Assumptions

This intervention can be divided either as minor or major. Minor re-annotation is considered every change of the gene names (in order to have all data in a consistent representation) and the characterisation of intronic orfs. Major changes are the finding of the gene boundaries in the cases where the annotation was not complete and any change of the submitted data concerning the genes, their introns and their boundaries. For determining protein and rRNA genes, BLAST search against the close relatives of the species whose mt genome is under examination was performed. For the trn genes, a tRNA-Scan with the tRNAscan-SE Search Server was employed.  The accepted by the MitoFun site gene names are presented in Table 1. tRNA genes are presented with the symbolism of "trn-One letter aminoacid code", (e.g. trnA for the tRNA of Alanine). The intron number and length mentioned in the Tables above each mt genome of Genome Browser correspond to all universal protein coding genes (i.e., atp6, atp8, atp9, cob, cox1-3, nad1-6, nad4L), and the two rRNA genes (rnl and rns).

Table 1: Gene nonmeclature used throughout MitoFun.

Gene name Product
Fungi Metazoa including Mammals*  
atp6 ATP6 A6 ATP synthase F0 subunit 6
atp8 ATP8 A8 ATP synthase F0 subunit 8
atp9 ATP9 A9 ATP synthase F0 subunit 9
cob COB CYTB/cytb Apocytochrome b
cox1 COX1 COI Cytochrome c oxidase subunit Ι
cox2 COX2 COII Cytochrome c oxidase subunit II
cox3 COX3 COIII Cytochrome c oxidase subunit IΙΙ
nad1 NAD1 ND1 NADH dehydrogenase  subunit 1
nad2 NAD2 ND2 NADH dehydrogenase  subunit 2
nad3 NAD3 ND3 NADH dehydrogenase  subunit 3
nad4 NAD4 ND4 NADH dehydrogenase  subunit 4
nad4L NAD4L ND4L NADH dehydrogenase  subunit 4L
nad5 NAD5 ND5 NADH dehydrogenase  subunit 5
nad6 NAD6 ND6 NADH dehydrogenase  subunit 6
rns srRNA 16S ribosomal RNA Small ribosomal RNA subunit
rnl lrRNA LSU/23S ribosomal RNA Large ribosomal RNA subunit
rps3 rpS5/ S5 var1 Ribosomal protein S3
Intron     groupI /groupII
Intronic orf LAGLI-DADG, GIY-YIG   groupI intron, GIY-YIG endonuclease, LAGLI-DADG endonuclease
LAGLI-DADG LAGLI-DADG   LAGLI-DADG endonuclease
GIY-YIG     GIY-YIG endonuclease
Mitochondrial maturase     Mitochondrial maturase
Reverse transcriptase     Reverse transcriptase
a, b, c, …     Gene copies
1, 2, 3, …     Gene parts
rnpB     RNase P
trnX     Corresponding one letter  amino acid code for tRNA gene
RNA pol     RNA polymerase
DNA pol     DNA polymerase
_pseudo     pseudogenes
*Based on research article Boore J.L. (1999). Animal Mitochondrial Genomes. Nucleic Acids Research 27: 1767-1780.
In the few mt genomes where gene duplications exist, these are shown as "gene name_a, _b" and gene splitting in two parts are shown as "gene name_1, _2".
Contact:
The MitoFun Team welcomes suggestions, comments and submission of novel fungal mt genomes. Please feel free to contact any of the MitoFun Team Members.

Acknowledgements:
MitoFun is a collaborative project between the Department of Genetics and Biotechnology (Faculty of Biology, University of Athens) and the Bioinformatics Research Laboratory (Department of Biological Sciences, University of Cyprus).
This project was partially funded by the University of Athens (Kapodistrias grant no. 70/4/8804) and the University of Cyprus (Grant 3/311).
The MitoFun development team: Ioannis Kirmitzoglou, Maria Ntertili, Stella Tamana, Ioanna Kalvari, Michalis Vasiliadis, Vassili N. Kouvelis, Vasilis J. Promponas, and Milton A. Typas
© 2006-2013 Bioinformatics Research Laboratory, University of Cyprus
© 2006-2013 Department of Genetics and Biotechnology, University of Athens