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LOC130068684 ATAC-STARR-seq lymphoblastoid silent region 20998 [ Homo sapiens (human) ]

Gene ID: 130068684, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068684
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20998
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 LOC130068684 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 (130268600..130268679)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (128587401..128587480)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (129402574..129402653)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 15346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20989 Neighboring gene E74 like ETS transcription factor 4 Neighboring gene Sharpr-MPRA regulatory region 9263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29938 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:129255011-129255220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20995 Neighboring gene RAB33A, member RAS oncogene family Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:129280263-129281462 Neighboring gene apoptosis inducing factor mitochondria associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:129305519-129306473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29941 Neighboring gene zinc finger protein 280C Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:129413936-129414929 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:129414930-129415922 Neighboring gene RNA, U6 small nuclear 1130, pseudogene Neighboring gene SNRPN upstream reading frame protein-like

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_203098.1 

    Range
    101..180
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    130268600..130268679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    128587401..128587480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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