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LINC01140 long intergenic non-protein coding RNA 1140 [ Homo sapiens (human) ]

Gene ID: 339524, updated on 17-Sep-2024

Summary

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Official Symbol
LINC01140provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1140provided by HGNC
Primary source
HGNC:HGNC:27922
See related
Ensembl:ENSG00000267272 AllianceGenome:HGNC:27922
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 fat (RPKM 5.3), ovary (RPKM 2.7) and 21 other tissues See more
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Genomic context

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See LINC01140 in Genome Data Viewer
Location:
1p22.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (87129765..87169204)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (86972495..87011921)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (87595448..87634887)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene heparan sulfate 2-O-sulfotransferase 1 Neighboring gene uncharacterized LOC124904211 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:87482946-87483115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1285 Neighboring gene ubiquitin like modifier activating enzyme 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1286 Neighboring gene ubiquitin like modifier activating enzyme 2 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87612561-87613060 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87614396-87615060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87616858-87617456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87617457-87618055 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87666183-87666684 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87666685-87667184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1043 Neighboring gene long intergenic non-protein coding RNA 2801 Neighboring gene Sharpr-MPRA regulatory region 9281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1045 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87794473-87795050 Neighboring gene VISTA enhancer hs809 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87797046-87797684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87797685-87798323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1049 Neighboring gene LIM domain only 4

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 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. Exosome-Mediated lncRNA LINC01140 Attenuates Breast Cancer Progression by Regulating the Wnt/β-Catenin Pathway. Guo Z, et al. Crit Rev Eukaryot Gene Expr, 2023. PMID 37602451
  2. LINC01140 Targeting miR-452-5p/RGS2 Pathway to Attenuate Breast Cancer Tumorigenesis. Li X. Dis Markers, 2022. PMID 36299824, Free PMC Article
  3. High Levels of LINC01140 Expression Predict a Good Prognosis and Improve Radiotherapy in Sarcoma Patients. Hu X, et al. Crit Rev Eukaryot Gene Expr, 2021. PMID 34587432
  4. A three-lncRNA expression signature associated with the prognosis of gastric cancer patients. Song P, et al. Cancer Med, 2017 Jun. PMID 28444881, Free PMC Article
  5. LINC01140 Regulates Radiosensitivity of Nasopharyngeal Carcinoma Cells Through the ceRNA Network. Li J, et al. Cell Mol Biol (Noisy-le-grand), 2022 Apr 30. PMID 35988287

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exosome-Mediated lncRNA LINC01140 Attenuates Breast Cancer Progression by Regulating the Wnt/beta-Catenin Pathway.
    Title: Exosome-Mediated lncRNA LINC01140 Attenuates Breast Cancer Progression by Regulating the Wnt/β-Catenin Pathway.
  2. LINC01140 Targeting miR-452-5p/RGS2 Pathway to Attenuate Breast Cancer Tumorigenesis.
    Title: LINC01140 Targeting miR-452-5p/RGS2 Pathway to Attenuate Breast Cancer Tumorigenesis.
  3. LINC01140 Regulates Radiosensitivity of Nasopharyngeal Carcinoma Cells Through the ceRNA Network.
    Title: LINC01140 Regulates Radiosensitivity of Nasopharyngeal Carcinoma Cells Through the ceRNA Network.
  4. LINC01140 inhibits nonsmall cell lung cancer progression and cisplatin resistance through the miR-4742-5p/TACC1 axis.
    Title: LINC01140 inhibits nonsmall cell lung cancer progression and cisplatin resistance through the miR-4742-5p/TACC1 axis.
  5. High Levels of LINC01140 Expression Predict a Good Prognosis and Improve Radiotherapy in Sarcoma Patients.
    Title: High Levels of LINC01140 Expression Predict a Good Prognosis and Improve Radiotherapy in Sarcoma Patients.
  6. The long noncoding RNA LINC01140/miR-140-5p/FGF9 axis modulates bladder cancer cell aggressiveness and macrophage M2 polarization.
    Title: The long noncoding RNA LINC01140/miR-140-5p/FGF9 axis modulates bladder cancer cell aggressiveness and macrophage M2 polarization.
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 and candidate gene association study of cigarette smoking behaviors.
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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Markers

Potential readthrough

Included gene: HS2ST1

Clone Names

  • FLJ11317, MGC161518

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_026985.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL139139, BC041867, DB462107
    Related
    ENST00000590653.5

  2. NR_026986.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, compared to variant 1.
    Source sequence(s)
    AL139139, BC041867, DA398164, DB462107

  3. NR_026987.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon and uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AL139139, BC041867, DB100426, DB462107

  4. NR_026988.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) represents use of an alternate promoter and 5' exon, compared to variant 1.
    Source sequence(s)
    AL139139, BC041867, BI818944, DA981741

  5. NR_026989.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) represents use of an alternate promoter and alternate 5' and 3' exons, compared to variant 1.
    Source sequence(s)
    AL139139, BM679066, BM722117, DA981741
    Related
    ENST00000490006.6

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
    87129765..87169204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    86972495..87011921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_207357.1: Suppressed sequence

    Description
    NM_207357.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version

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