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LOC125138306 Sharpr-MPRA regulatory region 3557 [ Homo sapiens (human) ]

Gene ID: 125138306, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125138306
Gene description
Sharpr-MPRA regulatory region 3557
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 matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [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 (89177778..89178072)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (86932615..86932909)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene abhydrolase domain containing 2, acylglycerol lipase Neighboring gene RNA, U7 small nuclear 195 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:89682791-89683292 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:89683293-89683792 Neighboring gene high mobility group box 1 pseudogene 8 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:89710497-89711696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89738102-89738602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89738603-89739103 Neighboring gene Sharpr-MPRA regulatory region 8523 Neighboring gene vesicle-associated membrane protein-associated protein A-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10044 Neighboring gene retinaldehyde binding protein 1

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_080278.1 

    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
    89177778..89178072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    86932615..86932909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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