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LOC125387253 Sharpr-MPRA regulatory region 14532 [ Homo sapiens (human) ]

Gene ID: 125387253, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387253
Gene description
Sharpr-MPRA regulatory region 14532
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (31602866..31603160)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (33327105..33327399)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene HM13 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30160423-30160964 Neighboring gene uncharacterized LOC107985416 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30162848-30163017 Neighboring gene RNA, U6 small nuclear 384, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:30172998-30173500 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:30173501-30174004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30175011-30175512 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:30178306-30178806 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:30178807-30179307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30180469-30181234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30182001-30182766 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr20:30182767-30183531 and GRCh37_chr20:30183532-30184297 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30185063-30185828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30185829-30186593 Neighboring gene VISTA enhancer hs480 Neighboring gene uncharacterized LOC105372588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30192859-30193529 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30193530-30194199 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30194246-30194824 Neighboring gene inhibitor of DNA binding 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 17684

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.

Genomic

  1. NG_080929.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    31602866..31603160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    33327105..33327399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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