U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130057247 ATAC-STARR-seq lymphoblastoid silent region 6522 [ Homo sapiens (human) ]

Gene ID: 130057247, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130057247
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6522
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region 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
See LOC130057247 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (63802009..63802198)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (61609187..61609376)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (64094208..64094397)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9539 Neighboring gene Sharpr-MPRA regulatory region 15501 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:63851884-63852437 Neighboring gene ubiquitin specific peptidase 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:63882664-63883863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63892143-63892860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63893123-63893940 Neighboring gene USP3 antisense RNA 1 Neighboring gene F-box and leucine rich repeat protein 22 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:63958187-63958357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64006451-64006952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64006953-64007452 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:64014173-64014349 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64057331-64058088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64058904-64059404 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:64107893-64108654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64114122-64114622 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64125303-64126168 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64126169-64127032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64171093-64171988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9543 Neighboring gene Sharpr-MPRA regulatory region 4498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64186155-64186656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9546 Neighboring gene microRNA 422a Neighboring gene uncharacterized LOC101928988 Neighboring gene death associated protein kinase 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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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)

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_191668.1 

    Range
    101..290
    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
    63802009..63802198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    61609187..61609376
    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