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LOC125371427 Sharpr-MPRA regulatory region 1296 [ Homo sapiens (human) ]

Gene ID: 125371427, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371427
Gene description
Sharpr-MPRA regulatory region 1296
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 LOC125371427 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (55763238..55763532)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (55966366..55966660)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene transcription factor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13360 Neighboring gene uncharacterized LOC105372126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:53295077-53295576 Neighboring gene ribosomal protein L21 pseudogene 126 Neighboring gene uncharacterized LOC105372130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:53388528-53389317 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:53420614-53421813 Neighboring gene long intergenic non-protein coding RNA 1415 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:53500200-53501399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:53517802-53518302 Neighboring gene uncharacterized LOC107985183 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:53525319-53525818

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_080697.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    55763238..55763532
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    55966366..55966660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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