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LOC128927512 STARR-positive B cell enhancer ABC_E5540 [ Mus musculus (house mouse) ]

Gene ID: 128927512, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927512
Gene description
STARR-positive B cell enhancer ABC_E5540
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
Rr370087
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. Two subregions were identified as candidate cis-regulatory modules (CRMs) in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. They were validated as enhancers by CapStarr-seq reporter assays, with both showing weak activity in NIH3T3 fibroblasts. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC128927512 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 (35861289..35861686)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene poly (ADP-ribose) polymerase family, member 9 Neighboring gene STARR-seq mESC enhancer starr_40752 Neighboring gene predicted gene 15564 Neighboring gene karyopherin subunit alpha 1 Neighboring gene family with sequence similarity 162, member A Neighboring gene WD repeat domain 5B Neighboring gene STARR-seq mESC enhancer starr_40755 Neighboring gene mitochondrial matrix import factor 23

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_chr16:36041071-36041180
  • CapStarr-seq enhancer MGSCv37_chr16:36041215-36041402
  • regulatory region 370087

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_153766.2 

    Range
    101..498
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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
    35861289..35861686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version