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LOC125177353 Sharpr-MPRA regulatory region 14871 [ Homo sapiens (human) ]

Gene ID: 125177353, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177353
Gene description
Sharpr-MPRA regulatory region 14871
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75621151..75621445)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81669444..81669738)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11138 Neighboring gene Sharpr-MPRA regulatory region 12601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75600739-75601492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11139 Neighboring gene GABA type A receptor associated protein like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11141 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75626991-75627988 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75627989-75628985 Neighboring gene adenosine deaminase tRNA specific 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655412-75655932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655933-75656452 Neighboring gene H3K27ac hESC enhancers GRCh37_chr16:75656453-75656972 and GRCh37_chr16:75656973-75657492 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75663368-75664567 Neighboring gene lysyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75681635-75682592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75682593-75683548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11146 Neighboring gene TERF2 interacting protein

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_080421.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    75621151..75621445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    81669444..81669738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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