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LOC128925422 CapStarr-seq enhancer MGSCv37_chr6:34267489-34267672 [ Mus musculus (house mouse) ]

Gene ID: 128925422, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128925422
Gene description
CapStarr-seq enhancer MGSCv37_chr6:34267489-34267672
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
Rr368048
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 LOC128925422 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 (34294305..34294607)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:34126896-34127097 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:34132037-34132238 Neighboring gene STARR-seq mESC enhancer starr_15530 Neighboring gene predicted gene 13855 Neighboring gene predicted gene, 32533 Neighboring gene STARR-seq mESC enhancer starr_15531 Neighboring gene STARR-seq mESC enhancer starr_15532 Neighboring gene aldo-keto reductase family 1 member B Neighboring gene STARR-seq mESC enhancer starr_15533 Neighboring gene STARR-seq mESC enhancer starr_15534 Neighboring gene aldo-keto reductase family 1, member B8 Neighboring gene cancer susceptibility candidate 4 pseudogene Neighboring gene RIO kinase 2 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

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • STARR-positive B cell enhancer mm9_chr6:34267370-34267670
  • regulatory region 368048

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_151116.2 

    Range
    101..403
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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_000072.7 Reference GRCm39 C57BL/6J

    Range
    34294305..34294607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version