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LOC125078094 Sharpr-MPRA regulatory region 14002 [ Homo sapiens (human) ]

Gene ID: 125078094, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078094
Gene description
Sharpr-MPRA regulatory region 14002
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 unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078094 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (62066790..62067084)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (59870763..59871057)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903501 Neighboring gene vacuolar protein sorting 13 homolog C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:62359400-62359915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6505 Neighboring gene VPS13C divergent transcript Neighboring gene C2 calcium dependent domain containing 4A Neighboring gene nucleophosmin 1 pseudogene 47 Neighboring gene MPRA-validated peak2366 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:62407814-62408044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:62456935-62457534 Neighboring gene C2 calcium dependent domain containing 4B

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_080230.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    62066790..62067084
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    59870763..59871057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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