Mouse strain assembly hub - May 3, 2017

This assembly hub contains 16 different strains of mice as the primary sequence, along with strain-specific gene annotations. Viewing this assembly hub on mm10, there will be a multiple alignment between the reference and 16 different strains of mice plus rat. The creation of this hub was made possible thanks to the Mouse Genomes Project.

How to view the hub

You can easily load this hub from our Public Hubs page or by clicking these links to any of our official websites:

To manually attach this hub to other genome browsers:

  1. From the blue navigation bar, go to My Data -> Track Hubs
  2. Then select the My Hubs tab and enter this URL into the textbox:
  3. Once you have added the URL to the entry form, press the Add Hub button to add the hub.

After adding the hub, you will be redirected to the mm10 gateway page. To view one of the new mice strains as the primary sequence, at the top of the phylogenetic tree diagram on the gateway page, click on mouse strain assemblies (16). This will allow you to choose between the 16 different strains from the drop-down menu.

Data resource links

UCSC genome
Ensembl genome
NCBI data
NCBI data
assembly name/
hub data
Jackson Laboratory/
strain data
129S1_SvImJ Mus musculus SAMN04489811 GCA_001624185.1 129S1_SvImJ_v1 002448
A_J Mus musculus SAMN04489813 GCA_001624215.1 A_J_v1 000646
AKR_J Mus musculus SAMN04489815 GCA_001624295.1 AKR_J_v1 000648
CAST_EiJ Mus musculus castaneus SAMN04489822 GCA_001624445.1 CAST_EiJ_v1 000928
CBA_J Mus musculus SAMN04489823 GCA_001624475.1 CBA_J_v1 000656
DBA_2J Mus musculus SAMN04489824 GCA_001624505.1 DBA_2J_v1 000671
FVB_NJ Mus musculus SAMN04489825 GCA_001624535.1 FVB_NJ_v1 001800
NOD_ShiLtJ Mus musculus SAMN04489827 GCA_001624675.1 NOD_ShiLtJ_v1 001976
NZO_HlLtJ Mus musculus SAMN04489828 GCA_001624745.1 NZO_HlLtJ_v1 002105
PWK_PhJ Mus musculus musculus SAMN04489829 GCA_001624775.1 PWK_PhJ_v1 003715
WSB_EiJ Mus musculus domesticus SAMN04489831 GCA_001624835.1 WSB_EiJ_v1 001145
SPRET_EiJ Mus spretus SAMN04489830 GCA_001624865.1 SPRET_EiJ_v1 001146
BALB_cJ Mus musculus SAMN04489816 GCA_001632525.1 BALB_cJ_v1 000651
C57BL_6NJ Mus musculus SAMN04489821 GCA_001632555.1 C57BL_6NJ_v1 005304
C3H_HeJ Mus musculus SAMN04489818 GCA_001632575.1 C3H_HeJ_v1 000659
LP_J Mus musculus SAMN04489826 GCA_001632615.1 LP_J_v1 000676

Note: In the browser, insertions may be missing from visualizations for alignments between these strains due to missing 'i' rows in the MAF files for these mouse strain assemblies.