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LOC125146383 Sharpr-MPRA regulatory region 15077 [ Homo sapiens (human) ]

Gene ID: 125146383, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146383
Gene description
Sharpr-MPRA regulatory region 15077
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - 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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See LOC125146383 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4000728..4001022)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4027969..4028273)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4011545-4012044 Neighboring gene adenylate cyclase 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4031926-4032449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4032450-4032972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4037243-4037742 Neighboring gene uncharacterized LOC124903633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4046659-4047440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4047441-4048221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4061099-4061744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4061745-4062389 Neighboring gene Sharpr-MPRA regulatory region 11986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4075057-4075558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4075559-4076058 Neighboring gene uncharacterized LOC124900373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4109664-4110164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4135427-4136150 Neighboring gene Sharpr-MPRA regulatory region 10289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4158443-4158942 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4163377-4163587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7145 Neighboring gene DBI pseudogene 3

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_080312.1 

    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
    4000728..4001022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    4027969..4028273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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