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LINC02540 long intergenic non-protein coding RNA 2540 [ Homo sapiens (human) ]

Gene ID: 105377860, updated on 10-Oct-2023

Summary

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Official Symbol
LINC02540provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 2540provided by HGNC
Primary source
HGNC:HGNC:53573
See related
Ensembl:ENSG00000236635 AllianceGenome:HGNC:53573
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
Low expression observed in reference dataset See more
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Genomic context

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See LINC02540 in Genome Data Viewer
Location:
6q14.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (76522448..76593623, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (77699529..77770675, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (77232165..77303340, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:76820442-76820982 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:76820983-76821521 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:76829469-76830098 Neighboring gene RNA, U6 small nuclear 248, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:76830099-76830727 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:77011078-77011263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:77088669-77089170 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:77132408-77132991 Neighboring gene NANOG hESC enhancer GRCh37_chr6:77135272-77135773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:77161364-77161864 Neighboring gene RNA, U6 small nuclear 261, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:77264768-77265312 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:77270552-77271091 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:77271631-77272170 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:77272171-77272708 Neighboring gene RNA, U6 small nuclear 84, pseudogene Neighboring gene 52 kDa repressor of the inhibitor of the protein kinase-like Neighboring gene uncharacterized LOC105377861 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:77413212-77414041 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94632 Neighboring gene NANOG hESC enhancer GRCh37_chr6:77418612-77419138

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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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)

Genotypes

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_149101.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL591030
    Related
    ENST00000455554.2

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    76522448..76593623 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    77699529..77770675 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases