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LOC125418058 Sharpr-MPRA regulatory region 8261 [ Homo sapiens (human) ]

Gene ID: 125418058, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125418058
Gene description
Sharpr-MPRA regulatory region 8261
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125418058 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (30083171..30083465)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (28449091..28449385)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene glutamate ionotropic receptor kainate type subunit 1 Neighboring gene GRIK1 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18349 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:31022541-31023740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18350 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:31068852-31069038 Neighboring gene GRIK1 antisense RNA 1 Neighboring gene MPRA-validated peak4398 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:31300943-31301519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:31311600-31312101 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:31387153-31387691 Neighboring gene claudin 17 Neighboring gene long intergenic non-protein coding RNA 307

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_081084.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    30083171..30083465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    28449091..28449385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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