U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130068873 ATAC-STARR-seq lymphoblastoid silent region 21106 [ Homo sapiens (human) ]

Gene ID: 130068873, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC130068873
Gene description
ATAC-STARR-seq lymphoblastoid silent region 21106
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 LOC130068873 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154457849..154458018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152694359..152694528)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153665032-153665532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153666887-153667386 Neighboring gene GDP dissociation inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153672115-153672682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153673251-153673818 Neighboring gene family with sequence similarity 50 member A Neighboring gene microRNA 6858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153687524-153688076 Neighboring gene plexin A3 Neighboring gene Sharpr-MPRA regulatory region 3405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21109 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153707495-153707994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30063 Neighboring gene L antigen family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153713643-153714401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153714402-153715160 Neighboring gene ubiquitin like 4A

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_203287.1 

    Range
    101..270
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154457849..154458018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152694359..152694528
    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