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    LINC00501 long intergenic non-protein coding RNA 501 [ Homo sapiens (human) ]

    Gene ID: 100820709, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC00501provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 501provided by HGNC
    Primary source
    HGNC:HGNC:43439
    See related
    Ensembl:ENSG00000203645 AllianceGenome:HGNC:43439
    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
    Low expression observed in reference dataset See more
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    Genomic context

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    See LINC00501 in Genome Data Viewer
    Location:
    3q26.32
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (177294442..177323435)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (180097600..180126595)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (177012230..177041223)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene TBL1X/Y related 1 Neighboring gene Sharpr-MPRA regulatory region 13561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:176870313-176870813 Neighboring gene RNA, U6 small nuclear 681, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10853 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:176911488-176912078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:176914847-176915356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:176915357-176915864 Neighboring gene uncharacterized LOC107986053 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:177001817-177002549 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177006212-177006426 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:177011460-177012659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20838 Neighboring gene MPRA-validated peak4933 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20839 Neighboring gene Sharpr-MPRA regulatory region 10654 Neighboring gene Sharpr-MPRA regulatory region 4767 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177062319-177062838 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:177063359-177063876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20842 Neighboring gene Sharpr-MPRA regulatory region 9868 Neighboring gene argininosuccinate synthetase 1 pseudogene 7 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177077317-177078158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177083633-177084134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20847 Neighboring gene MPRA-validated peak4934 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:177174687-177175886 Neighboring gene long intergenic non-protein coding RNA 578 Neighboring gene NANOG hESC enhancer GRCh37_chr3:177205476-177205977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177234333-177235097 Neighboring gene RN7SK pseudogene 52 Neighboring gene uncharacterized LOC124906306

    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. Upregulation of LINC00501 by H3K27 acetylation facilitates gastric cancer metastasis through activating epithelial-mesenchymal transition and angiogenesis. Dou R, et al. Clin Transl Med, 2023 Oct. PMID 37867401, Free PMC Article
    2. The LINC00501-HSP90B1-STAT3 positive feedback loop promotes malignant behavior in gastric cancer cells. Pei M, et al. Cell Signal, 2023 Aug. PMID 37156452
    3. 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

    What's a GeneRIF?
    1. The LINC00501-HSP90B1-STAT3 positive feedback loop promotes malignant behavior in gastric cancer cells.
      Title: The LINC00501-HSP90B1-STAT3 positive feedback loop promotes malignant behavior in gastric cancer cells.
    2. Upregulation of LINC00501 by H3K27 acetylation facilitates gastric cancer metastasis through activating epithelial-mesenchymal transition and angiogenesis.
      Title: Upregulation of LINC00501 by H3K27 acetylation facilitates gastric cancer metastasis through activating epithelial-mesenchymal transition and angiogenesis.
    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)

    See Variation Viewer (GRCh38)

    General gene information

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    Markers

    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_047465.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC117465
      Related
      ENST00000425388.2

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      177294442..177323435
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      180097600..180126595
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    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.

    Molecular Biology Databases
    Research Materials