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LOC128927822 STARR-seq mESC enhancer starr_44826 [ Mus musculus (house mouse) ]

Gene ID: 128927822, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927822
Gene description
STARR-seq mESC enhancer starr_44826
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
Rr370389
Summary
This genomic region represents an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) reporter assay in metastable (SL) mouse embryonic stem cells, where it was defined as a C1 class enhancer that overlaps an active chromatin signature. 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 NIH3T3 fibroblasts. This locus additionally includes a B cell regulatory element that was identified by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and which was validated as an enhancer by STARR-seq in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC128927822 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (65548912..65550530)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC118568359 Neighboring gene microRNA 122 Neighboring gene STARR-positive B cell enhancer ABC_E9983 Neighboring gene STARR-seq mESC enhancer starr_44824 Neighboring gene alpha-kinase 2 Neighboring gene STARR-positive B cell enhancer ABC_E3231 Neighboring gene STARR-positive B cell enhancer ABC_E2511 Neighboring gene STARR-positive B cell enhancer ABC_E7595 Neighboring gene STARR-seq mESC enhancer starr_44825 Neighboring gene predicted gene, 41757 Neighboring gene STARR-positive B cell enhancer ABC_E7596 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:65590163-65590272 Neighboring gene STARR-positive B cell enhancer mm9_chr18:65590289-65590590 Neighboring gene predicted gene, 46618 Neighboring gene MALT1 paracaspase

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_chr18:65576029-65576212
  • STARR-positive B cell enhancer ABC_E7597
  • regulatory region 370389

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_153429.2 

    Range
    101..1719
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    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_000084.7 Reference GRCm39 C57BL/6J

    Range
    65548912..65550530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version