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LOC130060058 ATAC-STARR-seq lymphoblastoid silent region 8057 [ Homo sapiens (human) ]

Gene ID: 130060058, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060058
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8057
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 LOC130060058 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 (4950040..4950269)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4840387..4840616)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4853335..4853564)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11555 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:4843813-4844007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11556 Neighboring gene ring finger protein 167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4847507-4848050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8056 Neighboring gene profilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4854946-4855680 Neighboring gene enolase 3 Neighboring gene sperm associated antigen 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4868801-4869478 Neighboring gene uncharacterized LOC124900387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4870157-4870834 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4870835-4871511 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:4872157-4873356 Neighboring gene calmodulin binding transcription activator 2 Neighboring gene microRNA 6864

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_194479.1 

    Range
    101..330
    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
    4950040..4950269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4840387..4840616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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