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LOC125316785 Sharpr-MPRA regulatory region 12537 [ Homo sapiens (human) ]

Gene ID: 125316785, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316785
Gene description
Sharpr-MPRA regulatory region 12537
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 3:PromF, promoter flanking). [provided by RefSeq, May 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 (69141788..69142082)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (70018380..70018674)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily A member 6 Neighboring gene Sharpr-MPRA regulatory region 12590 Neighboring gene SEC24 homolog A pseudogene 1 Neighboring gene microRNA 4524b Neighboring gene microRNA 4524a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12652 Neighboring gene MPRA-validated peak2964 silencer Neighboring gene ATP binding cassette subfamily A member 10 Neighboring gene MPRA-validated peak2965 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:67209122-67210042 Neighboring gene MPRA-validated peak2966 silencer Neighboring gene uncharacterized LOC100133319 Neighboring gene ATP binding cassette subfamily A member 5 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 4

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_080604.1 

    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
    69141788..69142082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    70018380..70018674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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