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LOC119407413 CRISPRi-FlowFISH-validated HDAC6 regulatory element 4 [ Homo sapiens (human) ]

Gene ID: 119407413, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119407413
Gene description
CRISPRi-FlowFISH-validated HDAC6 regulatory element 4
Gene type
biological region
Feature type(s)
regulatory: 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 negatively-acting cis-regulatory element for the HDAC6 (histone deacetylase 6) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Nov 2020]
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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 (49003655..49004155)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48414135..48414635)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48860065..48860565)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12141 Neighboring gene potassium voltage-gated channel subfamily D member 1 Neighboring gene GRIP1 associated protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48840212-48840468 Neighboring gene Sharpr-MPRA regulatory region 9113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29627 Neighboring gene Sharpr-MPRA regulatory region 2669 Neighboring gene transcription factor binding to IGHM enhancer 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48900209-48901072 Neighboring gene CRISPRi-FlowFISH-validated PQBP1 regulatory element 4 Neighboring gene Sharpr-MPRA regulatory region 13918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20833 Neighboring gene coiled-coil domain containing 120

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. 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)

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_070983.1 

    Range
    101..601
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    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
    49003655..49004155
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791820.1 Reference GRCh38.p14 PATCHES

    Range
    162490..162990
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48414135..48414635
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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