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LOC125467790 Sharpr-MPRA regulatory region 6851 [ Homo sapiens (human) ]

Gene ID: 125467790, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467790
Gene description
Sharpr-MPRA regulatory region 6851
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jun 2022]
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Genomic context

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Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (149470958..149471252)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (147736698..147736992)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ALF transcription elongation factor 2 Neighboring gene RN7SK pseudogene 267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:148228003-148228504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:148228505-148229004 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148264804-148265396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30014 Neighboring gene uncharacterized LOC122319696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148517664-148518235 Neighboring gene uncharacterized LOC107985667 Neighboring gene IDS recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148585415-148585963 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:148586087-148586588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30015 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:148591963-148593162 Neighboring gene Sharpr-MPRA regulatory region 15241 Neighboring gene IDSP1 recombination region Neighboring gene iduronate 2-sulfatase Neighboring gene iduronate 2-sulfatase 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_081259.1 

    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
    149470958..149471252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    147736698..147736992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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