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LOC123453203 Sharpr-MPRA regulatory region 15257 [ Homo sapiens (human) ]

Gene ID: 123453203, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123453203
Gene description
Sharpr-MPRA regulatory region 15257
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 DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184241921..184242215)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (187051205..187051499)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (183959709..183960003)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20904 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:183908066-183909265 Neighboring gene ATP binding cassette subfamily F member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14958 Neighboring gene von Willebrand factor A domain containing 5B2 Neighboring gene EEF1AKMT4-ECE2 readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:183965331-183966074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:183966075-183966818 Neighboring gene microRNA 1224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20907 Neighboring gene EEF1A lysine methyltransferase 4 Neighboring gene ALG3 alpha-1,3- mannosyltransferase

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_077455.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    184241921..184242215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    187051205..187051499
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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