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LOC129664124 ReSE screen-validated silencer GRCh37_chr17:66287460-66287634 [ Homo sapiens (human) ]

Gene ID: 129664124, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129664124
Gene description
ReSE screen-validated silencer GRCh37_chr17:66287460-66287634
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 LOC129664124 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 (68291263..68291952)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (69167837..69168526)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (66287404..66288093)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8890 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66196439-66197255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8893 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8895 Neighboring gene Rho GTPase activating protein 27 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66224773-66225658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8896 Neighboring gene archaelysin family metallopeptidase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66242704-66243250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66243251-66243796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8898 Neighboring gene solute carrier family 16 member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12644 Neighboring gene arylsulfatase G Neighboring gene Sharpr-MPRA regulatory region 10227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66340482-66340982 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66340983-66341483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12647 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66374359-66374878 Neighboring gene MPRA-validated peak2959 silencer Neighboring gene tRNA-undetermined (NNN) 5-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409262-66409920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409921-66410577 Neighboring gene protein kinase cAMP-dependent type I regulatory subunit alpha Neighboring gene microRNA 635 Neighboring gene WD repeat domain, phosphoinositide interacting 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 8899

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_161130.2 

    Range
    101..790
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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
    68291263..68291952
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    69167837..69168526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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