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LOC116309162 CRISPRi-validated cis-regulatory element chrX.2695 [ Homo sapiens (human) ]

Gene ID: 116309162, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116309162
Gene description
CRISPRi-validated cis-regulatory element chrX.2695
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a high-confidence cis-regulatory element for both the ABCD1 (ATP binding cassette subfamily D member 1) and IRAK1 (interleukin 1 receptor associated kinase 1) genes on chromosome X based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC116309162 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153985283..153986017)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152258993..152259727)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153250743..153251468)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene host cell factor C1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153234675-153234853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153235869-153236718 Neighboring gene HCFC1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21079 Neighboring gene transmembrane protein 187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30047 Neighboring gene microRNA 3202-2 Neighboring gene microRNA 3202-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153265676-153266176 Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153277410-153278394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153278395-153279378 Neighboring gene interleukin 1 receptor associated kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153285318-153286287 Neighboring gene microRNA 718

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. Human renin binding protein: complete genomic sequence and association of an intronic T/C polymorphism with the prorenin level in males. Knöll A, et al. Hum Mol Genet, 1997 Sep. PMID 9285790
  2. 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
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  5. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 30049
  • ATAC-STARR-seq lymphoblastoid active region 30050

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_067129.2 

    Range
    101..835
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153985283..153986017
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152258993..152259727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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