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LOC125384567 Sharpr-MPRA regulatory region 5115 [ Homo sapiens (human) ]

Gene ID: 125384567, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384567
Gene description
Sharpr-MPRA regulatory region 5115
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (4242362..4242656)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (4276702..4276996)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4141411-4142344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4148169-4148870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12641 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:4175883-4176064 Neighboring gene spermine oxidase Neighboring gene MPRA-validated peak4129 silencer Neighboring gene long intergenic non-protein coding RNA 1433 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4197441-4198178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17493 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:4202467-4202967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4212957-4213457 Neighboring gene adrenoceptor alpha 1D Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:4244845-4245360 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:4306716-4307915 Neighboring gene uncharacterized LOC124904862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4501639-4502140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4502141-4502640 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:4526897-4527638 Neighboring gene uncharacterized LOC105372510

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_080890.1 

    Range
    101..395
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    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
    4242362..4242656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    4276702..4276996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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