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    LINC01089 long intergenic non-protein coding RNA 1089 [ Homo sapiens (human) ]

    Gene ID: 338799, updated on 4-Jan-2024

    Summary

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    Official Symbol
    LINC01089provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1089provided by HGNC
    Primary source
    HGNC:HGNC:27886
    See related
    Ensembl:ENSG00000212694 AllianceGenome:HGNC:27886
    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
    LIMT
    Expression
    Ubiquitous expression in spleen (RPKM 8.0), prostate (RPKM 8.0) and 24 other tissues See more
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    Genomic context

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    See LINC01089 in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121795267..121802946, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (121791937..121799611, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122233173..122240852, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122101860-122102399 Neighboring gene uncharacterized LOC105370034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122109697-122110623 Neighboring gene MORN repeat containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122124874-122125860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4986 Neighboring gene transmembrane protein 120B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122165743-122166363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122194907-122195407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122204395-122204898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122207988-122208500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4987 Neighboring gene Sharpr-MPRA regulatory region 8824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122216872-122217390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122217391-122217909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122227166-122227882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122230665-122231496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122231502-122232042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122232583-122233123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122236367-122236906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122235825-122236366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122236907-122237446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122237447-122237986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4997 Neighboring gene ras homolog family member F, filopodia associated Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122248237-122249046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122249091-122249703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4998 Neighboring gene SET domain containing 1B, histone lysine methyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122252006-122252512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122276754-122277424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122278096-122278765 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122293687-122294886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122297907-122298424 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122298425-122298941 Neighboring gene Sharpr-MPRA regulatory region 2080 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene Sharpr-MPRA regulatory region 2229 Neighboring gene transcript inducer of AURKA lysosomal degradation Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326353-122326966 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326967-122327580 Neighboring gene proteasome 26S subunit, non-ATPase 9 Neighboring gene RNA, U7 small nuclear 170 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. The crosstalk between LINC01089 and hippo pathway inhibits osteosarcoma progression. Zhang H, et al. J Bone Miner Metab, 2022 Nov. PMID 36399257
    2. Long Non-Coding RNA 001089 is a Prognostic Marker and Inhibits Glioma Cells Proliferation and Invasion. Gu J, et al. Clin Lab, 2019 Mar 1. PMID 30868865
    3. LncRNA-LINC01089 inhibits lung adenocarcinoma cell proliferation and promotes apoptosis via sponging miR-543. Xu Y, et al. Tissue Cell, 2021 Oct. PMID 33892399
    4. LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer. Sas-Chen A, et al. EMBO Mol Med, 2016 Sep. PMID 27485121, Free PMC Article
    5. The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma. Zhi F, et al. PLoS One, 2015. PMID 26252651, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis.
      Title: Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis.
    2. LINC01089, suppressed by YY1, inhibits lung cancer progression by targeting miR-301b-3p/HPDG axis.
      Title: LINC01089, suppressed by YY1, inhibits lung cancer progression by targeting miR-301b-3p/HPDG axis.
    3. The crosstalk between LINC01089 and hippo pathway inhibits osteosarcoma progression.
      Title: The crosstalk between LINC01089 and hippo pathway inhibits osteosarcoma progression.
    4. LncRNA-LINC01089 inhibits lung adenocarcinoma cell proliferation and promotes apoptosis via sponging miR-543.
      Title: LncRNA-LINC01089 inhibits lung adenocarcinoma cell proliferation and promotes apoptosis via sponging miR-543.
    5. LINC01089 inhibits the progression of cervical cancer via inhibiting miR-27a-3p and increasing BTG2.
      Title: LINC01089 inhibits the progression of cervical cancer via inhibiting miR-27a-3p and increasing BTG2.
    6. LINC01089 suppresses lung adenocarcinoma cell proliferation and migration via miR-301b-3p/STARD13 axis.
      Title: LINC01089 suppresses lung adenocarcinoma cell proliferation and migration via miR-301b-3p/STARD13 axis.
    7. Glioma tissues exhibit loss of LINC01089 (LncRNA001089) expression, which is associated with poor prognosis in glioma patients.
      Title: Long Non-Coding RNA 001089 is a Prognostic Marker and Inhibits Glioma Cells Proliferation and Invasion.
    8. Interestingly, EGF rapidly downregulates LINC01089 (here renamed LncRNA Inhibiting Metastasis; LIMT) expression by enhancing histone deacetylation at the respective promoter.
      Title: LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer.
    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)

    Genotypes

    General gene information

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    Markers

    Potential readthrough

    Included gene: RHOF

    Other Names

    • long non coding RNA inhibiting metastasis

    Clone Names

    • FLJ37163, FLJ38855, AC084018.1

    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_002809.3 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC038786, BM669713

    2. NR_152735.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084018
      Related
      ENST00000542933.5

    3. NR_152736.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK311480, BM669713, CN398873

    4. NR_152737.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084018

    5. NR_152738.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084018, AK095700, AK311480, BM669713, CD516035

    6. NR_152739.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084018

    7. NR_152740.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084018, AK095700, AK311480, BG035222, BM669713

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      121795267..121802946 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      121791937..121799611 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_178538.2: Suppressed sequence

      Description
      NM_178538.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version

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