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LOC112543431 Sharpr-MPRA regulatory region 12053 [ Homo sapiens (human) ]

Gene ID: 112543431, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543431
Gene description
Sharpr-MPRA regulatory region 12053
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). It also displayed weak activation by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2018]
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Genomic context

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See LOC112543431 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (604809..605103)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (759175..759469)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (604809..605103)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene centrin 1 Neighboring gene RN7SK pseudogene 146 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:596737-596866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:597469-597968 Neighboring gene clusterin like 1 Neighboring gene uncharacterized LOC105371952 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:641155-642354 Neighboring gene TYMS opposite strand RNA Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:657377-657878 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:657879-658378 Neighboring gene thymidylate synthetase

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

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)

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_057382.1 

    Range
    101..395
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    604809..605103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    759175..759469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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