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LOC129664419 ReSE screen-validated silencer GRCh37_chr19:33071921-33072097 [ Homo sapiens (human) ]

Gene ID: 129664419, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129664419
Gene description
ReSE screen-validated silencer GRCh37_chr19:33071921-33072097
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 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]
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Genomic context

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See LOC129664419 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (32580940..32581669)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35099705..35100434)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33071846..33072575)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene DPY19L3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10481 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:32911836-32912044 Neighboring gene dpy-19 like C-mannosyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14429 Neighboring gene Sharpr-MPRA regulatory region 12835 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33051335-33051521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14430 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:33083895-33085094 Neighboring gene programmed cell death 5 Neighboring gene ankyrin repeat domain 27 Neighboring gene small nucleolar RNA, H/ACA box 68B Neighboring gene Sharpr-MPRA regulatory region 4203 Neighboring gene ribosomal protein S12 pseudogene 31

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 10482

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_161425.2 

    Range
    101..830
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    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    32580940..32581669
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    35099705..35100434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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