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LOC125177492 Sharpr-MPRA regulatory region 3811 [ Homo sapiens (human) ]

Gene ID: 125177492, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177492
Gene description
Sharpr-MPRA regulatory region 3811
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 DNase matched - 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 (46889563..46889857)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (47751027..47751321)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 37 member A2 Neighboring gene uncharacterized LOC101929777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44909071-44909718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44909719-44910366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44910367-44911014 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:44922250-44922415 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:44941221-44941463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44941567-44942392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44953785-44954385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:44955695-44956194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:44967346-44967846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:44971730-44972350 Neighboring gene Wnt family member 9B Neighboring gene uncharacterized LOC112268191 Neighboring gene long intergenic non-protein coding RNA 1974

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_080547.1 

    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
    46889563..46889857
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187663.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1408980..1409274
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    47751027..47751321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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