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LOC125177464 Sharpr-MPRA regulatory region 7659 [ Homo sapiens (human) ]

Gene ID: 125177464, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177464
Gene description
Sharpr-MPRA regulatory region 7659
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (38463528..38463822)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (39326556..39326850)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene suppressor of cytokine signaling 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36570079-36571013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:36571014-36571949 and GRCh37_chr17:36571950-36572884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36574173-36574722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36574723-36575272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36575776-36576704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36577634-36578562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36580149-36580794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36584872-36585780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36585781-36586688 Neighboring gene Rho GTPase activating protein 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36592213-36592713 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36597014-36597516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36605280-36606221 Neighboring gene uncharacterized LOC101929494 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36607163-36608104 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:36614287-36614452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36616590-36617218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36621073-36621864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36625516-36626152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36628374-36628874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36640731-36641252 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36649489-36649990 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36649991-36650490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36655308-36655834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36655835-36656359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36665002-36665819 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36665820-36666636 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:36706969-36707178 Neighboring gene SRC kinase signaling inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36717306-36717859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36718413-36718965 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36719518-36720070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36718966-36719517 Neighboring gene uncharacterized LOC105371761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36720624-36721176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36721177-36721728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36722271-36722779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36734639-36735366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36735367-36736094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36748159-36748740 Neighboring gene uncharacterized LOC124903992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36749033-36749534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36749535-36750034

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

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_080519.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    38463528..38463822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    2498835..2499129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    39326556..39326850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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