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LOC125146365 Sharpr-MPRA regulatory region 1759 [ Homo sapiens (human) ]

Gene ID: 125146365, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146365
Gene description
Sharpr-MPRA regulatory region 1759
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 DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146365 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (98794760..98795054)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (96559143..96559437)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene insulin like growth factor 1 receptor Neighboring gene uncharacterized LOC124903560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316261-99316843 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316844-99317425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99319525-99320432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99320433-99321339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99340181-99340972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99342674-99343369 Neighboring gene microRNA 4714 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:99365701-99366259 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99366260-99366818 Neighboring gene NANOG hESC enhancer GRCh37_chr15:99370256-99370757 Neighboring gene uncharacterized LOC124903561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99427064-99427656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99427657-99428249 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:99439536-99440735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99451095-99451595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10145 Neighboring gene pyroglutamyl-peptidase I like

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_080295.1 

    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
    98794760..98795054
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    96559143..96559437
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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