U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116268472 CRISPRi-validated cis-regulatory element chr15.2471 [ Homo sapiens (human) ]

Gene ID: 116268472, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116268472
Gene description
CRISPRi-validated cis-regulatory element chr15.2471
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 ETFA (electron transfer flavoprotein subunit alpha) gene on chromosome 15 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (76313653..76314074)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (74184782..74185203)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (76605994..76606415)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 266 Neighboring gene uncharacterized LOC101929439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9875 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76482438-76482591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488419-76488980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488981-76489540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76489541-76490100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491300-76491944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491945-76492588 Neighboring gene NANOG hESC enhancer GRCh37_chr15:76526655-76527344 Neighboring gene electron transfer flavoprotein subunit alpha Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603062-76603562 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603563-76604063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9877 Neighboring gene TYRO3P protein tyrosine kinase pseudogene Neighboring gene Sharpr-MPRA regulatory region 228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76629623-76630434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76632479-76633234 Neighboring gene uncharacterized LOC124903532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76638487-76638988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6688 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76663676-76663893 Neighboring gene tRNA-Lys (anticodon CTT) 16-1 Neighboring gene S-phase cyclin A associated protein in the ER Neighboring gene ISL LIM homeobox 2

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

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)

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_066987.1 

    Range
    101..522
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    76313653..76314074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    74184782..74185203
    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