Database or information of mouse (MM) mitochondrial cDNA/RNAs

Question

[mhyunjunkang]

Dear All,

I would like to get sequence data and annotation of all of the mouse mitochondrial cDNA (or mitochondrial genes). However, I have no idea where to get this. Could you let me know any websites/database? It would really help me out.

Thanks in advance. HJ

[GenoMax]

1. Do this search at Mouse Genome Informatics site.
2. Click on the MouseMine button.
3. In the new MouseMine portal page that opens up. Filter the list as appropriate. If you want everything then click on export button (you will see the following dialog). Select FASTA sequence and download file.
4. Do one more export to get the GFF3 annotations as a separate file.

[mhyunjunkang]

Thank you for the information. But the FASTA sequences are not available in that way....

Answer 1

[GenoMax]

Let us try BioMart at Ensembl instead.

1. Go to http://ensembl.org (you may be redirected to a nearby mirror)
2. Click on BioMart link at the top of browser
3. Choose database Ensembl genes 92 (as of this writing)
4. Choose dataser --> Mouse genes (GRCm38)
5. Click on Filters --> Region --> Chromosome/Scaffold --> Select MT
6. Click Attributes in left column --> Sequence in right column
7. Under Sequences choose the type (unspliced transcript may be ok)
8. Expand header information --> Choose ID's you would like to include in fasta header
9. Click on Count button at top of page (should be 37 genes)
10. Click Results --> Export all results to file (click on unique only to avoid duplicates --> Go