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LOC129664182 ReSE screen-validated silencer GRCh37_chr17:80452439-80452776 [ Homo sapiens (human) ]

Gene ID: 129664182, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129664182
Gene description
ReSE screen-validated silencer GRCh37_chr17:80452439-80452776
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 HepG2 liver carcinoma 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 LOC129664182 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 (82494563..82494935)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83363486..83363858)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80452439..80452811)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene hexosaminidase D Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13010 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80416539-80417371 Neighboring gene cytochrome b-245 chaperone 1 Neighboring gene NARF antisense RNA 2 Neighboring gene nuclear prelamin A recognition factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13011 Neighboring gene tRNA-iMet (anticodon CAT) 1-8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9218 Neighboring gene Sharpr-MPRA regulatory region 5709 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80493259-80493844 Neighboring gene forkhead box K2 Neighboring gene Sharpr-MPRA regulatory region 7485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80510130-80510754 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80511221-80511392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80520843-80521344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80521345-80521844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80524020-80524908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80528855-80529354 Neighboring gene uncharacterized LOC124904132 Neighboring gene ARF like GTPase 2 binding protein pseudogene 9 Neighboring gene FOXK2 antisense RNA 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 silent region 9215

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_161188.2 

    Range
    101..473
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82494563..82494935
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83363486..83363858
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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