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LOC125078093 Sharpr-MPRA regulatory region 7352 [ Homo sapiens (human) ]

Gene ID: 125078093, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078093
Gene description
Sharpr-MPRA regulatory region 7352
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078093 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 (60945210..60945504)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (58748334..58748628)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene RAR related orphan receptor A Neighboring gene uncharacterized LOC124903500 Neighboring gene uncharacterized LOC102724802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:61150768-61151321 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61151721-61152920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9518 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:61199430-61199931 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61200438-61201637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9519 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:61224144-61225343 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:61239167-61239924 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61265032-61266231 Neighboring gene uncharacterized LOC107984805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:61438991-61439492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:61465732-61466232 Neighboring gene uncharacterized LOC105370841

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_080229.1 

    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
    60945210..60945504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    58748334..58748628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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