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LOC115995536 CRISPRi-validated cis-regulatory element chr3.5443 [ Homo sapiens (human) ]

Gene ID: 115995536, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995536
Gene description
CRISPRi-validated cis-regulatory element chr3.5443
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 cis-regulatory element for the ST6GAL1 (ST6 beta-galactoside alpha-2,6-sialyltransferase 1) gene on chromosome 3 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:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (186871297..186871900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (189689089..189689692)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (186589086..186589689)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14988 Neighboring gene MCF2L2 pseudogene 1 Neighboring gene adiponectin enhancer region Neighboring gene adiponectin, C1Q and collagen domain containing Neighboring gene ADIPOQ antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6282 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186582731-186583380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186586160-186586957 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186591921-186592909 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186597846-186598346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186598347-186598847 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186604299-186605262 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186605263-186606225 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:186611033-186611552 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:186612594-186613114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186614677-186615197 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:186615198-186615717 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:186615718-186616238 Neighboring gene ribosomal protein S20 pseudogene 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186626722-186627417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:186627418-186628112 Neighboring gene ribosomal protein L29 pseudogene 9

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_066617.1 

    Range
    101..704
    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
    186871297..186871900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    189689089..189689692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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