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LOC125177472 Sharpr-MPRA regulatory region 7873 [ Homo sapiens (human) ]

Gene ID: 125177472, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177472
Gene description
Sharpr-MPRA regulatory region 7873
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 1:Tss, active promoter, TSS/CpG island region). [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 (40648057..40648351)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (41512435..41512729)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38716282-38716799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38720363-38721279 Neighboring gene C-C motif chemokine receptor 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12155 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:38738644-38738789 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:38744874-38746073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12157 Neighboring gene Sharpr-MPRA regulatory region 2180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12162 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 Neighboring gene keratin 222 Neighboring gene uncharacterized LOC105371775 Neighboring gene keratin 224, pseudogene

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_080527.1 

    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
    40648057..40648351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    41512435..41512729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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