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LOC130058614 ATAC-STARR-seq lymphoblastoid silent region 7249 [ Homo sapiens (human) ]

Gene ID: 130058614, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058614
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7249
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 LOC130058614 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (21158734..21158913)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (21089658..21089837)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (21170055..21170234)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene defective in cullin neddylation 1 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20911499-20912284 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20912285-20913070 Neighboring gene LYR motif containing 1 Neighboring gene dynein axonemal heavy chain 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:20982344-20983543 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20985044-20985544 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21059143-21059715 Neighboring gene uncharacterized LOC107984888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10547 Neighboring gene Sharpr-MPRA regulatory region 1818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:21170492-21170992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10551 Neighboring gene lipid droplet assembly factor 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21233480-21234004 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21234005-21234530 Neighboring gene uncharacterized LOC105371123 Neighboring gene zona pellucida glycoprotein 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_193035.1 

    Range
    101..280
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    21158734..21158913
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    21089658..21089837
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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