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LOC125384593 Sharpr-MPRA regulatory region 10094 [ Homo sapiens (human) ]

Gene ID: 125384593, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384593
Gene description
Sharpr-MPRA regulatory region 10094
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125384593 in Genome Data Viewer
Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (22534011..22534305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (22593461..22593755)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372563 Neighboring gene uncharacterized LOC105372564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22493383-22493884 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22543873-22544400 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22544401-22544926 Neighboring gene long intergenic non-protein coding RNA 261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22548490-22549308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22549309-22550126 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:22552037-22552636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22558127-22559082 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22559083-22560038 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22560039-22560994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22562671-22563242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:22563243-22563815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22565240-22565995 Neighboring gene forkhead box A2

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

Variation

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See variants in ClinVar

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_080916.1 

    Range
    101..395
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    22534011..22534305
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    22593461..22593755
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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