Table 1. Mitochondrial group II intron-encoded ORFs and related ORFs.
| Species namea |
Organism class |
Host gene |
Intron |
ORF
domainsb |
YxDDc |
Sized |
Framee |
Accession numberf |
| Saccharomyces cerevisiae (S.c.) | Yeast | cox1 | I1 | RT-X-Zn | + | 778 | Fusion | V00694 |
| Saccharomyces cerevisiae (S.c.) | Yeast | cox1 | I2 | RT-X-Zn | + | 785 | Fusion | V00694 |
| Kluyveromyces lactis (K.l.) | Yeast | cox1 | I1 | RT-X-Zn | + | 786 | Fusion | X57546 |
| Schizosaccharomyces pombe (S.p.) | Yeast | cob1 | I1 | RT-X-Zn | + | 807 | Fusion | X54421 |
| Schizosaccharomyces pombe (S.p.) | Yeast | cox1 | I1 | RT-X-Zn | + | 787 | Fusion | SP0251292 |
| Schizosaccharomyces pombe (S.p.) | Yeast | cox2 | I1 | RT-X-Zn | + (FADD) | 778 | Fusion | SP0251293 |
| Venturia inaequalis (V.i.) | Fungus | cob1 | I1 | RT-X | + | 707 | Fusion | AF004559 |
| Allomyces macrogynus (A.m.) | Fungus | cox1 | I3 | RT-X-Zn | + | 785 | Fusion | U41288 |
| Podospora anserina (P.a.) | Fungus | cox1 | I1 | RT-X-Zn | + | 787 | Fusion | X55026 |
| Podospora anserina (P.a.) | Fungus | cox1 | I4 | RT-X-Zn | + | 789 | Fusion | X55026 |
| Podospora anserina (P.a.) | Fungus | ND5 | I4 | RT-X | – (YANV) | 779 | Fusion | X55026 |
| Podospora comata (P.co.) | Fungus | cox1 | I1 | RT-X-Zn | + | 783 | Fusion | Z69899 |
| Podospora curvicolla (P.cu.) | Fungus | ND5 | I1 | RT-X | – (YANV) | 745 | Fusion | Z69898 |
| Neurospora crassa (N.c.) | Fungus | cox1 | I1 | RT-X-Zn | + | 835 | Fusion | X14669 |
| Cryphonectria parasitica (C.p.) | Fungus | N.D.g | N.D.g | RT-X-Zn | + | 778 | N.D.g | AF218567 |
| Marchantia polymorpha (M.p.) | Liverwort | atpA | I1 | RT-X-Zn | + | 1064 | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | atpA | I2 | RT-X | + | 909 | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | atp9 | I1 | RT-X | – (YADN) | 771h | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | cox1 | I1 | RT-X-Zn | – (YAGN) | 914i | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | cox1 | I2 | RT-X-Zn | + | 836j | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | cob1 | I3 | RT-X-Zn | + | 949 | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | cox2 | I2 | RT-X | + | 743 | Fusion | M68929 |
| Marchantia polymorpha (M.p.) | Liverwort | SSU rDNA | I1 | RT-X-Zn | + | 502k | Free | M68929 |
| Arabidopsis thaliana (A.t.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 656 | Free | X98300 |
| Glycine max (G.m.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 668 | Free | U09988 |
| Oenothera berteriana (O.b.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 655 | Free | M63034 |
| Solanum tuberosum (S.t.) | Green plant | nad1 | I4 | RT(2–7)-X | – (YADN) | 674 | Free | AJ003130 |
| Triticum aestivum (T.a.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 678 | Free | X57965 |
| Vicia faba (V.f.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 665 | Free | M30176 |
| Zea mays (Z.m.) | Green plant | nad1 | I4 | RT(2–7)-X | + | 653 | Free | U09987 |
| Porphyra purpurea (P.p.) | Red alga | LSU rDNA | I1 | RT-X-Zn | + | 544 | Free | AF114794 |
| Porphyra purpurea (P.p.) | Red alga | LSU rDNA | I2 | RT-X-Zn | + | 546 | Free | AF114794 |
| Pylaiella littoralis (P.li.) | Brown alga | LSU rDNA | I1 | RT-X-Zn | + | 308 | Free | Z48620 |
| Pylaiella littoralis (P.li.) | Brown alga | LSU rDNA | I2 | RT-X-Zn | + | 318 | Free | Z48620 |
| Pylaiella littoralis (P.li.) | Brown alga | cox1 | I1 | RT-X-Zn | + | 765 | Free | Z72500 |
| Pylaiella littoralis (P.li.) | Brown alga | cox1 | I2 | RT-X-Zn | + | 810 | Free | Z72500 |
| Pylaiella littoralis (P.li.) | Brown alga | cox1 | I3 | RT-X-Zn | + | 748 | Free | Z72500 |
| Free-standing ORFs | ||||||||
| Marchantia polymorpha (M.p.) | Liverwort | - | Orf732 | RT-X | + (FADD) | 732 | Free | M68929 |
| Porphyra purpurea (P.p.) | Red alga | - | rtl | X-Zn | – | 211 | Free | AF114794 |
aSpecies abbreviations used in this manuscript are shown in parentheses.
bThe presence of conserved domains: RT, reverse transcriptase domain; X, domain X (putative splicing function); Zn, Zn domain (nuclease activity). In cases where the complete RT domain is not present, subdomains are indicated in parentheses (0–7).
cThe presence of a catalytic YxDD motif in subdomain 5 of the RT. Deviations from YxDD are indicated, with FxDD considered to be functional since it is common in other RTs (32).
dSize (amino acids) of the ORF. For ORFs in-frame with the upstream exon, the length was calculated based on the first amino acid fully coded within the intron. However, these sizes are inaccurate since the encoded proteins are processed at their N-termini.
eFusion: ORF is translated in-frame with the upstream exon. Free: start codon for ORF is contained within the intron.
fAccession numbers are for DNA database entries except where noted.
gNo data. The complete flanking sequence was not reported.
hPublished size is 681 amino acids; a single frameshift in domain X replaces 34 C-terminal amino acids with 124 amino acids similar to other domain X sequences (8).
iPublished size is 887 amino acids; a single termination readthrough adds 27 amino acids with similarity to other Zn domains.
jPublished size is 742 amino acids; a single termination readthrough adds 94 amino acids with similarity to the Zn domain (9).
kPublished size is 501 amino acids; two frameshifts and a termination readthrough add 72 amino acids with similarity to the Zn domain (9).