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LOC125078055 Sharpr-MPRA regulatory region 15538 [ Homo sapiens (human) ]

Gene ID: 125078055, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078055
Gene description
Sharpr-MPRA regulatory region 15538
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078055 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 (34927808..34928102)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (32733018..32733312)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene GJD2 divergent transcript Neighboring gene uncharacterized LOC107984776 Neighboring gene tubulin alpha pseudogene 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:35166353-35167552 Neighboring gene aquarius intron-binding spliceosomal factor Neighboring gene ribosomal protein L36a pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:35260004-35260568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9184 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:35277351-35278003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9186 Neighboring gene zinc finger protein 770

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_080191.1 

    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
    34927808..34928102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    32733018..32733312
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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