U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129929077 ATAC-STARR-seq lymphoblastoid silent region 23 [ Homo sapiens (human) ]

Gene ID: 129929077, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC129929077
Gene description
ATAC-STARR-seq lymphoblastoid silent region 23
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 LOC129929077 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1040780..1040989)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (470917..471126)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L39 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:948847-949738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:949739-950630 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:950916-951136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18 Neighboring gene ISG15 ubiquitin like modifier Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:956772-957971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:959156-960132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:960133-961108 Neighboring gene agrin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:965235-966104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:967845-968714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 22 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:974926-975604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 24 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:989815-989997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:994105-994948 Neighboring gene uncharacterized LOC100288175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:995794-996637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:997280-997780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1000356-1000856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1000857-1001357 Neighboring gene uncharacterized LOC105378948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 27 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1004678-1005443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1009379-1009878 Neighboring gene ring finger protein 223

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_162134.1 

    Range
    101..310
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1040780..1040989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    470917..471126
    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