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LOC130068020 ATAC-STARR-seq lymphoblastoid silent region 20690 [ Homo sapiens (human) ]

Gene ID: 130068020, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068020
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20690
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 LOC130068020 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (19887002..19887141)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (19469909..19470048)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (19905120..19905259)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase 15 Neighboring gene eukaryotic translation initiation factor 5 pseudogene 2 Neighboring gene SH3 domain containing kinase binding protein 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:19643274-19644473 Neighboring gene uncharacterized LOC124905255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:19740595-19741095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:19820680-19821600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29470 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:19880674-19881280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29476 Neighboring gene uncharacterized LOC124905256 Neighboring gene BCLAF1 and THRAP3 family member 3 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:20001035-20001226 Neighboring gene uncharacterized LOC729609

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_202435.1 

    Range
    101..240
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    19887002..19887141
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    19469909..19470048
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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