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LOC125048446 Sharpr-MPRA regulatory region 2360 [ Homo sapiens (human) ]

Gene ID: 125048446, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048446
Gene description
Sharpr-MPRA regulatory region 2360
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125048446 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (76832686..76832980)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71042389..71042683)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5958 Neighboring gene vasohibin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77241882-77242840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8772 Neighboring gene VASH1 antisense RNA 1 Neighboring gene angel homolog 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77278266-77278840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77278841-77279414 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:77288377-77289157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77294675-77295362 Neighboring gene leucine rich repeat containing 74A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77350573-77351390 Neighboring gene RN7SK pseudogene 17 Neighboring gene ribosomal protein L22 pseudogene 2

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_080142.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    76832686..76832980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71042389..71042683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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