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LOC130005658 ATAC-STARR-seq lymphoblastoid silent region 3314 [ Homo sapiens (human) ]

Gene ID: 130005658, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005658
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3314
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 LOC130005658 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 (46700375..46700494)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46856391..46856510)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (46721925..46722044)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene autophagy and beclin 1 regulator 1 Neighboring gene microRNA 3160-1 Neighboring gene microRNA 3160-2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3313 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:46559175-46559678 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46559679-46560184 Neighboring gene Sharpr-MPRA regulatory region 9650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46587793-46588293 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4681 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:46605824-46606668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:46615325-46615825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4683 Neighboring gene Sharpr-MPRA regulatory region 32 Neighboring gene harbinger transposase derived 1 Neighboring gene autophagy related 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46715957-46716456 Neighboring gene Rho GTPase activating protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4684 Neighboring gene zinc finger protein 408 Neighboring gene coagulation factor II, thrombin

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_185103.1 

    Range
    101..220
    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
    46700375..46700494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46856391..46856510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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