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

Gene ID: 100130417, updated on 10-Oct-2023

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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Location:
1p36.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (916818..919692, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (346462..349336, complement)
105.20220307 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)

Genotypes

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_2023_10

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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