emap, The Edinburgh Mouse Atlas Project
MusBanks, a database which associates user's arbitrary keywords with mouse bio-resources via biomolecular network information.
Announcement of the NIEHS, October 2006
SNP data are available at NCBI Single Nucleotide Polymorphism (dbSNP)

Strains (IMGT Index)

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The mouse genome

Waterston, R.H. et al.
"Initial sequencing and comparative analysis of the mouse genome"
Nature, 420, 520-562 (2002) PMID: 12466850
Nature: the mouse genome
Mouse Genome Project (BCM)
Mouse Genome Browser Gateway, UCSC Genome Browser
Mouse Ensembl Genome Server, The Sanger Institute and EBI
Mouse Genome Resources, NCBI
- BLAST Mouse Sequences, NCBI
- Mus musculus (house mouse) genome view, NCBI Map Viewer
- Display of multiple assemblies (C57BL/6J reference assembly, mixed strain WGS assembly from Celera, MGSCv3 assembly, partial assemblies from other strains) NCBI Map Viewer.
The NIEHS project (2004-2006) Announcement of the NIEHS, October 2004
- "15 mouse strains will be sequenced within the next two years: 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BTBR T+ tf/J, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, MOLF/EiJ, KK/HlJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ. These strains will be sequenced in reference to C57BL/6J".
- About the NIEHS projet, February 2006
  Two things- this project is sponsored by NIEHS and is being carried out by Perlegen. Technically, they are not sequencing other strains but are doing extensive SNP discovery. They are taking the non-repetitive portion of C57BL/6J and tiling this on arrays. They then hybridize with DNA from other strains to detect SNPs. So- there will not be complete genome assemblies from these other strains, but there will be lots of polymorphism information.
  Here is a link to the site (Deanna Church, NIH/NLM/NCBI, e-mail to mgi list 02/02/2006).
- The sequence maps Mouse genome on NCBI Map viewer include the reference assembly as well as several alternate assemblies. The reference assembly represents the C57BL/6J genome and includes contigs assembled from finished (phase 3) high throughput genomic sequence (HTGs), single fragment HTGS phase 2 and WGS contigs. A hand-curated tiling path was used to guide the assembly of the reference genome. The alternate assemblies include a mixed-strain WGS assembly from Celera, the MGSCv3 assembly, and several BAC-based partial assemblies from other strains (129 substrain, A/J, B6/CBAF1J, Balb/c, C3H, and NOD) (08/05/2006). The July 2001 combined whole genome shotgun (WGS) assembly from Celera of Mus musculus contains 27 million Celera reads on four Mus musculus strains (129X1/SvJ, 129S1/SvImJ, DBA/2J and A/J), 13 million reads on C57BL/6J from the NCBI Trace Archive, 0.4 million BAC end sequences from TIGR, and unfinished and finished BACs pulled from NCBI (Nature, 420, 520-562 (2002)).
  For detailed information about whole genome sequencing and Celera's assembly process, see Venter, J.C. et al., Science 291:1304-1351 (2001) PMID: 11181995.
  Annotation was added to the WGS scaffolds in June 2007.
What is the best estimate of mouse genome size in cM and in terms of number of genes?
1. Estimates of the genome size in cM are given at MGI - Mouse Facts. You can also get the current length of individual chromosomes in cM from MGI's Linkage Map Query Form. For example, Chromosome 1 is 127.0 cM. Please also bear in mind that crossovers are not randomly distributed. For a discussion, see section 7.2.3 in Lee Silver's Mouse Genetics (Paul Szauter, e-mail to mgi list 06/10/2004).
2. Stats on the current mouse genome assembly can be found at NCBI MapViewer Statistics. There are also statistics for several non-sequence based maps on this page. The current assembly is roughly 2.56 Gb. The current working estimate of the actual size is 2.75 Gb- but this is just an estimate. We'll likely have a better handle on that near the end of 2005, when the mouse genome is slated to be finished. For an explanation of how the genome is assembled NCBI Mouse Contig Info. It is quite likely the genome is bigger than 2.5 Gb- There is a paper by Bailey et al. that provides some evidence that the MGSCv3 under represents segmental duplication. The problem, of course, is that we still don't quite know what the level of segmental duplication actually is in the mouse. For a gene based view of Homology/Orthology you can use HomoloGene (Deanna Church, e-mail to mgi list 06/10/2004 and to M.-P. Lefranc 03/01/2005).
3. The UCSC Genome Bioinformatics Group is estimating 41,208 known genes in its latest release http://genome.ucsc.edu. We are currently annotating believed orthologs by doing blastz alignments, and then using Jim Kent's chaining and netting to filter those alignments. We identified over 3 million net elements from mm5 to hg17 (the latest human). You can view these in the genome browser using the "Human Chain" and "Human Net" annotations. We recommend using the nets for looking for orthologs. You can also download our datasets from http://hgdownload.cse.ucsc.edu/downloads.html. We also have a public MySQL server if you wish to examine the datasets on our server. You can use our table browser to intersect chains and nets with known genes. We provide detailed documentation for the methods used to derive each annotation on our site (Heather Trumbower, e-mail to mgi list 06/10/2004).

