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LOC114827945 VISTA enhancer mm1644 [ Mus musculus (house mouse) ]

Gene ID: 114827945, updated on 9-Aug-2024

Summary

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Gene symbol
LOC114827945
Gene description
VISTA enhancer mm1644
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
Rr1935
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 heart and blood vessels of transgenic mice. Two subregions were also 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 high-throughput CapStarr-seq reporter assays, with both subregions showing weak activity in NIH3T3 fibroblasts, and one subregion additionally showing weak activity in P5424 T cells. Another subregion was identified as a putative B cell regulatory element by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and was validated as an enhancer 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 LOC114827945 in Genome Data Viewer
Location:
15; 15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (77681960..77685499)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (77797760..77801299)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene apolipoprotein L 9b Neighboring gene apolipoprotein L 8 Neighboring gene myosin, heavy polypeptide 9, non-muscle Neighboring gene STARR-seq mESC enhancer starr_39115 Neighboring gene STARR-seq mESC enhancer starr_39117 Neighboring gene STARR-positive B cell enhancer ABC_E8905 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:77664820-77665003 Neighboring gene STARR-positive B cell enhancer ABC_E140 Neighboring gene STARR-positive B cell enhancer ABC_E5493 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:77680033-77680254 Neighboring gene predicted gene, 22107 Neighboring gene STARR-seq mESC enhancer starr_39123 Neighboring gene predicted gene, 53901

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
  3. Gene regulatory networks STARR-ing B cells. Martínez de Paz A, et al. Nat Immunol, 2020 Feb. PMID 31873293, Free PMC Article
  4. 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_chr15:77629273-77629474
  • CapStarr-seq enhancer MGSCv37_chr15:77631019-77631202
  • STARR-positive B cell enhancer ABC_E11594
  • regulatory region 1935

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_065301.1 

    Range
    101..3640
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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_000081.7 Reference GRCm39 C57BL/6J

    Range
    77681960..77685499
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version