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    LINC02609 long intergenic non-protein coding RNA 2609 [ Homo sapiens (human) ]

    Gene ID: 105378853, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC02609provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2609provided by HGNC
    Primary source
    HGNC:HGNC:27140
    See related
    Ensembl:ENSG00000233593 AllianceGenome:HGNC:27140
    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
    Broad expression in liver (RPKM 2.7), testis (RPKM 2.3) and 21 other tissues See more
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    Genomic context

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    See LINC02609 in Genome Data Viewer
    Location:
    1p22.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (90782984..90851650, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (90627369..90696134, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (91248541..91317207, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, C/D box 3G Neighboring gene NANOG hESC enhancer GRCh37_chr1:91149838-91150358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91171602-91172396 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91176541-91177109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91190371-91190926 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91190927-91191482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91192039-91192594 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91193268-91194089 Neighboring gene BarH like homeobox 2 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91227242-91228098 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91253233-91253482 Neighboring gene uncharacterized LOC124904217 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:91275093-91275704 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91277119-91277260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91300317-91300956 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:91304224-91304748 Neighboring gene VISTA enhancer hs612 Neighboring gene long intergenic non-protein coding RNA 2788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:91316240-91316740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1063 Neighboring gene long intergenic non-protein coding RNA 1763 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:91356676-91357355 Neighboring gene phosphorylase kinase regulatory subunit alpha 1 pseudogene

    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. HIF-2α/LINC02609/APOL1-mediated lipid storage promotes endoplasmic reticulum homeostasis and regulates tumor progression in clear-cell renal cell carcinoma. Xiao H, et al. J Exp Clin Cancer Res, 2024 Jan 23. PMID 38263248, Free PMC Article
    2. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Wang AG, et al. Biochem Biophys Res Commun, 2006 Jul 7. PMID 16712791
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HIF-2alpha/LINC02609/APOL1-mediated lipid storage promotes endoplasmic reticulum homeostasis and regulates tumor progression in clear-cell renal cell carcinoma.
      Title: HIF-2α/LINC02609/APOL1-mediated lipid storage promotes endoplasmic reticulum homeostasis and regulates tumor progression in clear-cell renal cell carcinoma.
    Submit: New GeneRIF Correction

    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)

    General gene information

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    Clone Names

    • FLJ12836

    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_135038.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BJ993392, BJ993393, CB164346

    2. NR_147930.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC091614, AK022898, AL590094
      Related
      ENST00000606660.1

    3. NR_147931.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC091614, AL590094
      Related
      ENST00000443802.4

    4. NR_147932.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL590094, BC036441
      Related
      ENST00000455680.5

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      90782984..90851650 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      90627369..90696134 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_135039.1: Suppressed sequence

      Description
      NR_135039.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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    Research Materials