Mouse Omics

Welcome to the Mouse Omics of LongGeneDB.

Please enter the name of a mouse long gene,  you will obtain the gene’s profiles of conservation among 60 species, histone modifications (H3K4me3, H3K4me1, and H3K27ac) in 14 tissues, gene expression in 22 tissues, higher-order chromatin organization (Hi-C), and single-cell transcriptome

Please enter a gene name: (e.g. Shank2, Cdkl5, Cntnap2, Kcnip1)



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The conservation of the Shank2 gene region.
The plot below shows the conservation of the gene region of Shank2. The phylogenetic p-value (phyloP) scores, which were calculated by the PHAST package for multiple alignments of 59 vertebrate genomes to the mouse genome, were obtained from the UCSC Genome Browser (http://hgdownload.cse.ucsc.edu/goldenpath/mm10/phyloP60way/).
TSS, transcription start site.
TES, transcription end site.

The glire subset includes mm10, cavPor3, dipOrd1, hetGla2, ochPri2, oryCun2, rn5, and speTri2.
The euarchontoglire subset includes the glire subset, tupBel1, calJac3, gorGor3, hg19, micMur1, nomLeu2, otoGar3, panTro4, papHam1, ponAbe2, rheMac3, saiBol1, and tarSyr1.
The placental subset includes the euarchontoglire subset, ailMel1, bosTau7, canFam3, choHof1, dasNov3, echTel1, equCab2, eriEur1, felCat5, loxAfr3, myoLuc2, oviAri1, proCap1, pteVam1, sorAra1, susScr3, triMan1, turTru2, and vicPac1.
The all 60 species list includes the placental subset, anoCar2, chrPic1, danRer7, fr3, gadMor1, galGal4, gasAcu1, latCha1, macEug2, melGal1, melUnd1, monDom5, oreNil2, ornAna1, oryLat2, petMar1, sarHar1, taeGut1, tetNig2, and xenTro3.

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The histone modification profiles at Shank2 gene region.
The plots below show the histone modification profiles at Shank2 gene region measured by ChIP-seq.
H3K27ac, acetylation at the 27th lysine residue of the histone H3 protein.
H3K4me1, mono-methylation at the 4th lysine residue of the histone H3 protein.
H3K4me3, tri-methylation at the 4th lysine residue of the histone H3 protein.
RPM, reads per million uniquely mapped reads.

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The gene expression profile of Shank2 in 22 mouse tissues.
The plot below shows the gene expression profile of Shank2 in 22 mouse tissues measured by mRNA-seq. FPKM, fragments per kilobase of exonic region per million uniquely mapped read pairs.

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The higher-order chromatin organization at Shank2 gene region.
The heatmap below shows the higher-order chromatin organization at Shank2 gene region and the upstream and downstream 100 kb regions. Chromatin organizations were measured by Hi-C in the mouse cortex.
Heatmap legend, Pearson’s Correlation Coefficient of Hi-C normalized interaction.

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The expression profile of Shank2 in 24 cell types.
The plot below shows the expression profile of Shank2 in 24 cell types in the mouse cortex. Gene expression levels were measured by single nuclear RNA-seq.
Slc17a7 is a marker gene for excitatory neurons.
Gad1 is a marker gene for inhibitory neurons.
Slc1a3 is a marker gene for glial cells.

0:  layer 2/3 excitatory neurons     1:  layer 4 excitatory neurons
  2:  layer 5 excitatory neurons        3:  striatum MSNs
  4:  layer 2 excitatory neurons        5:  layer 6 excitatory neurons
6:  GAD2+ inhibitory neurons        7:  PV+ inhibitory neurons
  8:  layer 5 excitatory neurons        9:  layer 5 excitatory neurons
10:  SST+ inhibitory neurons         11:  oligodendrocytes
12:  layer 4 excitatory neurons      13:  layer 6 excitatory neurons
14:  VIP+ inhibitory neurons          15:  unknown cells
16:  isocortex neurons                   17:  hippocampus neurons
18:  unknown excitatory neurons   19:  NPY+ inhibitory neurons
20:  thalamus neurons                   21:  claustrum neurons
22:  astrocytes                               23: oligodendrocyte precursor cells

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