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LOC125138295 Sharpr-MPRA regulatory region 2833 [ Homo sapiens (human) ]

Gene ID: 125138295, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125138295
Gene description
Sharpr-MPRA regulatory region 2833
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 DNase matched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125138295 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (79874247..79874541)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (77737254..77737548)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (80166589..80166883)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 667, pseudogene Neighboring gene uncharacterized LOC124903536 Neighboring gene ST20-MTHFS readthrough Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:80146049-80146550 Neighboring gene methenyltetrahydrofolate synthetase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6725 Neighboring gene suppressor of tumorigenicity 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9936 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:80216673-80217333 Neighboring gene ST20 antisense RNA 1 Neighboring gene farnesyl diphosphate synthase pseudogene 9

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

See Variation Viewer (GRCh37.p13)

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_080267.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    79874247..79874541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    77737254..77737548
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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