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LINC00506 long intergenic non-protein coding RNA 506 [ Homo sapiens (human) ]

Gene ID: 100846978, updated on 4-Mar-2025

Summary

Official Symbol
LINC00506provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 506provided by HGNC
Primary source
HGNC:HGNC:43557
See related
Ensembl:ENSG00000281392 AllianceGenome:HGNC:43557
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

See LINC00506 in Genome Data Viewer
Location:
3p12.1-p11.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (87089280..87157069)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (87163632..87231418)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (87138430..87206219)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene vestigial like family member 3 Neighboring gene MPRA-validated peak4738 silencer Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20109 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:87245748-87246279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20114 Neighboring gene microRNA 4795 Neighboring gene charged multivesicular body protein 2B

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
EBI GWAS Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
EBI GWAS Catalog

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_047469.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC107204, AC108709
    Related
    ENST00000629295.1
  2. NR_104153.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon and contains two alternate 3' exons, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC108709, DA542035

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    87089280..87157069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    87163632..87231418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)