U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116268465 CRISPRi-validated cis-regulatory element chr15.1149 [ Homo sapiens (human) ]

Gene ID: 116268465, updated on 10-Dec-2024

Summary

Go to the top of the page Help
Gene symbol
LOC116268465
Gene description
CRISPRi-validated cis-regulatory element chr15.1149
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 high-confidence cis-regulatory element for the SCG3 (secretogranin III) and TMOD2 (tropomodulin 2) genes on chromosome 15, and with lower confidence for the LYSMD2 (LysM domain containing 2) gene, 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
See LOC116268465 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (51652106..51652686)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49459575..49460155)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (51944303..51944883)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:51678296-51678796 Neighboring gene gliomedin Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:51682661-51683516 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:51741640-51742839 Neighboring gene Dmx like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:51861014-51861520 Neighboring gene Sharpr-MPRA regulatory region 1269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6432 Neighboring gene uncharacterized LOC105370816 Neighboring gene CRISPRi-validated cis-regulatory element chr15.1151 Neighboring gene Sharpr-MPRA regulatory region 12802 Neighboring gene secretogranin III Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9406 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6438 Neighboring gene LysM domain containing 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_066980.1 

    Range
    101..681
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    51652106..51652686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    49459575..49460155
    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