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LOC130009065 ATAC-STARR-seq lymphoblastoid silent region 5021 [ Homo sapiens (human) ]

Gene ID: 130009065, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009065
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5021
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 LOC130009065 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (122774410..122774619)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122769818..122770027)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123258957..123259166)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123214153-123214820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123218665-123219164 Neighboring gene hydroxycarboxylic acid receptor 1 Neighboring gene Sharpr-MPRA regulatory region 1215 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:123235867-123236728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7236 Neighboring gene density regulated re-initiation and release factor Neighboring gene Sharpr-MPRA regulatory region 13845 Neighboring gene coiled-coil domain containing 62 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123274450-123275003 Neighboring gene MPRA-validated peak2023 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123296784-123296959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7238 Neighboring gene MPRA-validated peak2024 silencer Neighboring gene uncharacterized LOC124903040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123329929-123330760 Neighboring gene huntingtin interacting protein 1 related Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123338415-123338915 Neighboring gene Sharpr-MPRA regulatory region 11411 Neighboring gene uncharacterized LOC124903039 Neighboring gene VPS37B subunit of ESCRT-I

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_188737.1 

    Range
    101..310
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    122774410..122774619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    122769818..122770027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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