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LOC130057186 ATAC-STARR-seq lymphoblastoid silent region 6491 [ Homo sapiens (human) ]

Gene ID: 130057186, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057186
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6491
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 LOC130057186 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (59536688..59536807)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (57338405..57338524)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59828887..59829006)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9493 Neighboring gene family with sequence similarity 81 member A Neighboring gene ribosomal protein L7a pseudogene 75 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:59721031-59721227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9497 Neighboring gene ribosomal protein L21 pseudogene 114 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:59826686-59827885 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:59835403-59836602 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:59840860-59841630 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:59841631-59842401 Neighboring gene ribosomal protein L21 pseudogene 117 Neighboring gene RNA, 5S ribosomal pseudogene 396

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 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_191607.1 

    Range
    101..220
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    59536688..59536807
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    57338405..57338524
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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