Other sequence features
- All genes are encoded on the same strand.
- A single continuous ORF (cox1/2) encodes cox1 and cox2.
- Overlapping genes, with number of overlapping nucleotides indicated, are:
nad5-nad11: 1
cob-nad4L: 1
rpl11-rps12: 35
rps12-rps7: 29
rps19-rps3: 1
rpl16-rpl14: 38
rpl14-rpl5: 1
orfB-orf124: 11
nad3-nad9: 10
nad9-nad7: 19
trnK(ctt)-trnQ(ttg): 1
Ribosomal RNA genes (2): rns, rnl; no rrn5
Transfer RNA genes (16, including trnX,
which encodes a tRNA with a predicted 8-nt anticodon loop):
trnQ,K,E,I1,L1,I2,A,P,D,M,F,X,H,L2,Y,W
Ribosomal protein genes (16)
small subunit (10 genes):
rps2,3,4,7,8,11,12,13,14,19
large subunit (6 genes):
rpl2,5,6,11,14,16
Genes for respiration and oxidative phosphorylation (16; 17 if cox1/2 is counted as two genes)
Respiratory chain (13): nad1,2,3,4,4L,5,6,7,9,11; cob; cox1/2,3
ATP synthase complex (3): atp1(= A),6,9
Genes with similarity to unassigned mitochondrial ORFs in other organisms (2)
orf142 (ymf19 = angiosperm orfB); orf124 (ymf39 = angiosperm orf25)
Intronic ORFs (3, all in Group I rnl introns; see below)
I1orf (ymf46; AcLSU.m1, 142 aa),
I2orf (ymf47; AcLSU.m2, 168 aa),
I3orf (ymf48; AcLSU.m3, 164 aa)
Unique ORFs (3)
orf83 (ymf49), orf115 (ymf50), orf349 (ymf51)
Codon usage
Table below refers to all protein-coding genes, including intronic and unidentified ORFs.
Codons are in uppercase letters, anticodons of corresponding tRNAs in lowercase letters.
( - ) indicates that tRNAs corresponding to these codons are not encoded in A. castellanii mtDNA.
( % ) denotes proportional codon usage for each amino acid.
Codon usage table assumes 'super wobble' ('2 out of 3' reading) when the first anticodon
position is occupied by an unmodified U.
# # # #
TTT F(gaa) 851 88% TCT S( - ) 271 35% TAT Y(gua) 371 73% TGT C( - ) 71 72%
TTC F(gaa) 112 12% TCC S( - ) 74 10% TAC Y(gua) 138 27% TGC C( - ) 28 28%
TTA L2(uaa)662 54% TCA S( - ) 162 21% TAA ter * 23 72% TGA W( ? ) 69 58%
TTG L2(uaa)159 13% TCG S( - ) 42 5% TAG ter * 9 28% TGG W(cca) 50 42%
CTT L1(uag)207 17% CCT P(ugg) 128 48% CAT H(gug) 114 74% CGT R( - ) 69 19%
CTC L1(uag) 15 1% CCC P(ugg) 23 9% CAC H(gug) 40 26% CGC R( - ) 17 5%
CTA L1(uag)129 11% CCA P(ugg) 71 26% CAA Q(uug) 138 74% CGA R( - ) 23 6%
CTG L1(uag) 44 4% CCG P(ugg) 45 17% CAG Q(uug) 49 26% CGG R( - ) 4 1%
ATT I(gau) 441 48% ACT T( - ) 168 43% AAT N( - ) 504 79% AGT S( - ) 156 20%
ATC I1(gau) 67 7% ACC T( - ) 53 14% AAC N( - ) 130 21% AGC S( - ) 71 9%
ATA I2(cau)408 45% ACA T( - ) 132 34% AAA K( ? ) 569 76% AGA R( - ) 160 44%
ATG M(cau) 199 100% ACG T( - ) 34 9% AAG K(cuu) 175 24% AGG R( - ) 88 24%
GTT V( - ) 348 57% GCT A(ugc) 191 51% GAT D(guc) 201 83% GGT G( - ) 291 58%
GTC V( - ) 51 8% GCC A(ugc) 53 14% GAC D(guc) 41 17% GGC G( - ) 79 16%
GTA V( - ) 157 26% GCA A(ugc) 100 27% GAA E(uuc) 187 73% GGA G( - ) 82 16%
GTG V( - ) 58 9% GCG A(ugc) 30 8% GAG E(uuc) 69 27% GGG G( - ) 50 10%
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Additional tRNA features
Editing of the acceptor stem (demonstrated or predicted) in 13 out of 16 tRNAs.
One potential tRNA (X) has an 8-nt AC loop.
'Missing' tRNAs are probably imported from the cytosol.
The tRNA M has features of an initiator Met tRNA.
How do tRNA K (cuu) and tRNA W (cca) read AAA and UGA, respectively?
Possibly C-to-U editing or some other modification occurs at the first anticodon position,
or a particular tRNA structure allows decoding of both cognate codons,
despite the presence of an unmodified C residue at the wobble position.