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LOC112163547 Sharpr-MPRA regulatory region 713 [ Homo sapiens (human) ]

Gene ID: 112163547, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163547
Gene description
Sharpr-MPRA regulatory region 713
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. A subregion was validated as a functional enhancer 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 unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). An overlapping accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC112163547 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131230024..131230386)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131269947..131270309)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (131714569..131714863)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene adhesion G protein-coupled receptor D1 Neighboring gene uncharacterized LOC107984452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131616699-131617331 Neighboring gene long intergenic non-protein coding RNA 1257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131689145-131689646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7360 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:131707318-131707489 Neighboring gene uncharacterized LOC105370082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131719246-131719855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131746328-131746828 Neighboring gene uncharacterized LOC107987177 Neighboring gene ribosomal protein S6 pseudogene 20

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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

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

  • ReSE screen-validated silencer GRCh37_chr12:131714735-131714931

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_056571.2 

    Range
    101..463
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    131230024..131230386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    131269947..131270309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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