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LOC125316771 Sharpr-MPRA regulatory region 14154 [ Homo sapiens (human) ]

Gene ID: 125316771, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316771
Gene description
Sharpr-MPRA regulatory region 14154
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 4:PromP, inactive/poised promoter, highly conserved). [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 (64974411..64974705)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (65844380..65844674)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376844 Neighboring gene leucine rich repeat containing 37 member A3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8853 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:62915421-62915921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62915997-62916498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62916499-62916998 Neighboring gene RDM1 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 3243 Neighboring gene uncharacterized LOC107985000 Neighboring gene SLC16A6 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12602 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:62962191-62962354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8856 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:62971753-62972623 Neighboring gene AMZ2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12605 Neighboring gene uncharacterized LOC124904044 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63023805-63024744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:63024745-63025684 Neighboring gene G protein subunit alpha 13 Neighboring gene NANOG hESC enhancer GRCh37_chr17:63043783-63044416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8859

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_080590.1 

    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
    64974411..64974705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    65844380..65844674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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