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LOC124292589 Sharpr-MPRA regulatory region 15637 [ Homo sapiens (human) ]

Gene ID: 124292589, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124292589
Gene description
Sharpr-MPRA regulatory region 15637
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 histone modification. 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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (69307511..69308127)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (81474152..81474768)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (71922749..71923043)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene tight junction protein 2 Neighboring gene uncharacterized LOC124902175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28447 Neighboring gene Sharpr-MPRA regulatory region 4978 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71856696-71857196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71857197-71857697 Neighboring gene uncharacterized LOC124902176 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:71897736-71898504 Neighboring gene NANOG hESC enhancer GRCh37_chr9:71898508-71899009 Neighboring gene BRAF-activated non-protein coding RNA Neighboring gene endosomal transmembrane epsin interactor 1 Neighboring gene uncharacterized LOC124902177 Neighboring gene Sharpr-MPRA regulatory region 1664

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 hESC enhancer GRCh37_chr9:71922427-71923012

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_078833.2 

    Range
    101..717
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    69307511..69308127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    81474152..81474768
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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