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    LINC02593 long intergenic non-protein coding RNA 2593 [ Homo sapiens (human) ]

    Gene ID: 100130417, updated on 17-Sep-2024

    Summary

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    Official Symbol
    LINC02593provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2593provided by HGNC
    Primary source
    HGNC:HGNC:53933
    See related
    Ensembl:ENSG00000223764 AllianceGenome:HGNC:53933
    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 prostate (RPKM 8.5), adrenal (RPKM 5.3) and 18 other tissues See more
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    Genomic context

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    See LINC02593 in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (916818..919692, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (346462..349336, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (852198..855072, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:802261-802760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2 Neighboring gene family with sequence similarity 41 member C Neighboring gene tubulin beta 8 class VIII pseudogene 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:833348-833508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3 Neighboring gene uncharacterized LOC284600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:848070-848570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:848571-849071 Neighboring gene collagen alpha-1(III) chain-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:855570-856506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:858348-858926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:860592-861138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:864095-864596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:865404-865904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:865905-866405 Neighboring gene sterile alpha motif domain containing 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:873315-874026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4 Neighboring gene NOC2 like nucleolar associated transcriptional repressor Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:893904-894761

    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. Identification of a five-lncRNA signature for predicting the risk of tumor recurrence in patients with breast cancer. Li J, et al. Int J Cancer, 2018 Nov 1. PMID 29707762, Free PMC Article
    2. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? Nathan JA, et al. EMBO J, 2013 Feb 20. PMID 23314748, Free PMC Article
    3. TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. Banks CA, et al. Mol Cell Proteomics, 2016 Nov. PMID 27609421, Free PMC Article
    4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Clone Names

    • FLJ39609, AL645608.1

    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_026874.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL645608, BC144023, BX108591, DB264280

    2. NR_122045.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site at an internal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AL645608, BC144023, BC144024, BX108591, DB264280
      Related
      ENST00000417705.1

    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
      916818..919692 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      346462..349336 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175912.2: Suppressed sequence

      Description
      NM_175912.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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