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LOC116276504 CRISPRi-validated cis-regulatory element chr19.2258 [ Homo sapiens (human) ]

Gene ID: 116276504, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276504
Gene description
CRISPRi-validated cis-regulatory element chr19.2258
Gene type
biological region
Feature type(s)
regulatory: silencer, 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 TRMT1 (tRNA methyltransferase 1) gene on chromosome 19 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress 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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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13841816..13843324)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13967949..13969457)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13952630..13954138)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene miR-23a/27a/24-2 cluster host gene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10212 Neighboring gene microRNA 27a Neighboring gene microRNA 23a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14144 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:13958655-13958860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13964511-13965456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13975386-13976271 Neighboring gene nanos C2HC-type zinc finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10217 Neighboring gene microRNA 181c Neighboring gene microRNA 181d

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
  4. 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 silent region 10213
  • ATAC-STARR-seq lymphoblastoid silent region 10214

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_067055.1 

    Range
    101..1609
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13841816..13843324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160022.1 Reference GRCh38.p14 PATCHES

    Range
    53657..55165
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13967949..13969457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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