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LOC128925533 CapStarr-seq enhancer MGSCv37_chr6:115938993-115939194 [ Mus musculus (house mouse) ]

Gene ID: 128925533, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128925533
Gene description
CapStarr-seq enhancer MGSCv37_chr6:115938993-115939194
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
Rr368157
Summary
This locus includes a subregion that 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. This locus also 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 (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC128925533 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (115965936..115966360)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr6:115895647-115895947 Neighboring gene rhodopsin Neighboring gene rhodopsin enhancer region Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:115921305-115921458 Neighboring gene H1.8 linker histone Neighboring gene plexin D1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:115939698-115939944 Neighboring gene predicted gene, 53336 Neighboring gene transmembrane and coiled coil domains 1 Neighboring gene STARR-positive B cell enhancer ABC_E3672 Neighboring gene STARR-positive B cell enhancer ABC_E6473 Neighboring gene H2A histone family, member Z pseudogene

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

  • STARR-positive B cell enhancer ABC_E10403
  • regulatory region 368157

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_151221.2 

    Range
    101..525
    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_000072.7 Reference GRCm39 C57BL/6J

    Range
    115965936..115966360
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version