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LOC125177500 Sharpr-MPRA regulatory region 4171 [ Homo sapiens (human) ]

Gene ID: 125177500, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177500
Gene description
Sharpr-MPRA regulatory region 4171
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 matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177500 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 (50274548..50274842)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51141626..51141920)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48335091-48335661 Neighboring gene uncharacterized LOC124904028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48354331-48354878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48354879-48355426 Neighboring gene transmembrane protein 92 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8693 Neighboring gene TMEM92 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr17:48380397-48381379 Neighboring gene NANOG hESC enhancer GRCh37_chr17:48388769-48389287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12381 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:48395384-48395963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48395964-48396542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8696 Neighboring gene Sharpr-MPRA regulatory region 10047 Neighboring gene xylosyltransferase 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_080555.1 

    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
    50274548..50274842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    51141626..51141920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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