U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130009376 ATAC-STARR-seq lymphoblastoid silent region 5174 [ Homo sapiens (human) ]

Gene ID: 130009376, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC130009376
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5174
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 LOC130009376 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (23579241..23579720)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (22785730..22786210)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24066632-24067132 Neighboring gene uncharacterized LOC124903135 Neighboring gene NANOG hESC enhancer GRCh37_chr13:24081975-24082502 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:24100455-24101050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24141962-24142474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24142475-24142986 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5175 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32745 Neighboring gene TNF receptor superfamily member 19 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:24192537-24193038 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:24195169-24195668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24205756-24206564 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24206565-24207373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24213321-24213822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24228053-24228554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24269883-24270456 Neighboring gene uncharacterized LOC105370113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7462 Neighboring gene mitochondrial intermediate peptidase Neighboring gene MT-CO3 pseudogene 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

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_188997.1 

    Range
    101..580
    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    23579241..23579720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    22785730..22786210
    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