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    LINC00052 long intergenic non-protein coding RNA 52 [ Homo sapiens (human) ]

    Gene ID: 145978, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LINC00052provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 52provided by HGNC
    Primary source
    HGNC:HGNC:26455
    See related
    Ensembl:ENSG00000259527 AllianceGenome:HGNC:26455
    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
    TMEM83; NCRNA00052
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LINC00052 in Genome Data Viewer
    Location:
    15q25.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (87576929..87579686)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (85331488..85334245)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (88120160..88122917)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984735 Neighboring gene uncharacterized LOC102724465 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:87911835-87913034 Neighboring gene RNA, U6 small nuclear 185, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:88052812-88053364 Neighboring gene MPRA-validated peak2412 silencer Neighboring gene uncharacterized LOC124903579 Neighboring gene uncharacterized LOC124903580

    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. Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses. Sanchez-Lopez JM, et al. RNA Biol, 2024 Jan. PMID 38832821, Free PMC Article
    2. Long Non-Coding RNA LINC00052 Targets miR-548p/Notch2/Pyk2 to Modulate Tumor Budding and Metastasis of Human Breast Cancer. Huang X, et al. Biochem Genet, 2023 Feb. PMID 35918619
    3. LINC00052 ameliorates acute kidney injury by sponging miR-532-3p and activating the Wnt signaling pathway. Li X, et al. Aging (Albany NY), 2020 Nov 24. PMID 33231561, Free PMC Article
    4. Changes in the transcriptome profile of breast cancer cells grown as spheroids. Muñoz-Galindo L, et al. Biochem Biophys Res Commun, 2019 Sep 3. PMID 31301772
    5. LINC00052 upregulates EPB41L3 to inhibit migration and invasion of hepatocellular carcinoma by binding miR-452-5p. Zhu L, et al. Oncotarget, 2017 Sep 8. PMID 28969024, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses.
      Title: Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses.
    2. Long Non-Coding RNA LINC00052 Targets miR-548p/Notch2/Pyk2 to Modulate Tumor Budding and Metastasis of Human Breast Cancer.
      Title: Long Non-Coding RNA LINC00052 Targets miR-548p/Notch2/Pyk2 to Modulate Tumor Budding and Metastasis of Human Breast Cancer.
    3. LINC00052 ameliorates acute kidney injury by sponging miR-532-3p and activating the Wnt signaling pathway.
      Title: LINC00052 ameliorates acute kidney injury by sponging miR-532-3p and activating the Wnt signaling pathway.
    4. Long noncoding RNA LINC00052 suppressed the proliferation, migration and invasion of glioma cells by upregulating KLF6.
      Title: Long noncoding RNA LINC00052 suppressed the proliferation, migration and invasion of glioma cells by upregulating KLF6.
    5. tumor spheroids can induce changes in the transcriptome of cultured cells, including deregulation of linc00052 in breast cancer
      Title: Changes in the transcriptome profile of breast cancer cells grown as spheroids.
    6. our data indicated that the LINC00052 also remarkably suppressed pancreatic tumor growth via modulating miR-330-3p in vivo
      Title: LINC00052 functions as a tumor suppressor through negatively modulating miR-330-3p in pancreatic cancer.
    7. Study found a positive relationship between LINC00052 and miR-101-3p, and a negative relationship between miR-101-3p and SOX9 in hepatocellular carcinoma (HCC) tissues. Besides, miR-101-3p was involved in LINC00052 inhibiting HCC cells proliferation and metastasis. At the molecular level, LINC00052 downgulated SOX9 to inhibit HCC cells proliferation and metastasis by interacting with miR-101-3p.
      Title: LINC00052/miR-101-3p axis inhibits cell proliferation and metastasis by targeting SOX9 in hepatocellular carcinoma.
    8. High LINC00052 levels predict activation of HER3-mediated signaling, promoting breast cancer growth.
      Title: HER3 and LINC00052 interplay promotes tumor growth in breast cancer.
    9. LINC00052 could regulate NTRK3 expression by forming complementary base pairing with miR-128 and miR-485-3p to reduce the luciferase activity of NTRK3 3'UTR.
      Title: LINC00052 regulates the expression of NTRK3 by miR-128 and miR-485-3p to strengthen HCC cells invasion and migration.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Evidence for shared genetic risk between methamphetamine-induced psychosis and schizophrenia.
    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

    • transmembrane protein 83

    Clone Names

    • FLJ31461

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    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_026869.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK056023, BC066551
      Related
      ENST00000560153.3

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      87576929..87579686
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      85331488..85334245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152454.1: Suppressed sequence

      Description
      NM_152454.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96N35.1 GenPept UniProtKB/Swiss-Prot:Q96N35

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials