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LOC125387293 Sharpr-MPRA regulatory region 5066 [ Homo sapiens (human) ]

Gene ID: 125387293, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387293
Gene description
Sharpr-MPRA regulatory region 5066
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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50306052..50306346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52075656..52075950)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372656 Neighboring gene MPRA-validated peak4248 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48891163-48891664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48891665-48892164 Neighboring gene plaque enriched lncRNA in atherosclerotic and inflammatory bowel macrophage regulation Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48894009-48894546 Neighboring gene Sharpr-MPRA regulatory region 10045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48908810-48909546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48910660-48911160 Neighboring gene long intergenic non-protein coding RNA 1270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48921517-48922292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48925071-48925582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48925583-48926093 Neighboring gene long intergenic non-protein coding RNA 1271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48937461-48938045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48938046-48938631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48938632-48939216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18086 Neighboring gene uncharacterized LOC105372657 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:48971862-48972074

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_080968.1 

    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
    50306052..50306346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    52075656..52075950
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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