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LOC125446276 Sharpr-MPRA regulatory region 9198 [ Homo sapiens (human) ]

Gene ID: 125446276, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125446276
Gene description
Sharpr-MPRA regulatory region 9198
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125446276 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (23509292..23509868)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (23092848..23093424)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (23527409..23527985)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene patched domain containing 1 Neighboring gene HIKESHI pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:23523568-23524107 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:23526452-23526963 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:23677931-23678536 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:23678537-23679142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:23682591-23683125 Neighboring gene Sharpr-MPRA regulatory region 11823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20704 Neighboring gene peroxiredoxin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20705 Neighboring gene acyl-CoA thioesterase 9

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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:23527475-23527985

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_081207.2 

    Range
    101..677
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    23509292..23509868
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    23092848..23093424
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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