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LOC123464484 Sharpr-MPRA regulatory region 10063 [ Homo sapiens (human) ]

Gene ID: 123464484, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464484
Gene description
Sharpr-MPRA regulatory region 10063
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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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 (190120664..190121134)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (192937030..192937500)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (189838629..189838923)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene tumor protein p63 Neighboring gene microRNA 944 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:189652551-189653750 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:189655039-189656238 Neighboring gene methylthioadenosine phosphorylase pseudogene 2 Neighboring gene prolyl 3-hydroxylase 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:189759008-189759690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14998 Neighboring gene Sharpr-MPRA regulatory region 7173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20983 Neighboring gene P3H2 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:189879699-189880410 Neighboring gene RNA, U6 small nuclear 1109, pseudogene Neighboring gene NMNAT1 pseudogene 3

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 15000

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_077469.2 

    Range
    101..571
    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
    190120664..190121134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    192937030..192937500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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