U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116158523 CRISPRi-validated cis-regulatory element chr5.3240 [ Homo sapiens (human) ]

Gene ID: 116158523, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116158523
Gene description
CRISPRi-validated cis-regulatory element chr5.3240
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. A subregion was validated as a high-confidence cis-regulatory element for both the CYSTM1 (cysteine rich transmembrane module containing 1) and UBE2D2 (ubiquitin conjugating enzyme E2 D2) genes on chromosome 5 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139635653..139636517)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140160717..140161581)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (139015238..139016073)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 D2 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 15 Neighboring gene H3 histone pseudogene 25 Neighboring gene Sharpr-MPRA regulatory region 3558 Neighboring gene Sharpr-MPRA regulatory region 4362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139017982-139018548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139030154-139030654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23246 Neighboring gene CXXC5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139038513-139039362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139040914-139041480 Neighboring gene CXXC finger protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23248 Neighboring gene uncharacterized LOC124901084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16424

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16416

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_066665.2 

    Range
    101..965
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    139635653..139636517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    140160717..140161581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases