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LOC128462411 CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128391955-128393363 [ Homo sapiens (human) ]

Gene ID: 128462411, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462411
Gene description
CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128391955-128393363
Gene type
biological region
Feature type(s)
regulatory: silencer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for the ETS1 (ETS proto-oncogene 1, transcription factor) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in GM12878 lymphoblastoid cells. A subregion was also validated as an ETS1 regulatory element by CRISPRi-FlowFISH in Jurkat T cells. 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) massively parallel reporter assay (MPRA) in GM12878 cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (128522060..128523468)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (128555392..128556800)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902788 Neighboring gene uncharacterized LOC124902789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128292222-128292722 Neighboring gene Sharpr-MPRA regulatory region 2302 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:128318161-128319360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5720 Neighboring gene Sharpr-MPRA regulatory region 15716 Neighboring gene ETS proto-oncogene 1, transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5723 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:128362337-128363536 Neighboring gene Sharpr-MPRA regulatory region 9161 Neighboring gene uncharacterized LOC124902790 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:128401737-128402434 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:128402435-128403132 Neighboring gene microRNA 6090 Neighboring gene ETS1 antisense RNA 1

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-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 4054
  • CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128391955-128392615

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_149599.1 

    Range
    101..1509
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    128522060..128523468
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    128555392..128556800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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