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LOC125078042 Sharpr-MPRA regulatory region 14595 [ Homo sapiens (human) ]

Gene ID: 125078042, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078042
Gene description
Sharpr-MPRA regulatory region 14595
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 23:Low, low signal proximal to active elements). [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 (103033852..103034146)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (97270103..97270397)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene TNF receptor associated factor 3 Neighboring gene RNA, U6 small nuclear 1316, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:103352003-103353202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103357046-103357546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103357547-103358047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103366521-103367022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103367023-103367522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103379429-103380018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103380019-103380608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103380952-103381452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6134 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103390587-103390785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6136 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:103411482-103412681 Neighboring gene CDC42 binding protein kinase beta Neighboring gene amnion associated transmembrane protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103452779-103453413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103453414-103454047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103464738-103465284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9093 Neighboring gene Sharpr-MPRA regulatory region 6354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103486267-103486822 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103489632-103489899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103524373-103525023 Neighboring gene ribosomal protein L13 pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103541151-103541742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6141 Neighboring gene LBH domain containing 2

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_080177.1 

    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
    103033852..103034146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    97270103..97270397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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