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LOC125146360 Sharpr-MPRA regulatory region 11279 [ Homo sapiens (human) ]

Gene ID: 125146360, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146360
Gene description
Sharpr-MPRA regulatory region 11279
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 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 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125146360 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (96340800..96341359)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (94105385..94105944)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NR2F2 antisense RNA 1 Neighboring gene uncharacterized LOC124903584 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:96794933-96796132 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:96811550-96812164 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:96816434-96817633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96876956-96877918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:96885110-96885629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96884589-96885109 Neighboring gene uncharacterized LOC101927263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96897481-96898380 Neighboring gene microRNA 1469 Neighboring gene nuclear receptor subfamily 2 group F member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96901703-96902545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:96905583-96906432 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:96934820-96936019 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:96943980-96944194 Neighboring gene tubulin alpha pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 9726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96959267-96960130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96960131-96960994 Neighboring gene phosphoglycerate mutase 1 pseudogene 12

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:96884069-96884588

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_080290.2 

    Range
    101..660
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    96340800..96341359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    94105385..94105944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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