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LINC01539 long intergenic non-protein coding RNA 1539 [ Homo sapiens (human) ]

Gene ID: 100505474, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01539provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1539provided by HGNC
Primary source
HGNC:HGNC:51307
See related
Ensembl:ENSG00000267712 AllianceGenome:HGNC:51307
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
Restricted expression toward testis (RPKM 8.1) See more
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Genomic context

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See LINC01539 in Genome Data Viewer
Location:
18q21.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (56083356..56137536, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (56286115..56340236, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (53750587..53804767, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3092 Neighboring gene long intergenic non-protein coding RNA 3069 Neighboring gene long intergenic non-protein coding RNA 1905 Neighboring gene small nucleolar RNA SNORA73 family Neighboring gene uncharacterized LOC105372132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13362 Neighboring gene NANOG hESC enhancer GRCh37_chr18:54019108-54019609 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:54080945-54081494 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:54087957-54088683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:54230563-54231064 Neighboring gene uncharacterized LOC105372135

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. 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

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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Markers

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_040025.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AK057336, AK058169
    Related
    ENST00000587904.5

  2. NR_040026.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons, includes two alternate exons, and uses an alternate splice site, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC006305, AK057336
    Related
    ENST00000591974.5

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    56083356..56137536 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    56286115..56340236 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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