U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125024491 Sharpr-MPRA regulatory region 2203 [ Homo sapiens (human) ]

Gene ID: 125024491, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125024491
Gene description
Sharpr-MPRA regulatory region 2203
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC125024491 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (58152038..58152445)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (52358995..52359402)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene armadillo like helical domain containing 4 Neighboring gene polycomb group ring finger 3 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr14:58587185-58587752 Neighboring gene NANOG hESC enhancer GRCh37_chr14:58595390-58595891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5794 Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8440 Neighboring gene RNA, 7SL, cytoplasmic 598, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8442 Neighboring gene actin related protein 10

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 5795
  • ATAC-STARR-seq lymphoblastoid silent region 5796

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_080103.2 

    Range
    101..508
    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
    58152038..58152445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    52358995..52359402
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases