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LOC128927474 CapStarr-seq enhancer MGSCv37_chr16:11254345-11254532 [ Mus musculus (house mouse) ]

Gene ID: 128927474, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927474
Gene description
CapStarr-seq enhancer MGSCv37_chr16:11254345-11254532
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
Rr370051
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 P5424 T cells and 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 LOC128927474 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (11072116..11072459)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2610020C07 gene Neighboring gene STARR-positive B cell enhancer ABC_E7427 Neighboring gene STARR-positive B cell enhancer ABC_E8617 Neighboring gene G1 to S phase transition 1 Neighboring gene predicted gene, 57631 Neighboring gene microRNA 1945 Neighboring gene STARR-seq mESC enhancer starr_40101 Neighboring gene STARR-positive B cell enhancer mm9_chr16:11322815-11323116 Neighboring gene tumor necrosis factor receptor superfamily, member 17 Neighboring gene sorting nexin 29 Neighboring gene STARR-positive B cell enhancer mm9_chr16:11385888-11386189 Neighboring gene DEAH (Asp-Glu-Ala-His) box polypeptide 15 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 ABC_E948
  • regulatory region 370051

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_153101.2 

    Range
    101..444
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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_000082.7 Reference GRCm39 C57BL/6J

    Range
    11072116..11072459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version