U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129665010 ReSE screen-validated silencer GRCh37_chrX:135849488-135849656 [ Homo sapiens (human) ]

Gene ID: 129665010, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129665010
Gene description
ReSE screen-validated silencer GRCh37_chrX:135849488-135849656
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 includes an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. A subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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 LOC129665010 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (136767329..136767694)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (135076045..135076410)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (135849488..135849853)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21028 Neighboring gene CD40 ligand Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29993 Neighboring gene Rac/Cdc42 guanine nucleotide exchange factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29996 Neighboring gene RNA, U6 small nuclear 972, pseudogene Neighboring gene solute carrier family 25 member 6 pseudogene

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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 Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 21031
  • ATAC-STARR-seq lymphoblastoid silent region 21032

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_162048.2 

    Range
    101..466
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    136767329..136767694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    135076045..135076410
    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