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LOC115995518 CRISPRi-validated cis-regulatory element chr3.3676 [ Homo sapiens (human) ]

Gene ID: 115995518, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995518
Gene description
CRISPRi-validated cis-regulatory element chr3.3676
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 GATA2 (GATA binding protein 2) 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 (128411602..128411787)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (131153209..131153394)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128130445..128130630)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14701 Neighboring gene RUVBL1 antisense RNA 1 Neighboring gene RuvB like AAA ATPase 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:127819055-127819574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14702 Neighboring gene Sharpr-MPRA regulatory region 11416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:127865444-127866013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14703 Neighboring gene RNA, U6 small nuclear 823, pseudogene Neighboring gene Sharpr-MPRA regulatory region 8761 Neighboring gene eukaryotic elongation factor, selenocysteine-tRNA specific Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:127945585-127946085 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:127999447-127999964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128001517-128002034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128004261-128004760 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128005625-128006126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128035068-128035620 Neighboring gene Sharpr-MPRA regulatory region 3031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128053445-128054066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128054067-128054686 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:128062271-128062684 Neighboring gene Sharpr-MPRA regulatory regions 13692 and 14760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128087685-128088185 Neighboring gene Sharpr-MPRA regulatory region 10596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128107303-128107892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128107893-128108480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128118070-128118864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128118865-128119659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128120455-128121248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128126077-128126958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128128140-128128788 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3677 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3678 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3679 Neighboring gene CRISPRi-FlowFISH-validated RPN1 regulatory element 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128146331-128146889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128150709-128151289 Neighboring gene uncharacterized LOC124909428 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128151290-128151869 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128151870-128152450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128154435-128155122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20483 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128170962-128171462 Neighboring gene uncharacterized LOC124909429

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_066599.1 

    Range
    101..286
    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
    128411602..128411787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_019805490.1 Reference GRCh38.p14 PATCHES

    Range
    280721..280906
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    131153209..131153394
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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