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LOC125078027 Sharpr-MPRA regulatory region 3328 [ Homo sapiens (human) ]

Gene ID: 125078027, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078027
Gene description
Sharpr-MPRA regulatory region 3328
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (92755004..92755298)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (86986770..86987064)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene Ras and Rab interactor 3 Neighboring gene uncharacterized LOC124903364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93152626-93153253 Neighboring gene Sharpr-MPRA regulatory region 13986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6038 Neighboring gene Sharpr-MPRA regulatory region 11533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175978-93176602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175352-93175977 Neighboring gene legumain Neighboring gene MPRA-validated peak2238 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6039 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:93260331-93260478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93260501-93261045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93261046-93261589 Neighboring gene golgin A5 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:93312588-93313787 Neighboring gene long intergenic non-protein coding RNA 2833

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_080163.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    92755004..92755298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    86986770..86987064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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