Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids

Horn, David

doi:10.1186/1471-2164-9-2

BMC Genomics

Table 1 Codon usage across the trypanosomatid tandem gene set (see table 1 in the additional data file, >60,000 codons) and tRNA gene copy number (see table 2 in the additional data file) are shown. Overall favoured codons and all sixteen CU3 'wobble tRNA pairs' are indicated in bold text. T. cruzi has additional tRNA genes in many cases because the strain used for the sequencing project is a hybrid of two genotypes [19].

From: Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids

Am Acid	Codon	T. brucei Number	Fraction	tRNAs	T. cruzi Number	Fraction	tRNAs	L. major Number	Fraction	tRNAs
Ala	GCG	452	0.24	2	685	0.36	2	925	0.49	2
Ala	GCA	406	0.21	1	283	0.15	1	79	0.04	1
Ala	GCU	526	0.28	2	325	0.17	2	299	0.16	2
Ala	GCC	516	0.27	0	629	0.33	0	593	0.31	0
Arg	AGG	93	0.07	1	95	0.07	2	45	0.04	1
Arg	AGA	29	0.02	1	25	0.02	2	15	0.01	1
Arg	CGG	117	0.09	1	103	0.08	2	86	0.07	1
Arg	CGA	82	0.06	1	55	0.04	2	21	0.02	1
Arg	CGU	415	0.31	3	295	0.23	4	148	0.12	4
Arg	CGC	592	0.45	0	730	0.56	0	922	0.75	0
Asn	AAU	248	0.29	0	178	0.23	0	64	0.08	0
Asn	AAC	596	0.71	2	597	0.77	4	716	0.92	3
Asp	GAU	501	0.44	0	293	0.27	0	216	0.21	0
Asp	GAC	639	0.56	2	795	0.73	2	804	0.79	3
Cys	UGU	112	0.33	0	69	0.21	0	40	0.12	0
Cys	UGC	231	0.67	2	260	0.79	2	296	0.88	1
Gln	CAG	508	0.71	2	604	0.86	4	653	0.95	3
Gln	CAA	209	0.29	1	102	0.14	2	35	0.05	1
Glu	GAG	893	0.67	2	1084	0.8	4	1183	0.93	2
Glu	GAA	441	0.33	1	266	0.2	1	93	0.07	1
Gly	GGG	176	0.11	1	177	0.12	2	111	0.08	1
Gly	GGA	246	0.15	1	163	0.11	2	43	0.03	1
Gly	GGU	750	0.46	0	362	0.24	0	304	0.21	0
Gly	GGC	469	0.29	3	829	0.54	4	997	0.69	4
His	CAU	111	0.28	0	73	0.18	0	52	0.13	0
His	CAC	292	0.72	1	344	0.82	4	349	0.87	2
Ile	AUA	82	0.08	1	37	0.04	3	20	0.02	1
Ile	AUU	430	0.42	2	350	0.38	4	165	0.18	3
Ile	AUC	516	0.5	0	533	0.58	0	753	0.8	0
Leu	UUG	243	0.14	0	154	0.09	2	72	0.05	1
Leu	UUA	61	0.04	1	16	0.01	2	6	0	1
Leu	CUG	526	0.31	1	764	0.46	2	970	0.64	2
Leu	CUA	107	0.06	1	39	0.02	2	29	0.02	1
Leu	CUU	391	0.23	2	343	0.21	4	138	0.09	3
Leu	CUC	375	0.22	0	336	0.2	0	289	0.19	0
Lys	AAG	1248	0.78	3	1458	0.9	4	1457	0.96	3
Lys	AAA	350	0.22	1	158	0.1	2	66	0.04	1
Met	AUG	571	1	3	558	1	6	596	1	4
Phe	UUU	261	0.35	0	327	0.43	0	111	0.16	0
Phe	UUC	479	0.65	2	426	0.57	4	579	0.84	2
Pro	CCG	191	0.22	1	290	0.33	2	469	0.59	2
Pro	CCA	190	0.22	1	138	0.16	2	63	0.08	1
Pro	CCU	185	0.22	1	152	0.18	2	75	0.09	2
Pro	CCC	288	0.34	0	287	0.33	0	187	0.24	0
Ser	AGU	137	0.11	0	77	0.06	0	39	0.03	0
Ser	AGC	234	0.19	2	299	0.25	2	330	0.28	2
Ser	UCG	210	0.17	1	302	0.25	2	384	0.32	1
Ser	UCA	180	0.14	1	85	0.07	2	35	0.03	1
Ser	UCU	237	0.19	1	158	0.13	2	132	0.11	1
Ser	UCC	262	0.21	0	274	0.23	0	276	0.23	0
Thr	ACG	368	0.29	1	553	0.47	2	622	0.58	2
Thr	ACA	328	0.26	1	182	0.16	2	82	0.08	1
Thr	ACU	280	0.22	1	141	0.12	2	74	0.07	3
Thr	ACC	276	0.22	0	292	0.25	0	294	0.27	0
Trp	UGG	194	1	1	204	1	2	167	1	1
Tyr	UAU	177	0.31	0	83	0.15	0	39	0.07	0
Tyr	UAC	391	0.69	1	466	0.85	2	510	0.93	3
Val	GUG	805	0.47	1	1022	0.6	4	1115	0.69	2
Val	GUA	200	0.12	1	60	0.04	2	46	0.03	1
Val	GUU	449	0.26	2	318	0.19	2	141	0.09	2
Val	GUC	250	0.15	0	290	0.17	0	322	0.2	0

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com