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BAC library

Bacterial artificial chromosome (BAC) library from male MSM/Ms (Abe et al., Genome Res. 14: 2439-2447, 2004). MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It was believed that subspecies molossinus has contributed substantially to the genome constitution of common laboratory strains of mice, although the majority of their genome is derived from the west European subspecies M. m. domesticus. MSM BAC clones are available from the RIKEN BioResource Center DNA bank. Both ends of approximately 180,000 BAC clone inserts were sequenced, and ~63,000 BAC-end sequence (BES) pairs were mapped onto the C57BL/6J genome.Comparison of the MSM/Ms sequences with the B6 data provided a vast number of SNPs with defined genomic locations. The MSM/B6 polymorphism comparison is available at Mouse Polymorphism DB and from Ensembl Mouse Genome Server (Kuniya Abe and Toshihiko Shiroishi, e-mail 14/01/2005)

The mouse phenome

MMdb, MUGEN Mouse Database, a database of murine models of immune processes and immunological diseases
Mouse Genome Databases, Neurogenetics at UT Health Science Center, primers, integration of MIT and Roche SNP databases (last updated 2002).
MPD, the Mouse Phenome Database, JAX
The updated MPD SNP collection contains SNP records for ~ 540,000 genome-wide locations; there are 125 strains represented but most of the data are for ~20 commonly used strains. SNPs are mapped to Mouse Genome Build 33 / dbSNP Build 123 (Molly Bogue, e-mail 21/01/2005).
Search Mouse SNP between strains, NCBI
Distinguish C57BL/6J and C57BL/6N. More than 1600 SNP were tested against ~100 mouse inbred strains (Petkov P. et al., Genome Res, 2004, 14, 1806-1811, PMID: 15342563), these SNP were also tested against C57BL/6J vs C57BL/6N. C57BL/6 sublines are not identical (especially the N and J, as they have been separated for more than 50 years). Five polymorphisms can distinguish between these two sublines as they are now. If you know that you have C57BL/6 then you can test which subline (N vs J) with these SNPs.
- 08-015199792-M RS# rs3709624
  BL/6J = T
  BL/6N = C
- 11-004367508-M RS# rs3659787
  BL/6J = G
  BL/6N = A
- 13-041017317-M RS# rs3722313
  BL/6J = T
  BL/6N = C
- 15-057561875-M RS# rs3702158
  BL/6J = A
  BL/6N = G
- 19-049914266-M RS# rs3724876
  BL/6J = G
  BL/6N = T
(Michael V. Wiles, The Jackson Laboratory Bar Harbor, USA, e-mail to mgi list 30/06/2005)
2006 Johns Hopkins Phenotyping Symposium Mice and Beyond

The mouse QTL

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Mouse clone providers

MGI does not sell clones, but we can help you find a supplier of a suitable clone from an MGI gene detail page. Here is one example. Go to the Gene Detail Page for Myh6.

Scroll down to the Molecular Reagents section. Click on the number in parentheses next to the phrase "All nucleic" to view a list of genomic nd cDNA clones, and primers as well. Clicking the MGI identifiers in the Nucleotide Probe/Clone AccID column retrieves a detail page for a specific clone, which may contain links to suppliers of that clone.

Other tools for locating clones include Clonefinder at NCBI. This tool allows the user to find clones containing a specific object, such as a gene, or that are contained within a particular genomic region. CloneFinder is available for mouse only.

The NCBI Clone Registry integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.

Sources of clones include: