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LOC116268464 CRISPRi-validated cis-regulatory element chr14.2493 [ Homo sapiens (human) ]

Gene ID: 116268464, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116268464
Gene description
CRISPRi-validated cis-regulatory element chr14.2493
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 EIF5 (eukaryotic translation initiation factor 5) gene on chromosome 14 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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See LOC116268464 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (103313664..103314107)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (97549563..97550006)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (103780001..103780444)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103747748-103748546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103748547-103749344 Neighboring gene RAP2C pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103753471-103754274 Neighboring gene ribosomal protein L17 pseudogene 4 Neighboring gene uncharacterized LOC105370686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103768183-103768683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103777212-103778188 Neighboring gene uncharacterized LOC105378183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6148 Neighboring gene EIF5 divergent transcript Neighboring gene eukaryotic translation initiation factor 5

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_066979.1 

    Range
    101..544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    103313664..103314107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    97549563..97550006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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