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LOC129993382 ATAC-STARR-seq lymphoblastoid silent region 15802 [ Homo sapiens (human) ]

Gene ID: 129993382, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129993382
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15802
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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Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (171813325..171813374)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (175165599..175165648)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377535 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22151 Neighboring gene long intergenic non-protein coding RNA 2174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22152 Neighboring gene uncharacterized LOC441052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:172823942-172824554 Neighboring gene polypeptide N-acetylgalactosaminyltransferase like 6 Neighboring gene Sharpr-MPRA regulatory region 892 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:172914347-172914881 Neighboring gene uncharacterized LOC124900811 Neighboring gene ubiquitin conjugating enzyme E2 N pseudogene

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

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_172828.1 

    Range
    101..150
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    171813325..171813374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    175165599..175165648
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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