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Mouse Genome Information - Mouse Genome Assembly GRCm38


The laboratory mouse is a major model organism for basic mammalian biology, human disease, and genome evolution, and is extensively used for comparative genome analysis.

Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus; Mus musculus.


Summary

AssemblyMouse Genome Assembly GRCm38
GCF_000001635.26
Base Pairs3,482,409,794
Total Sequence Length (bp)2,818,974,548
Total Assembly Gap Length (bp)79,435,572
Gaps Between Scaffolds (bp)191
Number of Scaffolds336
Scaffold N50 (bp)52,589,046
Scaffold L5018
Number of Contigs885
Contig N50 (bp)32,273,079
Contig L5026
No. of NCBI chromosome records22

Gene Counts

Total Genes53210
Protein Coding genes22488
Non coding RNA16421
tRNA428
SnRNA926
rRNA63
Pseudogenes10939
miRNA Targets Confirmed816
miRNA Targets Predicted32320
Gene transcripts144514
Genes without orthologs33814
Genes with Orthologs19396

#Mouse Genes with Orthologs in...

Human19229
Rat17898
Chinchilla15965
Bonobo16757
Dog17040
Squirrel16139
Pig17018

Other

Exons516817
QTLS2668
SSLPs44341
Karyotype
 
Chromosomes
,
ChromosomeSequence LengthGap LengthGap CountContig CountRefSeq Id
1 195471971 3562732 41 8 NC_000067.6
2 182113224 3786573 28 7 NC_000068.7
3 160039680 3640814 12 4 NC_000069.6
4 156508116 4452505 43 3 NC_000070.6
5 151834684 3915010 34 12 NC_000071.6
6 149736546 3400000 10 4 NC_000072.6
7 145441459 3586031 32 5 NC_000073.6
8 129401213 3789781 14 5 NC_000074.6
9 124595110 3438092 36 7 NC_000075.6
10 130694993 3627229 30 3 NC_000076.6
11 122082543 3336598 7 2 NC_000077.6
12 120129022 3206600 6 2 NC_000078.6
13 120421639 3300446 11 5 NC_000079.6
14 124902244 3460131 13 2 NC_000080.6
15 104043685 3390370 12 3 NC_000081.6
16 98207768 3188000 6 2 NC_000082.6
17 94987271 3279807 39 3 NC_000083.6
18 90702639 3250000 7 3 NC_000084.6
19 61431566 3225710 7 2 NC_000085.6
X 171031299 7543293 97 20 NC_000086.7
Y 91744698 3620000 32 16 NC_000087.7
MT 16299 - - 1 NC_005089.1
References
Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. PMID: 12466850 

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.