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LOC125110351 Sharpr-MPRA regulatory region 8573 [ Homo sapiens (human) ]

Gene ID: 125110351, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125110351
Gene description
Sharpr-MPRA regulatory region 8573
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, Apr 2022]
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Genomic context

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See LOC125110351 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 (68666430..68666724)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66489306..66489600)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370873 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:68799611-68800181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68810923-68811424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68811425-68811924 Neighboring gene coronin 2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68842985-68843486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68871520-68872387 Neighboring gene Sharpr-MPRA regulatory region 3237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68882548-68883339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68892023-68892602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68893807-68894366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68900721-68901361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68906675-68907190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68933009-68933520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68933521-68934032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68934266-68934783 Neighboring gene uncharacterized LOC124903514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68943583-68944150 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:68944208-68944708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68961677-68962176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68966278-68966778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68987247-68987836 Neighboring gene heart enhancer 11 Neighboring gene cysteinyl-tRNA synthetase 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:69080134-69080641 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:69083767-69084268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:69084269-69084768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:69087559-69088131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9650 Neighboring gene acidic nuclear phosphoprotein 32 family member A Neighboring gene microRNA 4312

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_080252.1 

    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
    68666430..68666724
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    66489306..66489600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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