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LOC112997596 Sharpr-MPRA regulatory region 13785 [ Homo sapiens (human) ]

Gene ID: 112997596, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997596
Gene description
Sharpr-MPRA regulatory region 13785
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 associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer 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 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57173364..57174148)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58001668..58002453)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56469649..56469943)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22576 Neighboring gene Sharpr-MPRA regulatory region 9364 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56389593-56390094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56391121-56391620 Neighboring gene MPRA-validated peak5252 silencer Neighboring gene RLIG1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22577 Neighboring gene Sharpr-MPRA regulatory region 13834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22581 Neighboring gene GC-rich promoter binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56498073-56498573 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:56507443-56507608 Neighboring gene uncharacterized LOC107986381 Neighboring gene TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) pseudogene

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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 22578
  • ATAC-STARR-seq lymphoblastoid silent region 16030
  • ATAC-STARR-seq lymphoblastoid silent region 16031
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:56469191-56469778

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_061595.3 

    Range
    101..885
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    57173364..57174148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    58001668..58002453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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