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LOC125371506 Sharpr-MPRA regulatory region 8466 [ Homo sapiens (human) ]

Gene ID: 125371506, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371506
Gene description
Sharpr-MPRA regulatory region 8466
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 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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Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (31419172..31420317)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (33937724..33938869)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1791 Neighboring gene teashirt zinc finger homeobox 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31702527-31703027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:31744812-31745810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:31745811-31746808 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:31779704-31780204 Neighboring gene NANOG hESC enhancer GRCh37_chr19:31809776-31810277 Neighboring gene TSHZ3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31831709-31832233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31843549-31844050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31844051-31844550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31845493-31846136 Neighboring gene uncharacterized LOC124904794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31879539-31880040 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:31909131-31910077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:31939361-31939861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:31990532-31991116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:31991117-31991701 Neighboring gene long intergenic non-protein coding RNA 2841 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:32043944-32045143 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:32065114-32065673 Neighboring gene long intergenic non-protein coding RNA 3103

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

General gene information

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Other Names

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:31910078-31911024

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_080807.2 

    Range
    101..1246
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    31419172..31420317
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    33937724..33938869
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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