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LINC02520 long intergenic non-protein coding RNA 2520 [ Homo sapiens (human) ]

Gene ID: 100505530, updated on 10-Oct-2023

Summary

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Official Symbol
LINC02520provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 2520provided by HGNC
Primary source
HGNC:HGNC:53511
See related
AllianceGenome:HGNC:53511
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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Location:
6p21.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (37507348..37536280)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37330909..37361315)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37475124..37504056)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986531 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37400679-37401180 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17140 Neighboring gene cap methyltransferase 1 Neighboring gene MPRA-validated peak5792 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:37427605-37428259 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:37448259-37448959 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37456899-37457744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24459 Neighboring gene coiled-coil domain containing 167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37480625-37481226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37481227-37481828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37483099-37483883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37483884-37484668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24462 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:37487335-37487506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37504191-37504738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37513395-37514004 Neighboring gene uncharacterized LOC124901312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24468 Neighboring gene Sharpr-MPRA regulatory region 3834 Neighboring gene microRNA 4462

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. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. Need AC, et al. Hum Mol Genet, 2009 Dec 1. PMID 19734545, Free PMC Article
  2. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
  3. The DNA sequence and analysis of human chromosome 6. Mungall AJ, et al. Nature, 2003 Oct 23. PMID 14574404
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
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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Clone Names

  • FLJ20341, FLJ45825

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_126057.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AK127725, AL353597

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
    37507348..37536280
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    37330909..37361315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001039791.1: Suppressed sequence

    Description
    NM_001039791.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZS52.1 GenPept UniProtKB/Swiss-Prot:Q6ZS52

Gene LinkOut

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