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    LINC00520 long intergenic non-protein coding RNA 520 [ Homo sapiens (human) ]

    Gene ID: 645687, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC00520provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 520provided by HGNC
    Primary source
    HGNC:HGNC:19843
    See related
    Ensembl:ENSG00000258791 MIM:620533; AllianceGenome:HGNC:19843
    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
    LEENE; LASSIE; C14orf34; LncRNA00520
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LINC00520 in Genome Data Viewer
    Location:
    14q22.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (55781135..55796674, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (49986899..50002438, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (56247853..56263392, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903320 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:56219189-56219804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56219806-56220357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56220358-56220908 Neighboring gene ribosomal protein L13a pseudogene 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:56270173-56271372 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:56280398-56281597 Neighboring gene Sharpr-MPRA regulatory region 10894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:56328264-56328764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:56332166-56332666 Neighboring gene uncharacterized LOC105370511 Neighboring gene uncharacterized LOC102723670 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:56424611-56425199

    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. Endothelial cells LEENE on noncoding RNAs in diabetic vasculopathy. Kallapur A, et al. J Clin Invest, 2023 Feb 1. PMID 36719373, Free PMC Article
    2. Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. Tang X, et al. J Clin Invest, 2023 Feb 1. PMID 36512424, Free PMC Article
    3. LINC00520: A Potential Diagnostic and Prognostic Biomarker in Cancer. Zhang Q, et al. Front Immunol, 2022. PMID 35309319, Free PMC Article
    4. Long non-coding RNA LASSIE regulates shear stress sensing and endothelial barrier function. Stanicek L, et al. Commun Biol, 2020 May 26. PMID 32457386, Free PMC Article
    5. Characterization of lncRNA LINC00520 and functional polymorphisms associated with breast cancer susceptibility in Chinese Han population. Guo Q, et al. Cancer Med, 2020 Mar. PMID 31997582, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LINC00520 promotes colorectal cancer progression through miRNA-195-3p / NAT2 axis.
      Title: LINC00520 promotes colorectal cancer progression through miRNA-195-3p / NAT2 axis.
    2. Endothelial cells LEENE on noncoding RNAs in diabetic vasculopathy.
      Title: Endothelial cells LEENE on noncoding RNAs in diabetic vasculopathy.
    3. Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models.
      Title: Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models.
    4. LINC00520 up-regulates SOX5 to promote cell proliferation and invasion by miR-4516 in human hepatocellular carcinoma.
      Title: LINC00520 up-regulates SOX5 to promote cell proliferation and invasion by miR-4516 in human hepatocellular carcinoma.
    5. LINC00520: A Potential Diagnostic and Prognostic Biomarker in Cancer.
      Title: LINC00520: A Potential Diagnostic and Prognostic Biomarker in Cancer.
    6. SP1-induced overexpression of LINC00520 facilitates non-small cell lung cancer progression through miR-577/CCNE2 pathway and predicts poor prognosis.
      Title: SP1-induced overexpression of LINC00520 facilitates non-small cell lung cancer progression through miR-577/CCNE2 pathway and predicts poor prognosis.
    7. Characterization of lncRNA LINC00520 and functional polymorphisms associated with breast cancer susceptibility in Chinese Han population.
      Title: Characterization of lncRNA LINC00520 and functional polymorphisms associated with breast cancer susceptibility in Chinese Han population.
    8. Long non-coding RNA LINC00520 promotes the proliferation and metastasis of malignant melanoma by inducing the miR-125b-5p/EIF5A2 axis.
      Title: Long non-coding RNA LINC00520 promotes the proliferation and metastasis of malignant melanoma by inducing the miR-125b-5p/EIF5A2 axis.
    9. Overexpression of LINC00520 contributes to the aggravation of Acute kidney injury by targeting miR-27b-3p/ OSMR.
      Title: LINC00520 targeting miR-27b-3p regulates OSMR expression level to promote acute kidney injury development through the PI3K/AKT signaling pathway.
    10. LINC00520 expression is up-regulated in nasopharyngeal carcinoma (NPC) tissues and cells, and its overexpression is associated with poor prognosis. Its knockdown showed tumor-suppressive roles via repressing NPC cell proliferation and tumor growth. LINC00520 mediates its function through functioning as a ceRNA for miR-26b, releasing the miR-26b inhibitory role for its target gene USP39.
      Title: Long non-coding RNA 520 is a negative prognostic biomarker and exhibits pro-oncogenic function in nasopharyngeal carcinoma carcinogenesis through regulation of miR-26b-3p/USP39 axis.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    EBI GWAS Catalog
    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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    Markers

    Other Names

    • lncRNA activated by shear stress in the endothelium
    • lncRNA that enhances eNOS expression

    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_026796.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL355773, BG104219, BU171486
      Related
      ENST00000649691.1

    2. NR_026797.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon, compared to variant 1.
      Source sequence(s)
      AL355773, BG104219, BU171486, BU178088

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      55781135..55796674 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      49986899..50002438 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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