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LOC125371499 Sharpr-MPRA regulatory regions 11764 and 11751 [ Homo sapiens (human) ]

Gene ID: 125371499, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371499
Gene description
Sharpr-MPRA regulatory regions 11764 and 11751
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. Two adjacent subregions were validated as functional repressive elements by Sharpr-MPRA (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 24:Quies, heterochromatin/dead zone). One subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (24001227..24001821)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (24148847..24149441)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 726 Neighboring gene uncharacterized LOC100505851 Neighboring gene RNA, 28S ribosomal pseudogene Neighboring gene Sharpr-MPRA regulatory region 3900 Neighboring gene RNA, 5.8S ribosomal pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14397 Neighboring gene zinc finger protein 254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14400 Neighboring gene BCL2 interacting protein 3 pseudogene 40

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

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 11751
  • Sharpr-MPRA regulatory region 11764

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_080800.1 

    Range
    101..695
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    24001227..24001821
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    24148847..24149441
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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