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LOC125316787 Sharpr-MPRA regulatory region 1101 [ Homo sapiens (human) ]

Gene ID: 125316787, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316787
Gene description
Sharpr-MPRA regulatory region 1101
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, May 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 (72381788..72382082)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (73254867..73255161)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12668 Neighboring gene long intergenic non-protein coding RNA 2003 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70374994-70375570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70382797-70383298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70383299-70383798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12669 Neighboring gene Sharpr-MPRA regulatory region 2052 Neighboring gene long intergenic non-protein coding RNA 673 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:70417088-70418287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70426388-70426888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70464235-70464912 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70472481-70473394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12680 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:70511237-70511737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70513037-70513545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70552918-70553418 Neighboring gene Sharpr-MPRA regulatory region 2461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12681 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70598976-70599943 Neighboring gene long intergenic non-protein coding RNA 511 Neighboring gene ribosomal protein L32 pseudogene 33

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_080606.1 

    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
    72381788..72382082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    73254867..73255161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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