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LOC114827900 VISTA enhancer mm1677 [ Mus musculus (house mouse) ]

Gene ID: 114827900, updated on 9-Aug-2024

Summary

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Gene symbol
LOC114827900
Gene description
VISTA enhancer mm1677
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
Rr1968
Summary
This locus includes a conserved genomic element that can function as an enhancer. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic forebrain, hindbrain, midbrain, cranial nerve, neural tube and limb of transgenic mice. An overlapping 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 P5424 T cells. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC114827900 in Genome Data Viewer
Location:
1; 1
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (171843161..171846349)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (172015769..172018782)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_03043 Neighboring gene STARR-seq mESC enhancer starr_03044 Neighboring gene predicted gene 52845 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:173849407-173849647 Neighboring gene STARR-positive B cell enhancer ABC_E3330 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:173851483-173851687 Neighboring gene predicted gene, 37065 Neighboring gene SLAM family member 6 Neighboring gene STARR-seq mESC enhancer starr_03046 Neighboring gene STARR-positive B cell enhancer ABC_E5850 Neighboring gene VANGL planar cell polarity 2 Neighboring gene STARR-positive B cell enhancer ABC_E9498 Neighboring gene STARR-seq mESC enhancer starr_03049 Neighboring gene nescient helix loop helix 1 Neighboring gene nicastrin Neighboring gene coatomer protein complex subunit alpha

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_chr1:173945725-173946012
  • regulatory region 1968

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_065256.2 

    Range
    101..3289
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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_000067.7 Reference GRCm39 C57BL/6J

    Range
    171843161..171846349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version