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LOC130005086 ATAC-STARR-seq lymphoblastoid silent region 3028 [ Homo sapiens (human) ]

Gene ID: 130005086, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005086
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3028
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 LOC130005086 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 (777888..777987)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (829323..829422)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (777888..777987)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr11:746448-747096 and GRCh37_chr11:747097-747745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3025 Neighboring gene transaldolase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:762588-763787 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:765339-765752 Neighboring gene glutamine amidotransferase class 1 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3027 Neighboring gene uncharacterized LOC124900301 Neighboring gene GATD1 divergent transcript Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:783107-783794 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:783795-784482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3029 Neighboring gene cell cycle exit and neuronal differentiation 1 Neighboring gene solute carrier family 25 member 22 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:794229-794747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:795266-795784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:796302-796820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:797857-798373 Neighboring gene proapoptotic nucleolar protein 1

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_184531.1 

    Range
    101..200
    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
    777888..777987
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    829323..829422
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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