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LOC125387310 Sharpr-MPRA regulatory region 537 [ Homo sapiens (human) ]

Gene ID: 125387310, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387310
Gene description
Sharpr-MPRA regulatory region 537
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125387310 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (56804633..56805512)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (58582636..58583515)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55286729-55287342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55287343-55287956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55311142-55311780 Neighboring gene prothymosin alpha pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55317881-55318380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55334559-55335162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55335163-55335765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55350371-55351220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55363417-55364176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55364177-55364935 Neighboring gene RNA, U6 small nuclear 929, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55381821-55382451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55382452-55383081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55383713-55384341 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55406913-55407706 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55407707-55408500 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:55423625-55423770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55447159-55447691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55450301-55450946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55468204-55468808 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55472313-55472844 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55499864-55500713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55533349-55533974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55543166-55543675 Neighboring gene uncharacterized LOC105372683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55570502-55571030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55578655-55579522 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:55589742-55589905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55604837-55605336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55619775-55620276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55640151-55640652 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:55646149-55646712 Neighboring gene uncharacterized LOC105372685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55707263-55707764

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55379697-55380568

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_081035.2 

    Range
    101..980
    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
    56804633..56805512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    58582636..58583515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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