U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC111818956 Sharpr-MPRA regulatory regions 5244/11724 and 13137 [ Homo sapiens (human) ]

Gene ID: 111818956, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC111818956
Gene description
Sharpr-MPRA regulatory regions 5244/11724 and 13137
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 includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. Two overlapping subregions were also validated as functional enhancers by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). One subregion also displayed weak activation by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 23:Low, low signal proximal to active elements). This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (12436016..12437036)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (12715598..12716618)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (12293969..12294523)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12277688-12278525 Neighboring gene Putative protein FAM90A2P Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:12283742-12284386 Neighboring gene ALG1 like 12, pseudogene Neighboring gene family with sequence similarity 86 member B2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:12292881-12293524 Neighboring gene FAM86B2 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12302867-12303469 Neighboring gene defensin beta 109E (pseudogene) Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12338855-12339594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12344744-12345435 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12354567-12355426 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:12355427-12356286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:12358763-12359264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:12368735-12369234

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 18946
  • ATAC-STARR-seq lymphoblastoid silent region 18947
  • H3K27ac hESC enhancer GRCh37_chr8:12293525-12294167
  • Sharpr-MPRA regulatory region 11724
  • Sharpr-MPRA regulatory region 13137
  • Sharpr-MPRA regulatory region 5244

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_056203.3 

    Range
    101..1121
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    12436016..12437036
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    12715598..12716618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases