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LOC115995523 CRISPRi-validated cis-regulatory element chr3.4087 [ Homo sapiens (human) ]

Gene ID: 115995523, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995523
Gene description
CRISPRi-validated cis-regulatory element chr3.4087
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) gene on chromosome 3 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. An 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 HepG2 liver carcinoma cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (138875636..138876369)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (141616630..141617363)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (138594478..138595211)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta Neighboring gene ribosomal protein L23a pseudogene 40 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14766 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 25 Neighboring gene Sharpr-MPRA regulatory region 9070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138562234-138562975 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138581611-138582152 Neighboring gene Sharpr-MPRA regulatory region 8152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138598027-138598906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:138598907-138599785 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 3 Neighboring gene uncharacterized LOC124906289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14767

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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_chr3:138594654-138594839

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_066604.1 

    Range
    101..834
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    138875636..138876369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    141616630..141617363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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