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LOC123956139 Sharpr-MPRA regulatory region 5110 [ Homo sapiens (human) ]

Gene ID: 123956139, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956139
Gene description
Sharpr-MPRA regulatory region 5110
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956139 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (43073330..43073624)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (43231499..43231793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (43112929..43113223)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25905 Neighboring gene uncharacterized LOC105375253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25907 Neighboring gene mitochondrial ribosomal protein L32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:43086257-43086757 Neighboring gene Sharpr-MPRA regulatory region 4044 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:43098985-43099585 Neighboring gene uncharacterized LOC107986790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:43117009-43117801 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:43147486-43148000 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:43157882-43159081 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:43178144-43178740 Neighboring gene HECW1 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25908 Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene microRNA 3943 Neighboring gene RNA, U7 small nuclear 35 pseudogene

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_078334.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    43073330..43073624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    43231499..43231793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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