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LOC130005298 ATAC-STARR-seq lymphoblastoid silent region 3137 [ Homo sapiens (human) ]

Gene ID: 130005298, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005298
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3137
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 LOC130005298 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (9758103..9758502)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (9842813..9843212)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9779650..9780049)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4420 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:9697353-9697887 Neighboring gene NANOG hESC enhancer GRCh37_chr11:9700059-9700598 Neighboring gene ribosomal protein L21 pseudogene 97 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9733231-9733731 Neighboring gene RN7SK pseudogene 50 Neighboring gene switching B cell complex subunit SWAP70 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9740773-9741273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3138 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9785216-9785716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9786625-9787448 Neighboring gene uncharacterized LOC105369149 Neighboring gene long intergenic non-protein coding RNA 2709 Neighboring gene SBF2 antisense RNA 1 Neighboring gene protein GVQW1-like Neighboring gene SET binding factor 2

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_184743.1 

    Range
    101..500
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    9758103..9758502
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    9842813..9843212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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