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LOC113875028 Sharpr-MPRA regulatory region 7060 [ Homo sapiens (human) ]

Gene ID: 113875028, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875028
Gene description
Sharpr-MPRA regulatory region 7060
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer; flanking open chromatin of candidate enhancers) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113875028 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 (47048007..47048301)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46455008..46455302)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (46907409..46907703)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29577 Neighboring gene RP2 activator of ARL3 GTPase Neighboring gene long intergenic non-protein coding RNA 1545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29578 Neighboring gene Sharpr-MPRA regulatory region 4088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20797 Neighboring gene jade family PHD finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29579 Neighboring gene RNA, U6 small nuclear 1189, pseudogene Neighboring gene regucalcin Neighboring gene uncharacterized LOC105373193 Neighboring gene uncharacterized LOC107985720

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_063216.1 

    Range
    101..395
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    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
    47048007..47048301
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46455008..46455302
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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