U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC115947636 CRISPRi-validated cis-regulatory element chr2.7130 [ Homo sapiens (human) ]

Gene ID: 115947636, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC115947636
Gene description
CRISPRi-validated cis-regulatory element chr2.7130
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 high-confidence cis-regulatory element for the AGAP1 (ArfGAP with GTPase domain, ankyrin repeat and PH domain 1) gene on chromosome 2 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. [provided by RefSeq, Jun 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (235460434..235461258)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (235949954..235950778)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (236369078..236369902)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373940 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236182269-236182836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236233641-236234543 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236255926-236257125 Neighboring gene uncharacterized LOC105373941 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:236302767-236303966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236403941-236404814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236409110-236409715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236413687-236414193 Neighboring gene AGAP1 intronic transcript 1 Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 Neighboring gene trinucleotide repeat containing 17

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

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

  • ReSE screen-validated silencer GRCh37_chr2:236369201-236369397

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_066579.1 

    Range
    101..925
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    235460434..235461258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    235949954..235950778
    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