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LOC125384581 Sharpr-MPRA regulatory region 8773 [ Homo sapiens (human) ]

Gene ID: 125384581, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384581
Gene description
Sharpr-MPRA regulatory region 8773
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 LOC125384581 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 (11270661..11270955)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (11314307..11314601)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372527 Neighboring gene uncharacterized LOC105372528 Neighboring gene NANOG hESC enhancer GRCh37_chr20:11229310-11229856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:11241778-11242278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:11242279-11242779 Neighboring gene uncharacterized LOC124904960 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:11247394-11248593 Neighboring gene uncharacterized LOC339593 Neighboring gene uncharacterized LOC105372529 Neighboring gene ribosomal protein S11 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17548 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:11517622-11518319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:11589151-11589652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:11589653-11590152 Neighboring gene LIN28A pseudogene 3

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_080904.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    11270661..11270955
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    11314307..11314601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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