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LOC129663090 ReSE screen-validated silencer GRCh37_chr12:7023548-7023738 [ Homo sapiens (human) ]

Gene ID: 129663090, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129663090
Gene description
ReSE screen-validated silencer GRCh37_chr12:7023548-7023738
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 LOC129663090 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6914363..6914852)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6925543..6926032)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7023527..7024016)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369632 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:6995318-6995865 Neighboring gene DSTN pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7000801-7001348 Neighboring gene leucine rich repeat containing 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7024095-7024736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7024737-7025376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5891 Neighboring gene enolase 2 Neighboring gene uncharacterized LOC124902868 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7033606-7034306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7035007-7035706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4194 Neighboring gene atrophin 1 Neighboring gene atrophin 1 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:7052993-7053572 and GRCh37_chr12:7053573-7054152 Neighboring gene chromosome 12 open reading frame 57 Neighboring gene RNA, U7 small nuclear 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 4192

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_160096.2 

    Range
    101..590
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6914363..6914852
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6925543..6926032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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