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LOC109280113 VISTA enhancer mm1337 [ Mus musculus (house mouse) ]

Gene ID: 109280113, updated on 8-Feb-2024

Summary

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Gene symbol
LOC109280113
Gene description
VISTA enhancer mm1337
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
Mm1337; Rr1660
Summary
This locus represents a conserved genomic element that can function as an enhancer. It can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic liver of transgenic mice. 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 subregion was validated as an enhancer by high-throughput CapStarr-seq reporter assays showing weak activity in NIH3T3 fibroblasts. Two other subregions were identified as putative B cell regulatory elements by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and were validated as enhancers by STARR-seq (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC109280113 in Genome Data Viewer
Location:
9; 9
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (40982935..40985983)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (41071639..41074687)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene junctional cadherin complex regulator Neighboring gene ubiquitin specific peptidase 10 pseudogene Neighboring gene cytotoxic and regulatory T cell molecule Neighboring gene ubiquitin associated and SH3 domain containing, B Neighboring gene STARR-seq mESC enhancer starr_23876 Neighboring gene interferon-induced transmembrane protein 3-like Neighboring gene predicted gene, 35657

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. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, Free PMC Article
  2. 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

  • CapStarr-seq enhancer MGSCv37_chr9:40881665-40881871
  • STARR-positive B cell enhancer ABC_E11405
  • STARR-positive B cell enhancer mm9_chr9:40880221-40880522
  • regulatory region 1660

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_054382.1 

    Range
    101..3149
    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_000075.7 Reference GRCm39 C57BL/6J

    Range
    40982935..40985983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version