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LOC128925314 STARR-positive B cell enhancer ABC_E6377 [ Mus musculus (house mouse) ]

Gene ID: 128925314, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128925314
Gene description
STARR-positive B cell enhancer ABC_E6377
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
Rr367944
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 LOC128925314 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (123267081..123267382)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6444 Neighboring gene transmembrane protein 120B Neighboring gene STARR-seq mESC enhancer starr_14311 Neighboring gene STARR-seq mESC enhancer starr_14312 Neighboring gene STARR-positive B cell enhancer ABC_E10349 Neighboring gene STARR-positive B cell enhancer ABC_E4788 Neighboring gene ras homolog family member F (in filopodia) Neighboring gene STARR-positive B cell enhancer ABC_E1060 Neighboring gene STARR-positive B cell enhancer ABC_E8079 Neighboring gene STARR-seq mESC enhancer starr_14314 Neighboring gene expressed sequence AI480526 Neighboring gene STARR-positive B cell enhancer ABC_E2763 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:123591600-123591709 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:123599408-123599706 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:123599709-123599818 Neighboring gene SET domain containing 1B Neighboring gene STARR-positive B cell enhancer ABC_E6378 Neighboring gene predicted gene, 54284

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_chr5:123579110-123579293
  • regulatory region 367944

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_151016.2 

    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_000071.7 Reference GRCm39 C57BL/6J

    Range
    123267081..123267382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version