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LOC125177523 Sharpr-MPRA regulatory region 12460 [ Homo sapiens (human) ]

Gene ID: 125177523, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177523
Gene description
Sharpr-MPRA regulatory region 12460
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, 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 (59685048..59685342)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60553794..60554088)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371847 Neighboring gene RNA, U4 small nuclear 13, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57642652-57643194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8781 Neighboring gene DEAH-box helicase 40 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57695690-57696502 Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8782 Neighboring gene clathrin heavy chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:57760547-57761746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57780642-57781146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57781147-57781650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57784605-57785260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57794547-57795046 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene vacuole membrane protein 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:57831571-57832770 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57845677-57846178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57860713-57861526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57911971-57912470 Neighboring gene VISTA enhancer hs1656 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:57917673-57918402 Neighboring gene microRNA 21

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_080578.1 

    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
    59685048..59685342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    60553794..60554088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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