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LOC125177520 Sharpr-MPRA regulatory region 6256 [ Homo sapiens (human) ]

Gene ID: 125177520, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177520
Gene description
Sharpr-MPRA regulatory region 6256
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177520 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 (57948748..57949042)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (58822031..58822325)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55923593-55924200 Neighboring gene mitochondrial ribosomal protein S23 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:55927391-55927900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55937722-55938572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55938573-55939422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55939423-55940272 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:55945275-55946474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55951125-55951765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55951766-55952407 Neighboring gene CUE domain containing 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55953049-55953690 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55953691-55954331 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:55956376-55956928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55958036-55958588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55958589-55959141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55962626-55963126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55969929-55970670 Neighboring gene Sharpr-MPRA regulatory region 2303 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55977227-55977897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12452 Neighboring gene uncharacterized LOC107985065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55991179-55991679 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:56004573-56005088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12454 Neighboring gene Sharpr-MPRA regulatory region 4150 Neighboring gene NANOG hESC enhancer GRCh37_chr17:56029838-56030339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56043109-56043617 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:56046907-56047067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8755 Neighboring gene vascular endothelial zinc finger 1 Neighboring gene uncharacterized LOC101929185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12457 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:56082218-56083417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12459 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56084242-56084960 Neighboring gene serine and arginine rich splicing factor 1

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_080575.1 

    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
    57948748..57949042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    58822031..58822325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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