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LINC00539 long intergenic non-protein coding RNA 539 [ Homo sapiens (human) ]

Gene ID: 100652865, updated on 13-May-2022

Summary

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Official Symbol
LINC00539provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 539provided by HGNC
Primary source
HGNC:HGNC:43672
See related
Ensembl:ENSG00000224429 AllianceGenome:HGNC:43672
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
LINC00422
Expression
Broad expression in bone marrow (RPKM 1.5), testis (RPKM 1.2) and 22 other tissues See more
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Genomic context

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See LINC00539 in Genome Data Viewer
Location:
13q12.11
Exon count:
6
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (21303512..21344859, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (20496592..20539170, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (21877651..21918998, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370105 Neighboring gene estrogen-related receptor alpha pseudogene 2 Neighboring gene coiled-coil domain-containing protein 144B Neighboring gene mitochondrial intermediate peptidase pseudogene 3 Neighboring gene G protein-coupled receptor kinase 6 pseudogene 1 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 52 Neighboring gene RNA, 5S ribosomal pseudogene 25

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. Gene expression in proliferating human erythroid cells. Gubin AN, et al. Genomics, 1999 Jul 15. PMID 10409428
  2. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article

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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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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Other Names

  • long intergenic non-protein coding RNA 422

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_103840.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AL139380, BF185586, BQ007438, CD684045
    Related
    ENST00000692188.1

  2. NR_103841.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' exon and lacks three internal exons, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL139380, CD684045

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    21303512..21344859 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    20496592..20539170 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases