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LOC130066125 ATAC-STARR-seq lymphoblastoid silent region 13013 [ Homo sapiens (human) ]

Gene ID: 130066125, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066125
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13013
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 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 LOC130066125 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50112678..50113217)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (51882465..51883004)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (48729215..48729754)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48660109-48661056 Neighboring gene translation regulatory long non-coding RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48666284-48667078 Neighboring gene uncharacterized LOC105372655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48671143-48671728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18082 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:48681498-48681675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48689593-48690102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48690103-48690612 Neighboring gene PEDS1-UBE2V1 readthrough Neighboring gene ubiquitin conjugating enzyme E2 V1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:48715799-48716462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18083 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:48730039-48730606 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:48732458-48732614 Neighboring gene plasmanylethanolamine desaturase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48754882-48755569 Neighboring gene putative uncharacterized protein CCDC28A-AS1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48760275-48760910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13014 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:48782079-48783278 Neighboring gene long intergenic non-protein coding RNA 1275

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. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

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_200542.1 

    Range
    101..640
    Download
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    50112678..50113217
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    51882465..51883004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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