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LOC129936541 ATAC-STARR-seq lymphoblastoid silent region 14240 [ Homo sapiens (human) ]

Gene ID: 129936541, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936541
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14240
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 LOC129936541 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42013712..42013781)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42031670..42031739)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42055204..42055273)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene gem nuclear organelle associated protein 2 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42040771-42040982 Neighboring gene uncharacterized LOC107986077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42056327-42056828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42065830-42066748 Neighboring gene trafficking kinesin protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19730 Neighboring gene Sharpr-MPRA regulatory region 14156 Neighboring gene NANOG hESC enhancer GRCh37_chr3:42093014-42093515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19731 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42103275-42103494 Neighboring gene ribosomal protein L7a pseudogene 83 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42112363-42113074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42139608-42140430 Neighboring gene uncharacterized LOC124906231

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_169552.1 

    Range
    101..170
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    42013712..42013781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    42031670..42031739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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