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LOC125177495 Sharpr-MPRA regulatory region 1659 [ Homo sapiens (human) ]

Gene ID: 125177495, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177495
Gene description
Sharpr-MPRA regulatory region 1659
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 DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [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 (47362223..47362517)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48224873..48225167)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene integrin subunit beta 3 Neighboring gene uncharacterized LOC107985029 Neighboring gene Sharpr-MPRA regulatory region 4923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12309 Neighboring gene Sharpr-MPRA regulatory region 4395 Neighboring gene VISTA enhancer hs2033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45369753-45370253 Neighboring gene EFCAB13 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12311 Neighboring gene EF-hand calcium binding domain 13 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:45416653-45417154 Neighboring gene UDP-N-acetylglucosamine pyrophosphorylase 1 pseudogene Neighboring gene MPRA-validated peak2872 silencer Neighboring gene MPRA-validated peak2873 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8626 Neighboring gene nuclear factor, erythroid 2 like 3 pseudogene 2

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_080550.1 

    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
    47362223..47362517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48224873..48225167
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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