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LOC113875027 Sharpr-MPRA regulatory region 10799 [ Homo sapiens (human) ]

Gene ID: 113875027, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113875027
Gene description
Sharpr-MPRA regulatory region 10799
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113875027 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (46812534..46812828)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46219534..46219828)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (46671969..46672263)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 9 member A7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29573 Neighboring gene Y-box binding protein 1 pseudogene 8 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:46569386-46570585 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29574 Neighboring gene CHMP5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29576 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:46673232-46673357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29577 Neighboring gene RP2 activator of ARL3 GTPase Neighboring gene long intergenic non-protein coding RNA 1545

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_063215.1 

    Range
    101..395
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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
    46812534..46812828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46219534..46219828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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