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LOC125368548 Sharpr-MPRA regulatory region 7933 [ Homo sapiens (human) ]

Gene ID: 125368548, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125368548
Gene description
Sharpr-MPRA regulatory region 7933
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC125368548 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (11980430..11982044)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (12143144..12144758)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (11980429..11982043)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene G protein subunit alpha L Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9301 Neighboring gene uncharacterized LOC101927511 Neighboring gene metallophosphoesterase 1 Neighboring gene CRISPRi-validated cis-regulatory element chr18.397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:11951641-11952330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13098 Neighboring gene inositol monophosphatase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12038197-12038698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13099 Neighboring gene kinesin-like protein KIF1C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12058991-12059532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12059533-12060072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12060615-12061154 Neighboring gene single stranded DNA binding protein 4 pseudogene

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 9302

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_080663.2 

    Range
    101..1715
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    11980430..11982044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    12143144..12144758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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