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LOC130007123 ATAC-STARR-seq lymphoblastoid silent region 4096 [ Homo sapiens (human) ]

Gene ID: 130007123, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130007123
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4096
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 LOC130007123 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (134262133..134262182)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (134303978..134304027)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene non-SMC condensin II complex subunit D3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5770 Neighboring gene VPS26 retromer complex component B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4095 Neighboring gene thymocyte nuclear protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:134142736-134143291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5773 Neighboring gene acyl-CoA dehydrogenase family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4097 Neighboring gene galactosidase beta 1 like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:134180995-134181180 Neighboring gene ATPase H+/K+ transporting subunit beta pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4099 Neighboring gene galactosidase beta 1 like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:134228611-134229134

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_186567.1 

    Range
    101..150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    134262133..134262182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    134303978..134304027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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