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LOC123453200 Sharpr-MPRA regulatory region 15184 [ Homo sapiens (human) ]

Gene ID: 123453200, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123453200
Gene description
Sharpr-MPRA regulatory region 15184
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, Nov 2021]
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Genomic context

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See LOC123453200 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (183411601..183411895)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (186219017..186219311)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (183129389..183129683)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene MCF.2 cell line derived transforming sequence-like 2 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:182980890-182981594 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:182983517-182984716 Neighboring gene RNA, 5S ribosomal pseudogene 151 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:183003113-183004312 Neighboring gene uncharacterized LOC107986160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:183014350-183015174 Neighboring gene Sharpr-MPRA regulatory region 12547 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14939 Neighboring gene NANOG hESC enhancer GRCh37_chr3:183118178-183118679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14940 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:183152219-183153159 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:183165063-183165598 Neighboring gene small nucleolar RNA SNORA81 Neighboring gene small nucleolar RNA, H/ACA box 63D Neighboring gene small nucleolar RNA host gene 33

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

See Variation Viewer (GRCh37.p13)

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_077452.1 

    Range
    101..395
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    183411601..183411895
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    186219017..186219311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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