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LOC130005054 ATAC-STARR-seq lymphoblastoid silent region 2996 [ Homo sapiens (human) ]

Gene ID: 130005054, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130005054
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2996
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: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (316304..316353)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (354662..354711, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:311550-312155 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:313425-313980 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:313981-314536 Neighboring gene interferon induced transmembrane protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4266 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:316761-317316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4267 Neighboring gene uncharacterized LOC105376505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:318431-318986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:318987-319542 Neighboring gene interferon induced transmembrane protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:320655-321210 Neighboring gene interferon induced transmembrane protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4271 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:333329-333882 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:333883-334436 Neighboring gene CRISPRi-validated cis-regulatory element chr11.30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4272 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:353490-353656 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:354319-354895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:355877-356829 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:368032-368570 Neighboring gene beta-1,4-N-acetyl-galactosaminyltransferase 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:380111-380268

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_184499.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    316304..316353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    354662..354711 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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