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LOC130068072 ATAC-STARR-seq lymphoblastoid silent region 20722 [ Homo sapiens (human) ]

Gene ID: 130068072, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130068072
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20722
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 LOC130068072 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (29478789..29478948)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (29070885..29071044)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene interleukin 1 receptor accessory protein like 1 Neighboring gene uncharacterized LOC124900494 Neighboring gene RNA, 5S ribosomal pseudogene 500 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:29173264-29174047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:29194297-29194796 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:29243546-29244419 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:29315145-29315868 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:29326788-29327495 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:29327496-29328204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:29328205-29328911 Neighboring gene NANOG hESC enhancer GRCh37_chrX:29440069-29440570 Neighboring gene microRNA 4666b Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:29679893-29681092 Neighboring gene NANOG hESC enhancer GRCh37_chrX:29749637-29750178 Neighboring gene uncharacterized LOC124905284

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_202487.1 

    Range
    101..260
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    29478789..29478948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    29070885..29071044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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