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LINC00501 long intergenic non-protein coding RNA 501 [ Homo sapiens (human) ]

Gene ID: 100820709, updated on 6-Nov-2023

Summary

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Official Symbol
LINC00501provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 501provided by HGNC
Primary source
HGNC:HGNC:43439
See related
Ensembl:ENSG00000203645 AllianceGenome:HGNC:43439
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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Location:
3q26.32
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (177294442..177323435)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (180097600..180126595)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (177012230..177041223)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene TBL1X/Y related 1 Neighboring gene Sharpr-MPRA regulatory region 13561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:176870313-176870813 Neighboring gene RNA, U6 small nuclear 681, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10853 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:176911488-176912078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:176914847-176915356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:176915357-176915864 Neighboring gene uncharacterized LOC107986053 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:177001817-177002549 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177006212-177006426 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:177011460-177012659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20838 Neighboring gene MPRA-validated peak4933 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20839 Neighboring gene Sharpr-MPRA regulatory region 10654 Neighboring gene Sharpr-MPRA regulatory region 4767 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177062319-177062838 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:177063359-177063876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20842 Neighboring gene Sharpr-MPRA regulatory region 9868 Neighboring gene argininosuccinate synthetase 1 pseudogene 7 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:177077317-177078158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177083633-177084134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20847 Neighboring gene MPRA-validated peak4934 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:177174687-177175886 Neighboring gene long intergenic non-protein coding RNA 578 Neighboring gene NANOG hESC enhancer GRCh37_chr3:177205476-177205977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177234333-177235097 Neighboring gene RN7SK pseudogene 52 Neighboring gene uncharacterized LOC124906306

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

What's a GeneRIF?
  1. The LINC00501-HSP90B1-STAT3 positive feedback loop promotes malignant behavior in gastric cancer cells.
    Title: The LINC00501-HSP90B1-STAT3 positive feedback loop promotes malignant behavior in gastric cancer cells.
  2. Upregulation of LINC00501 by H3K27 acetylation facilitates gastric cancer metastasis through activating epithelial-mesenchymal transition and angiogenesis.
    Title: Upregulation of LINC00501 by H3K27 acetylation facilitates gastric cancer metastasis through activating epithelial-mesenchymal transition and angiogenesis.
Submit: New GeneRIF Correction

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_047465.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC117465
    Related
    ENST00000425388.1

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    177294442..177323435
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    180097600..180126595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases