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LOC125467755 Sharpr-MPRA regulatory region 15663 [ Homo sapiens (human) ]

Gene ID: 125467755, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467755
Gene description
Sharpr-MPRA regulatory region 15663
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element 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 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125467755 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 (56820156..56820450)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (56118960..56119254)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:56790193-56790694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29694 Neighboring gene ubiquinol-cytochrome c reductase binding protein pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56796358-56796874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56796875-56797391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56798078-56798669 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56798670-56799260 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56799261-56799852 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56804396-56805293 Neighboring gene negative regulator of P-body association Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:56805294-56806192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29701 Neighboring gene spindlin family member 3 Neighboring gene SPIN2 family pseudogene 1

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

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_081226.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    56820156..56820450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    56118960..56119254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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