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LOC117125590 CRISPRi-FlowFISH-validated DNASE2 regulatory element 2 [ Homo sapiens (human) ]

Gene ID: 117125590, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117125590
Gene description
CRISPRi-FlowFISH-validated DNASE2 regulatory element 2
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 (DHS) and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for the DNASE2 (deoxyribonuclease 2, lysosomal) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. A subregion identified as an erythroid DHS site was shown to function an enhancer that can activate the KLF1 (KLF transcription factor 1) promoter by reporter assays in K562 cells. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12883611..12884131)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13008060..13008580)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (12994425..12994945)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microtubule associated serine/threonine kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12963003-12963503 Neighboring gene microRNA 6794 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:12975591-12976379 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:12976380-12977167 Neighboring gene Sharpr-MPRA regulatory region 6054 Neighboring gene deoxyribonuclease 2, lysosomal Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated DNASE2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10180 Neighboring gene CRISPRi-FlowFISH-validated CALR, DHPS, JUNB, PRDX2, RAD23A, RNASEH2A and WDR83OS regulatory element Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14090 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:13001481-13002118 and GRCh37_chr19:13002119-13002756 Neighboring gene KLF transcription factor 1 Neighboring gene glutaryl-CoA dehydrogenase Neighboring gene ribosomal protein S6 pseudogene 25

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. Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors. Xiong Q, et al. BMC Genomics, 2013 Aug 28. PMID 23985037, Free PMC Article
  2. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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

  • KLF1-V enhancer

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_068128.1 

    Range
    101..621
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    12883611..12884131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13008060..13008580
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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