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LOC128924847 STARR-positive B cell enhancer ABC_E6083 [ Mus musculus (house mouse) ]

Gene ID: 128924847, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128924847
Gene description
STARR-positive B cell enhancer ABC_E6083
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
Rr367495
Summary
This genomic region was identified as a putative B cell regulatory element by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and was validated as an enhancer by STARR-seq (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. A subregion was identified as a candidate cis-regulatory module (CRM) 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. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC128924847 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (96487514..96487815)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene hemojuvelin BMP co-receptor Neighboring gene STARR-positive B cell enhancer mm9_chr3:96351291-96351592 Neighboring gene STARR-positive B cell enhancer ABC_E6082 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:96361830-96361983 Neighboring gene STARR-seq mESC enhancer starr_08439 Neighboring gene predicted gene 15441 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:96368663-96368826 Neighboring gene thioredoxin interacting protein Neighboring gene STARR-seq mESC enhancer starr_08441 Neighboring gene polymerase (RNA) III (DNA directed) polypeptide G like Neighboring gene STARR-seq mESC enhancer starr_08442 Neighboring gene STARR-positive B cell enhancer ABC_E3451 Neighboring gene ankyrin repeat domain 34A Neighboring gene RIKEN cDNA 6330549D23 gene Neighboring gene predicted gene, 52628 Neighboring gene Lix1-like

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

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • CapStarr-seq enhancer MGSCv37_chr3:96384146-96384329
  • regulatory region 367495

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_150595.2 

    Range
    101..402
    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_000069.7 Reference GRCm39 C57BL/6J

    Range
    96487514..96487815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version