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LOC113002593 Sharpr-MPRA regulatory region 10457 [ Homo sapiens (human) ]

Gene ID: 113002593, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113002593
Gene description
Sharpr-MPRA regulatory region 10457
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). An overlapping accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (78597026..78597370)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79078460..79078804)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (77892849..77893143)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77655493-77656089 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77656090-77656686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16120 Neighboring gene SCAMP1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:77687375-77687953 Neighboring gene secretory carrier membrane protein 1 Neighboring gene MPRA-validated peak5302 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77753154-77753763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77788199-77788702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22709 Neighboring gene Sharpr-MPRA regulatory region 4849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77800693-77801201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77805941-77806562 Neighboring gene LHFPL tetraspan subfamily member 2 Neighboring gene Sharpr-MPRA regulatory region 4833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77828783-77829282 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77838469-77839288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77839289-77840106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22713 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:77911679-77912878 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:77922186-77922385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77928669-77929170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77929171-77929670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16123 Neighboring gene uncharacterized LOC124900191 Neighboring gene high mobility group box 1 pseudogene 21 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:77995230-77996429 Neighboring gene Sharpr-MPRA regulatory region 2428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22719

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ReSE screen-validated silencer GRCh37_chr5:77892989-77893193

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_061604.2 

    Range
    101..445
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    78597026..78597370
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    79078460..79078804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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