U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129992566 ATAC-STARR-seq lymphoblastoid silent region 15404 [ Homo sapiens (human) ]

Gene ID: 129992566, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129992566
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15404
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 LOC129992566 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (48269648..48269777)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (48236590..48236719)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (48271665..48271794)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900886 Neighboring gene TXK tyrosine kinase Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:48114113-48115312 Neighboring gene RNA, U6 small nuclear 838, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:48129156-48130018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21537 Neighboring gene Sharpr-MPRA regulatory region 15119 Neighboring gene NANOG hESC enhancer GRCh37_chr4:48177274-48177775 Neighboring gene tec protein tyrosine kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:48187797-48188522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21547 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15405 Neighboring gene uncharacterized LOC105374445 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:48293363-48294358 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:48297678-48298877 Neighboring gene Sharpr-MPRA regulatory region 3457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21548 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:48343493-48344406 Neighboring gene SLAIN motif family member 2 Neighboring gene U6 snRNA-associated Sm-like protein LSm2

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_172012.1 

    Range
    101..230
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    48269648..48269777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    48236590..48236719
    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