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LOC116216156 CRISPRi-validated cis-regulatory element chr11.4413 [ Homo sapiens (human) ]

Gene ID: 116216156, updated on 10-Dec-2024

Summary

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Gene symbol
LOC116216156
Gene description
CRISPRi-validated cis-regulatory element chr11.4413
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 TSKU (tsukushi, small leucine rich proteoglycan) gene on chromosome 11 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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See LOC116216156 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (76224432..76224639)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76154148..76154355)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (75935476..75935683)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75897726-75898505 Neighboring gene Wnt family member 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75918003-75918670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75920005-75920671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75920672-75921338 Neighboring gene uncharacterized LOC112268079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3780 Neighboring gene long intergenic non-protein coding RNA 2761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75941095-75941596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75944436-75944982 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75945530-75946076 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75946077-75946622 Neighboring gene tRNA-Pro (anticodon AGG) 2-4 Neighboring gene tRNA-Pro (anticodon TGG) 2-1

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_066921.1 

    Range
    101..308
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    76224432..76224639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    76154148..76154355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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