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LOC129663045 ReSE screen-validated silencer GRCh37_chr11:116658726-116658949 [ Homo sapiens (human) ]

Gene ID: 129663045, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129663045
Gene description
ReSE screen-validated silencer GRCh37_chr11:116658726-116658949
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 K562 erythroleukemia cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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]
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Genomic context

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See LOC129663045 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (116788010..116788325)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (116802634..116802949)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (116658726..116659041)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene BUD13 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5555 Neighboring gene BUD13 divergent transcript Neighboring gene ZPR1 zinc finger Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3924 Neighboring gene enhancer-blocking element 11-1-2 overlapping APOA5 Neighboring gene apolipoprotein A5 Neighboring gene lncRNA regulator of hepatic lineages 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 5556

NCBI Reference Sequences (RefSeq)

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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_160051.2 

    Range
    101..416
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    116788010..116788325
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    116802634..116802949
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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