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LOC130065644 ATAC-STARR-seq lymphoblastoid silent region 12783 [ Homo sapiens (human) ]

Gene ID: 130065644, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065644
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12783
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 LOC130065644 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 (32358871..32359030)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (34083755..34083914)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (30946674..30946833)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30865306-30865816 Neighboring gene kinesin family member 3B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:30914131-30915330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17716 Neighboring gene ASXL transcriptional regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31033225-31033886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31035799-31036300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31044389-31045304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31045305-31046220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31046221-31047136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12787 Neighboring gene nucleolar protein 4 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31062343-31063114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31064659-31065430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12790 Neighboring gene uncharacterized LOC124904886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31084748-31085264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31093704-31094386 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31094387-31095068 Neighboring gene uncharacterized LOC101929698 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31098781-31099176

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_200061.1 

    Range
    101..260
    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
    32358871..32359030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    34083755..34083914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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