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LOC129664170 ReSE screen-validated silencer GRCh37_chr17:78807023-78807239 [ Homo sapiens (human) ]

Gene ID: 129664170, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129664170
Gene description
ReSE screen-validated silencer GRCh37_chr17:78807023-78807239
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 HepG2 liver carcinoma 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 LOC129664170 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80833085..80833439)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81738606..81738961)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78806885..78807239)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene regulatory associated protein of MTOR complex 1 Neighboring gene uncharacterized LOC101928855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78785069-78785570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78794217-78794820 Neighboring gene uncharacterized LOC124904076 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78801060-78801750 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78801751-78802440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78805646-78806418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78807964-78808735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78829045-78829576 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78829770-78830969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78831337-78832266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78847077-78848036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78852392-78852991 Neighboring gene uncharacterized LOC124904075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78933187-78933704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78937983-78938532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78939083-78939632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78943614-78944419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78944420-78945224 Neighboring gene uncharacterized LOC400627

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 12945

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_161176.2 

    Range
    101..455
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80833085..80833439
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81738606..81738961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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