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LOC125467771 Sharpr-MPRA regulatory region 15158 [ Homo sapiens (human) ]

Gene ID: 125467771, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467771
Gene description
Sharpr-MPRA regulatory region 15158
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 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125467771 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (107843059..107843353)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106279795..106280089)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:106968611-106969112 Neighboring gene TSC22 domain family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:106975096-106975705 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:106980023-106980600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:106992672-106993524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:106993525-106994376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107017786-107018363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107018364-107018940 Neighboring gene Sharpr-MPRA regulatory region 6089 Neighboring gene nuclear cap binding protein subunit 2 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20934 Neighboring gene midline 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107120928-107121436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107121437-107121945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29837 Neighboring gene uncharacterized LOC101928335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107162128-107162628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107162629-107163129 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:107178227-107179426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107179498-107180201 Neighboring gene TMEM230 pseudogene 1

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_081241.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    107843059..107843353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    106279795..106280089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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