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LOC130059094 ATAC-STARR-seq lymphoblastoid silent region 7528 [ Homo sapiens (human) ]

Gene ID: 130059094, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059094
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7528
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 LOC130059094 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57299925..57300134)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63095897..63096106)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (57333837..57334046)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903697 Neighboring gene ARF like GTPase 2 binding protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:57292150-57292362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57292975-57293530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57295195-57295750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:57295751-57296304 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:57296526-57297296 and GRCh37_chr16:57297297-57298066 Neighboring gene plasmolipin Neighboring gene Sharpr-MPRA regulatory region 12895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57317662-57318323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7527 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:57321027-57321239 Neighboring gene Sharpr-MPRA regulatory region 5344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7529 Neighboring gene tRNA-Leu (anticodon CAG) 2-1 Neighboring gene tRNA-Leu (anticodon CAG) 2-2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10890 Neighboring gene ribosomal protein L23a pseudogene 91

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_193515.1 

    Range
    101..310
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    57299925..57300134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    63095897..63096106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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