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LOC123575585 Sharpr-MPRA regulatory region 15640 [ Homo sapiens (human) ]

Gene ID: 123575585, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575585
Gene description
Sharpr-MPRA regulatory region 15640
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (146407806..146408100)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (146943640..146943934)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (145787369..145787663)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RBM27-POU4F3 Neighboring gene MPRA-validated peak5522 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:145724002-145724515 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:145725029-145725541 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81810 Neighboring gene POU class 4 homeobox 3 Neighboring gene uncharacterized LOC105378213 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81818 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81828 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:145826559-145827266 Neighboring gene transcription elongation regulator 1 Neighboring gene MPRA-validated peak5524 silencer Neighboring gene G protein-coupled receptor 151

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_077846.1 

    Range
    101..395
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    146407806..146408100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    146943640..146943934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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