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LOC123464473 Sharpr-MPRA regulatory region 9603 [ Homo sapiens (human) ]

Gene ID: 123464473, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464473
Gene description
Sharpr-MPRA regulatory region 9603
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123464473 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 (185749941..185750235)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (188565878..188566172)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (185467729..185468023)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SUMO specific peptidase 2 Neighboring gene ribosomal protein L34 pseudogene 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185359885-185360103 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185363553-185364440 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185369908-185370106 Neighboring gene insulin like growth factor 2 mRNA binding protein 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:185406257-185407456 Neighboring gene IGF2BP2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185442702-185443202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185445539-185446390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185446391-185447242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185449611-185450110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14976 Neighboring gene uncharacterized LOC124906313 Neighboring gene Sharpr-MPRA regulatory region 5696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487094-185487594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487595-185488095 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185491440-185492292 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:185496875-185497772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185497860-185498360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185501879-185502772 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185504559-185505450 Neighboring gene microRNA 548aq Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185507237-185508130 Neighboring gene VISTA enhancer hs1976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185516757-185517258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185517259-185517758 Neighboring gene NANOG hESC enhancer GRCh37_chr3:185520396-185520897 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:185525354-185525896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:185540833-185541696 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185542636-185542866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14978 Neighboring gene Sharpr-MPRA regulatory region 6530 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185623478-185623669 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185655136-185655863 Neighboring gene transformer 2 beta homolog

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_077459.1 

    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
    185749941..185750235
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    188565878..188566172
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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