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LOC116309154 CRISPRi-validated cis-regulatory element chrX.1004 [ Homo sapiens (human) ]

Gene ID: 116309154, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116309154
Gene description
CRISPRi-validated cis-regulatory element chrX.1004
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 PLP2 (proteolipid protein 2) gene on chromosome X based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49147999..49148149)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48559736..48559886)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49004334..49004484)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene WD repeat domain 45 Neighboring gene RNA, U4 small nuclear 52, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29628 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48974390-48974501 Neighboring gene G-patch domain and KOW motifs Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48979755-48980408 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48980409-48981062 Neighboring gene uncharacterized LOC105373195 Neighboring gene CRISPRi-validated cis-regulatory element chrX.1005 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 1 Neighboring gene RNA, 7SL, cytoplasmic 262, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49019052-49019751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20837 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49022309-49023254 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 10 Neighboring gene MAGI family member, X-linked

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_067121.1 

    Range
    101..251
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    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
    49147999..49148149
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791820.1 Reference GRCh38.p14 PATCHES

    Range
    306950..307100
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48559736..48559886
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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