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LINC02539 long intergenic non-protein coding RNA 2539 [ Homo sapiens (human) ]

Gene ID: 100507406, updated on 10-Oct-2023

Summary

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Official Symbol
LINC02539provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 2539provided by HGNC
Primary source
HGNC:HGNC:53572
See related
Ensembl:ENSG00000234956 AllianceGenome:HGNC:53572
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 1.3) See more
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Genomic context

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Location:
6q23.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (137730170..137739037, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (138918593..138927460, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (138051307..138060174, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901411 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90467 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:138020371-138021570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17586 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:138039958-138040164 Neighboring gene PTPN11 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25150 Neighboring gene wound and keratinocyte migration associated lncRNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25154 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:138196296-138197495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138200115-138200697 Neighboring gene TNF alpha induced protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25156 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:138246817-138248016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17592 Neighboring gene long intergenic non-protein coding RNA 2865 Neighboring gene suppressor of inflammatory macrophage apoptosis lncRNA

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)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Other Names

  • RP11-356I2.2

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_121618.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AL357060, BQ011120, N41668
    Related
    ENST00000411615.5

  2. NR_121619.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL357060, BF970945, BQ011120
    Related
    ENST00000668179.1

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    137730170..137739037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    138918593..138927460 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Molecular Biology Databases