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LOC129663641 ReSE screen-validated silencer GRCh37_chr15:71407710-71407887 [ Homo sapiens (human) ]

Gene ID: 129663641, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129663641
Gene description
ReSE screen-validated silencer GRCh37_chr15:71407710-71407887
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 two accessible chromatin subregions that were validated as silencers based on their 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 LOC129663641 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71115371..71115624)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (68938654..68938907)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (71407710..71407963)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:71364462-71365661 Neighboring gene uncharacterized LOC105370886 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:71377897-71378512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71412420-71412936 Neighboring gene ribosomal protein L5 pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:71446356-71447555 Neighboring gene thrombospondin type 1 domain containing 4 Neighboring gene cancer/testis associated 62 Neighboring gene THSD4 antisense RNA 1 Neighboring gene high mobility group box 1 pseudogene 6

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 6611
  • ATAC-STARR-seq lymphoblastoid silent region 6612

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_160647.2 

    Range
    101..354
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    71115371..71115624
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    68938654..68938907
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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