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LOC129663034 ReSE screen-validated silencer GRCh37_chr11:107991956-107992494 [ Homo sapiens (human) ]

Gene ID: 129663034, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129663034
Gene description
ReSE screen-validated silencer GRCh37_chr11:107991956-107992494
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 K562 erythroleukemia cells. This locus also includes an accessible chromatin subregion 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]
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Genomic context

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See LOC129663034 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 (108121229..108121778)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (108128766..108129315)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (107991956..107992505)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5479 Neighboring gene Sharpr-MPRA regulatory region 4319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5480 Neighboring gene cullin 5 Neighboring gene uncharacterized LOC124902748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5482 Neighboring gene MPRA-validated peak1447 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:108021496-108021664 Neighboring gene acetyl-CoA acetyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108047982 Neighboring gene nuclear protein, coactivator of histone transcription Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108089151 Neighboring gene NANOG hESC enhancer GRCh37_chr11:108089784-108090285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5487 Neighboring gene MPRA-validated peak1449 silencer Neighboring gene MPRA-validated peak1450 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108140516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:108147863-108148662 Neighboring gene ATM serine/threonine kinase Neighboring gene chromosome 11 open reading frame 65 Neighboring gene MPRA-validated peak1451 silencer

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 silent region 3876

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_160040.2 

    Range
    101..650
    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
    108121229..108121778
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    108128766..108129315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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