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LOC125316818 Sharpr-MPRA regulatory region 10297 [ Homo sapiens (human) ]

Gene ID: 125316818, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316818
Gene description
Sharpr-MPRA regulatory region 10297
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125316818 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82015673..82015967)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82882832..82883126)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79914359-79914943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79914944-79915527 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:79917211-79917773 and GRCh37_chr17:79917774-79918336 Neighboring gene notum, palmitoleoyl-protein carboxylesterase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79925163-79925740 Neighboring gene uncharacterized LOC124904087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9177 Neighboring gene uncharacterized LOC105371939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79934117-79934890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79934891-79935662 Neighboring gene ASPSCR1 tether for SLC2A4, UBX domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79947643-79948352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79949063-79949770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79951899-79952606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79958937-79959584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79961033-79961554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79961555-79962076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79962077-79962598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79963388-79963894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79966024-79966524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79972873-79973594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79974318-79975039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79979009-79979681 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79981231-79982154 Neighboring gene centromere protein X Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79987649-79988172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9180 Neighboring gene leucine rich repeat containing 45

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_080636.1 

    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
    82015673..82015967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82882832..82883126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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