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LOC113839543 Sharpr-MPRA regulatory region 7975 [ Homo sapiens (human) ]

Gene ID: 113839543, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839543
Gene description
Sharpr-MPRA regulatory region 7975
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an 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). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (16768787..16769685)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (16780630..16781528)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (16769389..16769683)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902125 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16435259-16436458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28216 Neighboring gene basonuclin zinc finger protein 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485208-16485860 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485861-16486512 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16514088-16514670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16514766-16515334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16515335-16515901 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16515916-16516476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16626962-16627495 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16653272-16653772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16704398-16705152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16706560-16707060 Neighboring gene VISTA enhancer hs307 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16726395-16726896 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16730147-16730694 Neighboring gene BNC2 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:16795834-16796335 Neighboring gene Sharpr-MPRA regulatory region 8712 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16809986-16810513 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16810514-16811042 Neighboring gene LSM1 homolog, mRNA degradation associated pseudogene 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_107116 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16867432-16868631 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16921666-16922273 Neighboring gene uncharacterized LOC124902126 Neighboring gene uncharacterized LOC105375983

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_chr9:16768785-16769530

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_063154.2 

    Range
    101..999
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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
    16768787..16769685
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    16780630..16781528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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