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LOC115995508 CRISPRi-validated cis-regulatory element chr3.1267 [ Homo sapiens (human) ]

Gene ID: 115995508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995508
Gene description
CRISPRi-validated cis-regulatory element chr3.1267
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 TRANK1 (tetratricopeptide repeat and ankyrin repeat containing 1) 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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See LOC115995508 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (36954887..36955096)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (36956258..36956467)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (36996378..36996587)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36863988-36864163 Neighboring gene long intergenic non-protein coding RNA 2033 Neighboring gene tetratricopeptide repeat and ankyrin repeat containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36899292-36899475 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36907187-36907362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19661 Neighboring gene CBX3 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19664 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36952104-36952272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19665 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:36964989-36965490 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:36965491-36965990 Neighboring gene Sharpr-MPRA regulatory region 3248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19668 Neighboring gene RNA, U6atac small nuclear 4, pseudogene Neighboring gene protease associated domain containing 1 pseudogene 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_066589.1 

    Range
    101..310
    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
    36954887..36955096
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    36956258..36956467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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