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LOC113875009 Sharpr-MPRA regulatory region 14523 [ Homo sapiens (human) ]

Gene ID: 113875009, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875009
Gene description
Sharpr-MPRA regulatory region 14523
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. It 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC113875009 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (129666332..129666626)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (127985120..127985414)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (128800309..128800603)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 13828 Neighboring gene OCRL inositol polyphosphate-5-phosphatase Neighboring gene NANOG hESC enhancer GRCh37_chrX:128698883-128699384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128734568-128735068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128735069-128735569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128783429-128783930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128783931-128784430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29917 Neighboring gene apelin Neighboring gene uncharacterized LOC105373334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20978 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:128851647-128852238 Neighboring gene uncharacterized LOC124905214 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:128852239-128852830

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_063197.1 

    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
    129666332..129666626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    127985120..127985414
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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