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LOC125384572 Sharpr-MPRA regulatory region 6239 [ Homo sapiens (human) ]

Gene ID: 125384572, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384572
Gene description
Sharpr-MPRA regulatory region 6239
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125384572 in Genome Data Viewer
Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (6519582..6519876)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (6560699..6560993)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene fibroblast growth factor receptor 3 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:6301432-6302266 Neighboring gene MPRA-validated peak4138 silencer Neighboring gene uncharacterized LOC124904866 Neighboring gene cancer susceptibility 20 Neighboring gene MPRA-validated peak4139 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:6571340-6572539 Neighboring gene Sharpr-MPRA regulatory region 6314 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:6593736-6594935 Neighboring gene OCT4 hESC enhancer GRCh37_chr20:6617898-6618411 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:6678222-6679421 Neighboring gene Sharpr-MPRA regulatory region 10991 Neighboring gene long intergenic non-protein coding RNA 1713 Neighboring gene BMP2 5' regulatory region Neighboring gene uncharacterized LOC105372517

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

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_080895.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    6519582..6519876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    6560699..6560993
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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