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LOC115995533 CRISPRi-validated cis-regulatory element chr3.5052 [ Homo sapiens (human) ]

Gene ID: 115995533, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995533
Gene description
CRISPRi-validated cis-regulatory element chr3.5052
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 MRPL47 (mitochondrial ribosomal protein L47) 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 (179301641..179302057)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (182105477..182105893)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (179019429..179019845)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA25 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14913 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:178905170-178905394 Neighboring gene potassium calcium-activated channel subfamily M regulatory beta subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:178980593-178981094 Neighboring gene LRR binding FLII interacting protein 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 12572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:179008749-179009491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20865 Neighboring gene zinc finger protein 639 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:179065206-179065735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20866 Neighboring gene mitofusin 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_066614.1 

    Range
    101..517
    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
    179301641..179302057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    182105477..182105893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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