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LOC125110350 Sharpr-MPRA regulatory region 1870 [ Homo sapiens (human) ]

Gene ID: 125110350, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125110350
Gene description
Sharpr-MPRA regulatory region 1870
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (68433870..68434164)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66256764..66257058)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68570079-68570980 Neighboring gene NANOG hESC enhancer GRCh37_chr15:68577826-68578327 Neighboring gene fem-1 homolog B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6587 Neighboring gene integrin subunit alpha 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68607402-68608268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68609715-68610215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68634197-68634792 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:68657127-68658326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68662273-68662774 Neighboring gene Sharpr-MPRA regulatory region 14581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68722903-68723662 Neighboring gene uncharacterized LOC124903513 Neighboring gene uncharacterized LOC105370873

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_080251.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    68433870..68434164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    66256764..66257058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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