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LOC130059862 ATAC-STARR-seq lymphoblastoid silent region 7941 [ Homo sapiens (human) ]

Gene ID: 130059862, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059862
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7941
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 LOC130059862 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (732073..732552)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (617133..617612)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene VPS53 subunit of GARP complex Neighboring gene uncharacterized LOC124903891 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:463241-464440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7940 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:475469-476353 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:487351-487501 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:504328-505527 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:560426-561625 Neighboring gene ribosomal protein S4X pseudogene 17 Neighboring gene Sharpr-MPRA regulatory region 8461 Neighboring gene Sharpr-MPRA regulatory region 15051 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:610400-610605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11438 Neighboring gene uncharacterized LOC124903893 Neighboring gene Sharpr-MPRA regulatory region 11717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7945 Neighboring gene TLC domain containing 3A Neighboring gene gem nuclear organelle associated protein 4 Neighboring gene diazepam binding inhibitor-like 5, pseudogene

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_194283.1 

    Range
    101..580
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    732073..732552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    617133..617612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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