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LOC130061502 ATAC-STARR-seq lymphoblastoid silent region 8883 [ Homo sapiens (human) ]

Gene ID: 130061502, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061502
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8883
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 LOC130061502 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (67995699..67995788)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (68870927..68871016)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (65991815..65991904)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L17 pseudogene 41 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:65820867-65821564 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:65821565-65822260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12632 Neighboring gene NANOG hESC enhancer GRCh37_chr17:65827101-65827602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12633 Neighboring gene bromodomain PHD finger transcription factor Neighboring gene Sharpr-MPRA regulatory region 4989 Neighboring gene RNA, 7SL, cytoplasmic 622, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8882 Neighboring gene chromosome 17 open reading frame 58 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66016003-66016576 Neighboring gene tRNA-Arg (anticodon CCG) 2-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66031597-66032144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12635 Neighboring gene karyopherin subunit alpha 2

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_194959.1 

    Range
    101..190
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    67995699..67995788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    68870927..68871016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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