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LOC122889048 Sharpr-MPRA regulatory region 5433 [ Homo sapiens (human) ]

Gene ID: 122889048, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889048
Gene description
Sharpr-MPRA regulatory region 5433
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889048 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (17877377..17877671)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (17879484..17879778)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (17918869..17919163)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909350 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:17901798-17902528 and GRCh37_chr3:17902529-17903258 Neighboring gene PDCL3 pseudogene 3 Neighboring gene pyrophosphatase (inorganic) 1 pseudogene Neighboring gene B-cell acute lymphoblastic leukemia associated long RNA 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:18088671-18088844 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:18140124-18141323 Neighboring gene VISTA enhancer hs250 Neighboring gene uncharacterized LOC124909351 Neighboring gene Sharpr-MPRA regulatory region 1190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:18371920-18372490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:18372491-18373060 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:18386263-18386883 Neighboring gene SATB homeobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14129 Neighboring gene SATB1 antisense RNA 1

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_077180.1 

    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
    17877377..17877671
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    17879484..17879778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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