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LOC130058732 ATAC-STARR-seq lymphoblastoid silent region 7311 [ Homo sapiens (human) ]

Gene ID: 130058732, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130058732
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7311
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 LOC130058732 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28623403..28623452)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (28772231..28772280, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4245 Neighboring gene sulfotransferase family 1A member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28610237-28610771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28610772-28611305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28612139-28612653 Neighboring gene uncharacterized LOC107984835 Neighboring gene sulfotransferase family 1A member 1 Neighboring gene uncharacterized LOC124903674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28623750-28624250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28624498-28625048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28625049-28625598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28626587-28627161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7312 Neighboring gene nuclear pore complex interacting protein family member B8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28677654-28678567 Neighboring gene small nucleolar RNA U13

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_193153.1 

    Range
    101..150
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    28623403..28623452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    28772231..28772280 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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