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LOC129661473 ReSE screen-validated silencer GRCh37_chr5:75852604-75853098 [ Homo sapiens (human) ]

Gene ID: 129661473, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129661473
Gene description
ReSE screen-validated silencer GRCh37_chr5:75852604-75853098
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 represents 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. This region was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia 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 LOC129661473 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (76556779..76557273)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (77038530..77039024)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (75852604..75853098)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75690574-75691074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75691075-75691575 Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:75699075-75699575 Neighboring gene IQ motif containing GTPase activating protein 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:75767824-75769023 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75794074-75794996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75794997-75795918 Neighboring gene sulfiredoxin 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22693 Neighboring gene uncharacterized LOC101929109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22694 Neighboring gene Sharpr-MPRA regulatory region 1022 Neighboring gene coagulation factor II thrombin receptor like 2

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 22691

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_158509.1 

    Range
    101..595
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    76556779..76557273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    77038530..77039024
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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