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LOC128926749 STARR-seq mESC enhancer starr_30594 [ Mus musculus (house mouse) ]

Gene ID: 128926749, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128926749
Gene description
STARR-seq mESC enhancer starr_30594
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rr369344
Summary
This genomic region represents an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) reporter assay in ground-state (2iL) and metastable (SL) mouse embryonic stem cells, where it was defined as a C1 class enhancer that overlaps an active chromatin signature. Two subregions were identified as putative B cell regulatory elements by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and were validated as enhancers by STARR-seq in lipopolysaccharide-activated mouse splenic B cells. This locus also includes a candidate cis-regulatory module (CRM) that was identified in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. That CRM was validated as an active enhancer by high-throughput CapStarr-seq reporter assays showing weak activity in P5424 T cells and NIH3T3 fibroblasts. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC128926749 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (97205498..97207467)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene aminopeptidase puromycin sensitive Neighboring gene predicted gene 11592 Neighboring gene STARR-seq mESC enhancer starr_30592 Neighboring gene STARR-seq mESC enhancer starr_30593 Neighboring gene predicted gene, 31005 Neighboring gene STARR-seq mESC enhancer starr_30595 Neighboring gene mitochondrial ribosomal protein L45 Neighboring gene predicted gene, 53647 Neighboring gene G protein-coupled receptor 179 Neighboring gene suppressor of cytokine signaling 7

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. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Vanhille L, et al. Nat Commun, 2015 Apr 15. PMID 25872643
  2. Gene regulatory networks STARR-ing B cells. Martínez de Paz A, et al. Nat Immunol, 2020 Feb. PMID 31873293, Free PMC Article
  3. Charting the cis-regulome of activated B cells by coupling structural and functional genomics. Chaudhri VK, et al. Nat Immunol, 2020 Feb. PMID 31873292
  4. STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells. Peng T, et al. Genome Biol, 2020 Sep 10. PMID 32912294, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • CapStarr-seq enhancer MGSCv37_chr11:97177079-97177266
  • STARR-positive B cell enhancer ABC_E11771
  • STARR-positive B cell enhancer ABC_E5271
  • regulatory region 369344

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_152392.2 

    Range
    101..2070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    97205498..97207467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version