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LOC116158514 CRISPRi-validated cis-regulatory element chr5.1234 [ Homo sapiens (human) ]

Gene ID: 116158514, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158514
Gene description
CRISPRi-validated cis-regulatory element chr5.1234
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 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 HMGCS1 (3-hydroxy-3-methylglutaryl-CoA synthase 1) gene on chromosome 5 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (43320854..43321182)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (43573689..43574017)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (43320956..43321284)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NIM1 serine/threonine protein kinase Neighboring gene tubulin alpha pseudogene 14 Neighboring gene Sharpr-MPRA regulatory region 4627 Neighboring gene 3-hydroxy-3-methylglutaryl-CoA synthase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22537 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:43313910-43314426 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:43314427-43314941 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:43315036-43316235 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:43335752-43336951 Neighboring gene 60S acidic ribosomal protein P1-like Neighboring gene C-C motif chemokine ligand 28 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15994

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

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_066656.1 

    Range
    101..429
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    43320854..43321182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    43573689..43574017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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