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LOC116216145 CRISPRi-validated cis-regulatory element chr11.3247 [ Homo sapiens (human) ]

Gene ID: 116216145, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116216145
Gene description
CRISPRi-validated cis-regulatory element chr11.3247
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 ATG2A (autophagy related 2A) 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 LOC116216145 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 (65479574..65479797)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65472877..65473100)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65247045..65247268)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65222520-65222823 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:65226769-65227414 Neighboring gene FAU pseudogene 4 Neighboring gene NEAT1-MALAT1 intergenic CAGE-defined mid-level expression enhancer Neighboring gene CRISPRi-validated cis-regulatory element chr11.3243 Neighboring gene NEAT1-MALAT1 intergenic CAGE-defined high expression enhancer Neighboring gene enhancer lncRNA neighbor of NEAT1 and MALAT1 Neighboring gene NEAT1-MALAT1 intergenic CAGE-defined low expression enhancer Neighboring gene VISTA enhancer hs1759 Neighboring gene long intergenic non-protein coding RNA 2736 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65259133-65259634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65260440-65260950 Neighboring gene Sharpr-MPRA regulatory region 14387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4977 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:65264508-65265707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4983 Neighboring gene metastasis associated lung adenocarcinoma transcript 1 Neighboring gene TALAM1 transcript, MALAT1 antisense RNA Neighboring gene MALAT1-associated small cytoplasmic RNA

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_066910.1 

    Range
    101..324
    Download
    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
    65479574..65479797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65472877..65473100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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