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LOC125467759 Sharpr-MPRA regulatory region 13592 [ Homo sapiens (human) ]

Gene ID: 125467759, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125467759
Gene description
Sharpr-MPRA regulatory region 13592
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125467759 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (65722787..65723081)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (64149200..64149494)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (64942649..64942943)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29713 Neighboring gene LAS1 like ribosome biogenesis factor Neighboring gene FERM domain containing 8 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29714 Neighboring gene moesin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29715 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:64924017-64924189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29717 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:64972237-64972435 Neighboring gene Nanog homeobox pseudogene 9 Neighboring gene eukaryotic translation termination factor 1 pseudogene 3

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_081229.1 

    Range
    101..395
    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
    65722787..65723081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    64149200..64149494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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