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LOC125446269 Sharpr-MPRA regulatory region 11092 [ Homo sapiens (human) ]

Gene ID: 125446269, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446269
Gene description
Sharpr-MPRA regulatory region 11092
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 (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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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See LOC125446269 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (9530809..9531386)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (9113391..9113972)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905242 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9260651-9261238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29398 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:9320474-9321673 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:9374111-9375310 Neighboring gene uncharacterized LOC107985634 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9382495-9382700 Neighboring gene chromodomain Y like protein pseudogene Neighboring gene MPRA-validated peak7356 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9420158-9420316 Neighboring gene Sharpr-MPRA regulatory region 2097 Neighboring gene Sharpr-MPRA regulatory region 7028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9431698-9432526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9471641-9472141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9490972-9491496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9500568-9501137 Neighboring gene transducin beta like 1 X-linked Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528031-9528532 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528533-9529032 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9536306-9537137 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9537138-9537968 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9554716-9555236 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9555237-9555756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561459-9561960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561961-9562460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9603687-9604186 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:9629664-9630863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9650484-9650984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9675799-9676456 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9676457-9677113 Neighboring gene uncharacterized LOC105373126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9732793-9733294 Neighboring gene G protein-coupled receptor 143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9761068-9761591 Neighboring gene shroom family member 2 Neighboring gene eukaryotic translation initiation factor 5 pseudogene 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
  3. 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

  • ATAC-STARR-seq lymphoblastoid silent region 20653
  • NANOG-H3K27ac hESC enhancer GRCh37_chrX:9498855-9499426

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_081200.2 

    Range
    101..678
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    9530809..9531386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    9113391..9113972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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