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LOC129660591 ReSE screen-validated silencer GRCh37_chr2:10262327-10262827 [ Homo sapiens (human) ]

Gene ID: 129660591, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129660591
Gene description
ReSE screen-validated silencer GRCh37_chr2:10262327-10262827
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 LOC129660591 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10122194..10122793)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10150906..10151505)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10262321..10262920)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10197717-10198660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10198661-10199603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10200462-10201324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10201325-10202185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10203342-10203940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10203941-10204538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10204790-10205668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10205669-10206546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10211417-10211918 Neighboring gene cystin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15296 Neighboring gene uncharacterized LOC124900536 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10231300-10231817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15297 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:10259653-10260596 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:10260597-10261539 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:10261588-10262143 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr2:10273128-10273791 Neighboring gene ribonucleotide reductase regulatory subunit M2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10282796-10283457 Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10303055-10303660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10303661-10304265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10309414-10310044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10311305-10311934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10311935-10312564 Neighboring gene microRNA 4261

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 11158

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_157628.2 

    Range
    101..700
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    10122194..10122793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    10150906..10151505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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