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LOC123881343 Sharpr-MPRA regulatory region 1028 [ Homo sapiens (human) ]

Gene ID: 123881343, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123881343
Gene description
Sharpr-MPRA regulatory region 1028
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (156773515..156773809)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (157975766..157976060)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (157094649..157094943)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901444 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157007142-157008069 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157008070-157008996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25314 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:157029670-157029847 Neighboring gene H3 histone pseudogene 28 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25315 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:157042423-157042971 Neighboring gene MPRA-validated peak6246 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25318 Neighboring gene uncharacterized LOC115308161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17712 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157099729-157100264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17715 Neighboring gene microRNA 4466 Neighboring gene AT-rich interaction domain 1B

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_078248.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    156773515..156773809
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    157975766..157976060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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