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

Gene ID: 100846978, updated on 10-Oct-2023

Summary

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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

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See LINC00506 in Genome Data Viewer
Location:
3p12.1-p11.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (87089280..87157069)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (87163632..87231418)
105.20220307 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

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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. Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. Takata R, et al. Nat Genet, 2010 Sep. PMID 20676098
  2. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Eeles RA, et al. Nat Genet, 2009 Oct. PMID 19767753, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, 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
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

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_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_2023_10

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)
Nucleotide Protein
Heading Accession and Version

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