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LOC128926527 STARR-positive B cell enhancer ABC_E8871 [ Mus musculus (house mouse) ]

Gene ID: 128926527, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128926527
Gene description
STARR-positive B cell enhancer ABC_E8871
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
Rr369131
Summary
This genomic region includes a B cell regulatory element that was identified by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing). It was validated as an enhancer by STARR-seq (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells, and also by standard reporter assays in CH12 B lymphoma 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 strong activity in P5424 T cells and weak activity in NIH3T3 fibroblasts. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC128926527 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 (11456267..11456699)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene zona pellucida binding protein Neighboring gene predicted gene, 26458 Neighboring gene TGF beta-inducible nuclear protein 1 pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr11:11361594-11361894 Neighboring gene sperm microtubule inner protein 7 Neighboring gene STARR-positive B cell enhancer ABC_E10664 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:11428864-11429017 Neighboring gene STARR-positive B cell enhancer ABC_E2348 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:11464295-11464600 Neighboring gene STARR-seq mESC enhancer starr_28596 Neighboring gene predicted gene, 29945 Neighboring gene predicted gene 11998 Neighboring gene RIKEN cDNA 4930512M02 gene Neighboring gene STARR-seq mESC enhancer starr_28597

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_chr11:11406270-11406453
  • STARR-positive B cell enhancer mm9_chr11:11406313-11406614
  • regulatory region 369131

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_152178.3 

    Range
    101..533
    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
    11456267..11456699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version