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LOC125048426 Sharpr-MPRA regulatory region 15027 [ Homo sapiens (human) ]

Gene ID: 125048426, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048426
Gene description
Sharpr-MPRA regulatory region 15027
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 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (68672052..68672346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (62878927..62879221)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RAD51 paralog B Neighboring gene uncharacterized LOC107984016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69073752-69074398 Neighboring gene Sharpr-MPRA regulatory region 11310 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:69086033-69086224 Neighboring gene uncharacterized LOC100996664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5868 Neighboring gene uncharacterized LOC124903333 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:69124801-69124929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69136154-69136654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69136655-69137155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69143042-69143542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69143543-69144043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69149771-69150316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69150317-69150861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69171588-69172111 Neighboring gene uncharacterized LOC105370547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69197453-69198006 Neighboring gene RNA, U6 small nuclear 921, pseudogene Neighboring gene ribosomal protein L12 pseudogene 7

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_080122.1 

    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
    68672052..68672346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    62878927..62879221
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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