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LOC123833529 Sharpr-MPRA regulatory region 2122 [ Homo sapiens (human) ]

Gene ID: 123833529, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123833529
Gene description
Sharpr-MPRA regulatory region 2122
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP). 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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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116370734..116371320)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117554768..117555354)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116692189..116692483)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S5 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:116592289-116592790 Neighboring gene RPS5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24985 Neighboring gene dermatan sulfate epimerase Neighboring gene TSPY like 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88171 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:116644935-116645502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116646525-116647026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24986 Neighboring gene uncharacterized LOC100287467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24987 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116692481-116692981 Neighboring gene Sharpr-MPRA regulatory region 1381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116720114-116720614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116720615-116721115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17494 Neighboring gene keratin 18 pseudogene 22 Neighboring gene CBX3 pseudogene 9

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 17492

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_078183.2 

    Range
    101..687
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    116370734..116371320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    117554768..117555354
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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