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LOC125371409 Sharpr-MPRA regulatory region 1146 [ Homo sapiens (human) ]

Gene ID: 125371409, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371409
Gene description
Sharpr-MPRA regulatory region 1146
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125371409 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (37175766..37176060)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (37368829..37369123)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene KIAA1328 Neighboring gene uncharacterized LOC105372069 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34527890-34528524 Neighboring gene uncharacterized LOC124904287 Neighboring gene VISTA enhancer hs590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:34745369-34745869 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:34797958-34798476 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:34798477-34798995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34829500-34830000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34830001-34830501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9407 Neighboring gene uncharacterized LOC105372068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34885971-34886552 Neighboring gene CUGBP Elav-like family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34902991-34903527 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:34921466-34922026 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:34942069-34943065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34948255-34949075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34952714-34953502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34953503-34954289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34983317-34984180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:35001359-35001962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:35009620-35010464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:35031250-35032144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:35044533-35045032 Neighboring gene small nucleolar RNA, H/ACA box 111

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_080679.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    37175766..37176060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    37368829..37369123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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