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LOC130060067 ATAC-STARR-seq lymphoblastoid silent region 8065 [ Homo sapiens (human) ]

Gene ID: 130060067, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060067
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8065
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 LOC130060067 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 (5191803..5192002)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (5085152..5085351)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (5095098..5095297)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11566 Neighboring gene ZNF232 antisense RNA 1 Neighboring gene zinc finger protein 232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5033804-5034304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040130-5040801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040802-5041472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5042145-5042815 Neighboring gene ubiquitin specific peptidase 6 Neighboring gene MPRA-validated peak2704 silencer Neighboring gene zinc finger protein 594 Neighboring gene ZNF594 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8066 Neighboring gene MPRA-validated peak2705 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11567 Neighboring gene SLP adaptor and CSK interacting membrane protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11569 Neighboring gene Sharpr-MPRA regulatory region 14928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5157813-5158318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5187866-5188384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8068 Neighboring gene rabaptin, RAB GTPase binding effector protein 1 Neighboring gene uncharacterized LOC105371505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:5265177-5265872

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_194488.1 

    Range
    101..300
    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
    5191803..5192002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    5085152..5085351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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