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LOC109279953 VISTA enhancer mm412 [ Mus musculus (house mouse) ]

Gene ID: 109279953, updated on 9-Aug-2024

Summary

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Gene symbol
LOC109279953
Gene description
VISTA enhancer mm412
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
Mm412; Rr1266
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 neural tube of transgenic mice. A subregion was also 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 P5424 T cells and NIH3T3 fibroblasts. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC109279953 in Genome Data Viewer
Location:
6; 6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (51834215..51835594)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (51857235..51858614)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene sorting nexin 10 Neighboring gene predicted gene, 53331 Neighboring gene STARR-seq mESC enhancer starr_15887 Neighboring gene STARR-seq mESC enhancer starr_15888 Neighboring gene STARR-positive B cell enhancer mm9_chr6:51663532-51663833 Neighboring gene predicted gene, 38811 Neighboring gene STARR-seq mESC enhancer starr_15891 Neighboring gene src family associated phosphoprotein 2 Neighboring gene STARR-seq mESC enhancer starr_15896 Neighboring gene STARR-seq mESC enhancer starr_15897 Neighboring gene STARR-seq mESC enhancer starr_15898 Neighboring gene STARR-seq mESC enhancer starr_15899 Neighboring gene STARR-seq mESC enhancer starr_15900 Neighboring gene Hoxa adjacent long noncoding RNA 1

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_chr6:51807852-51808039
  • regulatory region 1266

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_054225.1 

    Range
    101..1480
    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_000072.7 Reference GRCm39 C57BL/6J

    Range
    51834215..51835594
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version