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LOC116158526 CRISPRi-validated cis-regulatory element chr5.4044 [ Homo sapiens (human) ]

Gene ID: 116158526, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158526
Gene description
CRISPRi-validated cis-regulatory element chr5.4044
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a cis-regulatory element for the LARP1 (La ribonucleoprotein 1, translational regulator) gene on chromosome 5 based on multiplex CRISPR/Cas9-mediated perturbation in K562 erythroleukemia cells. An overlapping subregion was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), and it additionally displayed repressive activity by Sharpr-MPRA in K562 cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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See LOC116158526 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (154653469..154654421)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (155187456..155188408)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (154033029..154033981)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83489 Neighboring gene CIR1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153962321-153962904 Neighboring gene CIR1P1-LARP1 intergenic CAGE-defined high expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153983238-153983756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153983757-153984274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153990742-153991511 Neighboring gene microRNA 3141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:154026765-154027427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:154070395-154071038 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:154076347-154076858 Neighboring gene microRNA 1303 Neighboring gene La ribonucleoprotein 1, translational regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:154091948-154092494 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83490 Neighboring gene RNA, 7SL, cytoplasmic 803, pseudogene

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 10572

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_066668.2 

    Range
    101..1053
    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
    154653469..154654421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    155187456..155188408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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