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LOC119407408 CRISPRi-validated e-HDAC6 enhancer [ Homo sapiens (human) ]

Gene ID: 119407408, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119407408
Gene description
CRISPRi-validated e-HDAC6 enhancer
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 and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as an active enhancer by reporter assays in K562 erythroleukemia cells. A subregion was validated as a positively-acting cis-regulatory element for each of the GATA1 (GATA binding protein 1), HDAC6 (histone deacetylase 6) and PLP2 (proteolipid protein 2) genes based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 cells. An overlapping subregion was additionally validated as a GATA1 and HDAC6 positively-acting cis-regulatory element by CRISPRi in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48800418..48801257)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48210911..48211750)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48658825..48659325)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ACAA2 pseudogene 1 Neighboring gene RNA, U6 small nuclear 29, pseudogene Neighboring gene CRISPRi-validated e-GATA1 enhancer Neighboring gene CRISPRi-FlowFISH-validated GATA1, HDAC6 and PLP2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated HDAC6, PLP2 and PQBP1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 5 Neighboring gene GATA binding protein 1 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 6 Neighboring gene CRISPRi-FlowFISH-validated PQBP1 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48659902-48660415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29613 Neighboring gene histone deacetylase 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20823 Neighboring gene ES cell expressed Ras

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 mapping of functional enhancer-promoter connections with CRISPR interference. Fulco CP, et al. Science, 2016 Nov 11. PMID 27708057, Free PMC Article
  2. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  3. 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

  • CRISPRi-FlowFISH-validated GATA1, HDAC6 and PLP2 regulatory element 2

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_070980.2 

    Range
    101..940
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    48800418..48801257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48210911..48211750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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