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    GAPLINC gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNA [ Homo sapiens (human) ]

    Gene ID: 100505592, updated on 6-May-2024

    Summary

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    Official Symbol
    GAPLINCprovided by HGNC
    Official Full Name
    gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNAprovided by HGNC
    Primary source
    HGNC:HGNC:51308
    See related
    Ensembl:ENSG00000266835 AllianceGenome:HGNC:51308
    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
    LINC01540
    Expression
    Biased expression in placenta (RPKM 2.1), lung (RPKM 1.0) and 7 other tissues See more
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    Genomic context

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    See GAPLINC in Genome Data Viewer
    Location:
    18p11.31
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (3466250..3478978)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (3625722..3638452)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (3466248..3478976)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3425706-3426206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3426207-3426707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:3433772-3434272 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:3434707-3434917 Neighboring gene uncharacterized LOC124904237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3448381-3449002 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3449003-3449622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3452109-3452730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:3452731-3453350 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3451487-3452108 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:3455215-3455834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:3457616-3458176 Neighboring gene uncharacterized LOC105371965 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:3466751-3467438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:3469136-3469926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13048 Neighboring gene TGFB induced factor homeobox 1 Neighboring gene Sharpr-MPRA regulatory region 485 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:3554877-3555427 Neighboring gene small nucleolar RNA U13 Neighboring gene DLG associated protein 1 Neighboring gene RNA, 7SL, cytoplasmic 39, pseudogene

    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. Poor expression of long-chain noncoding RNA GAPLINC inhibits epithelial-mesenchymal transition, and invasion and migration of hepatocellular carcinoma cells. Zhang W, et al. Anticancer Drugs, 2019 Sep. PMID 31415284
    2. Clinical usefulness of gastric adenocarcinoma predictive long intergenic noncoding RNA in human malignancies: A meta-analysis. Liu W, et al. Pathol Res Pract, 2019 Jun. PMID 30904361
    3. GAPLINC is a predictor of poor prognosis and regulates cell migration and invasion in osteosarcoma. Liao S, et al. Biosci Rep, 2018 Oct 31. PMID 30177521, Free PMC Article
    4. Hypoxia Promotes Gastric Cancer Malignancy Partly through the HIF-1α Dependent Transcriptional Activation of the Long Non-coding RNA GAPLINC. Liu L, et al. Front Physiol, 2016. PMID 27729869, Free PMC Article
    5. A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock. Vollmers AC, et al. Proc Natl Acad Sci U S A, 2021 Feb 16. PMID 33568531, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Macrophage-enriched novel functional long noncoding RNAs LRRC75A-AS1 and GAPLINC regulate polarization and innate immune responses.
      Title: Macrophage-enriched novel functional long noncoding RNAs LRRC75A-AS1 and GAPLINC regulate polarization and innate immune responses.
    2. Serum Levels of Long Non-coding RNAs NEAT1, GAS5, and GAPLINC Altered in Rheumatoid Arthritis.
      Title: Serum Levels of Long Non-coding RNAs NEAT1, GAS5, and GAPLINC Altered in Rheumatoid Arthritis.
    3. A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock.
      Title: A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock.
    4. Long non-coding RNA GAPLINC promotes angiogenesis by regulating miR-211 under hypoxia in human umbilical vein endothelial cells.
      Title: Long non-coding RNA GAPLINC promotes angiogenesis by regulating miR-211 under hypoxia in human umbilical vein endothelial cells.
    5. Poor expression of long-chain noncoding RNA GAPLINC inhibits epithelial-mesenchymal transition, and invasion and migration of hepatocellular carcinoma cells.
      Title: Poor expression of long-chain noncoding RNA GAPLINC inhibits epithelial-mesenchymal transition, and invasion and migration of hepatocellular carcinoma cells.
    6. GAPLINC expression was significantly upregulated in both glioblastoma (GBM) tissues and cell lines. The overexpression of GAPLINC was associated with shorter overall and disease-free survival. GAPLINC silencing suppressed GBM cells proliferation, migration, and invasion, and promoted apoptosis. GAPLINC acted as a competing endogenous RNA to sponge miR-331-3p and knockdown of GAPLINC promoted the expression of miR-331-3p.
      Title: LncRNA GAPLINC promotes the growth and metastasis of glioblastoma by sponging miR-331-3p.
    7. Our results suggest that elevated GAPLINC was associated with poor clinical outcomes and might serve as a promising prognostic biomarker in cancer survivors
      Title: Clinical usefulness of gastric adenocarcinoma predictive long intergenic noncoding RNA in human malignancies: A meta-analysis.
    8. The in vitro studies showed knockdown of GAPLINC depressed osteosarcoma cell migration and invasion via inhibiting CD44 expression, but no effect on cell proliferation. In conclusion, GAPLINC may serve as a potential biomarker for predicting prognosis and developing therapy for osteosarcoma.
      Title: GAPLINC is a predictor of poor prognosis and regulates cell migration and invasion in osteosarcoma.
    9. GAPLINC promotes Non-Small Cell Lung Cancer tumorigenesis by regulating miR-661/eEF2K cascade.
      Title: Gastric Adenocarcinoma Predictive Long Intergenic Non-Coding RNA Promotes Tumor Occurrence and Progression in Non-Small Cell Lung Cancer via Regulation of the miR-661/eEF2K Signaling Pathway.
    10. GAPLINC has a role in promoting colorectal cancer invasion via binding to PSF/NONO and partly by stimulating the expression of SNAI2
      Title: Long noncoding RNA GAPLINC promotes invasion in colorectal cancer by targeting SNAI2 through binding with PSF and NONO.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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)

    Genotypes

    General gene information

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    Other Names

    • RP11-838N2.4
    • TCONS_00026238
    • gastric adenocarcinoma predictive long intergenic noncoding RNA
    • lncRNA-uc002kmd.1
    • long intergenic non-protein coding RNA 1540

    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_110428.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site and is shorter than variant 1.
      Source sequence(s)
      BM782281, BX107736

    2. NR_110429.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the longer transcript.
      Source sequence(s)
      AJ707365, AP001025
      Related
      ENST00000581442.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      3466250..3478978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      3625722..3638452
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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