U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130060758 ATAC-STARR-seq lymphoblastoid silent region 8456 [ Homo sapiens (human) ]

Gene ID: 130060758, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC130060758
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8456
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 LOC130060758 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39402256..39402645)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40266167..40266557)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transcription factor CP2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37400607-37401181 Neighboring gene F-box and leucine rich repeat protein 20 Neighboring gene microRNA 548BC Neighboring gene MPRA-validated peak2834 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37489325-37489835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37493495-37494252 Neighboring gene Sharpr-MPRA regulatory region 12086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8454 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37557132-37557424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8455 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37558864-37559028 Neighboring gene mediator complex subunit 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:37618166-37619365 Neighboring gene U6 spliceosomal RNA Neighboring gene cyclin dependent kinase 12

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

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_196022.1 

    Range
    101..490
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    39402256..39402645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40266167..40266557
    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