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LOC116158508 CRISPRi-validated cis-regulatory element chr4.2840 [ Homo sapiens (human) ]

Gene ID: 116158508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158508
Gene description
CRISPRi-validated cis-regulatory element chr4.2840
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 MGARP (mitochondria localized glutamic acid rich protein) gene on chromosome 4 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:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (139178555..139178679)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (142498164..142498288)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (140099709..140099833)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene E74 like ETS transcription factor 2 Neighboring gene RNA, 7SL, cytoplasmic 382, pseudogene Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14B pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:140073148-140073731 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140076063-140076645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140076646-140077228 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140080143-140080726 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:140080727-140081308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140083181-140083798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140084443-140085075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140085076-140085707 Neighboring gene uncharacterized LOC105379412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15698 Neighboring gene RNA, 7SL, cytoplasmic 311, pseudogene Neighboring gene RNA, U6 small nuclear 506, 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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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_066650.1 

    Range
    101..225
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    139178555..139178679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    142498164..142498288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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