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LOC115995516 CRISPRi-validated cis-regulatory element chr3.3177 [ Homo sapiens (human) ]

Gene ID: 115995516, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995516
Gene description
CRISPRi-validated cis-regulatory element chr3.3177
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 CD47 (CD47 molecule) 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 (108104250..108104804)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (110824038..110824592)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (107823097..107823651)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906265 Neighboring gene CD47 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14592 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14593 Neighboring gene uncharacterized LOC105374031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:107843148-107843648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20214 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:107849902-107851101 Neighboring gene long intergenic non-protein coding RNA 1215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20215 Neighboring gene intraflagellar transport 57 Neighboring gene MPRA-validated peak4760 silencer Neighboring gene MPRA-validated peak4761 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20216 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:107941185-107941478

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_066597.1 

    Range
    101..655
    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
    108104250..108104804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    110824038..110824592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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