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LOC125146356 Sharpr-MPRA regulatory region 9655 [ Homo sapiens (human) ]

Gene ID: 125146356, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146356
Gene description
Sharpr-MPRA regulatory region 9655
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element by the Sharpr-MPRA technique (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, Apr 2022]
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Genomic context

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See LOC125146356 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92120439..92120733)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (89882667..89882961)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903608 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:92396360-92396534 Neighboring gene Sharpr-MPRA regulatory region 9082 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:92424907-92425482 Neighboring gene solute carrier organic anion transporter family member 3A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:92493309-92494181 Neighboring gene uncharacterized LOC124903557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:92517318-92517818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:92517819-92518319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:92555079-92555579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10111 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:92634162-92634898 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:92660697-92661288 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:92661469-92662168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:92662868-92663566 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:92667565-92668555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:92690101-92691004 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:92707869-92708626 Neighboring gene Sharpr-MPRA regulatory region 10912 Neighboring gene uncharacterized LOC107987227 Neighboring gene double homeobox A pseudogene 6

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

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_080286.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    92120439..92120733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    89882667..89882961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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