539 long intergenic non-protein coding RNA 539 [ Homo sapiens (human) ]

    Gene ID: 100652865, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC00539provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 539provided by HGNC
    Primary source
    HGNC:HGNC:43672
    See related
    Ensembl:ENSG00000224429 AllianceGenome:HGNC:43672
    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
    LINC00422
    Expression
    Broad expression in bone marrow (RPKM 1.5), testis (RPKM 1.2) and 22 other tissues See more
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    Genomic context

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    See LINC00539 in Genome Data Viewer
    Location:
    13q12.11
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (21303512..21344859, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (20496592..20539170, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (21877651..21918998, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370105 Neighboring gene estrogen-related receptor alpha pseudogene 2 Neighboring gene coiled-coil domain-containing protein 144B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7435 Neighboring gene mitochondrial intermediate peptidase pseudogene 3 Neighboring gene G protein-coupled receptor kinase 6 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:21911141-21911723 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:21912641-21913197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:21916347-21916850 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:21920736-21920939 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 52 Neighboring gene RNA, 5S ribosomal pseudogene 25

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Gene expression in proliferating human erythroid cells. Gubin AN, et al. Genomics, 1999 Jul 15. PMID 10409428
    2. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    General gene information

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    Other Names

    • long intergenic non-protein coding RNA 422

    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_103840.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL139380, BF185586, BQ007438, CD684045
      Related
      ENST00000657403.1

    2. NR_103841.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' exon and lacks three internal exons, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AL139380, CD684045

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      21303512..21344859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      20496592..20539170 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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