Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

Cho, Myeongji; Kim, Hayeon; Son, Hyeon S.

doi:10.1186/s12985-019-1245-2

Virology Journal

Table 3 Domains and motifs of PyVs used in this study

From: Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

No.	Abbr.	Accession no.	DnaJ domain			LXCXE motif			Helicase domain
No.	Abbr.	Accession no.	Start	End	nt length	Start	End	a.a. sequence	Start	End	nt length
1	BatPyV4a	NC_038556.1	12	67	168	107	111	LRCDE	405	564	480
2	ApanPyV1	NC_019853.1	12	77	198	122	126	LFCNE	441	601	483
3	BatPyV5b-1	NC_026767.1	12	74	189	–	–	–	376	536	483
4	BatPyV5a	NC_026768.1	12	67	168	–	–	–	382	546	495
5	OraPyV-Bor	NC_013439.1	12	77	198	122	126	LFCDE	422	602	543
6	CardiodermaPyV	NC_020067.1	12	77	198	212	216	LYCDE	556	716	483
7	BatPyV4b	NC_028120.1	–	–	–	152	156	LLCEE	458	651	582
8	ChPyV	NC_014743.1	12	96	255	–	–	–	379	580	606
9	VmPyV1	NC_019844.1	12	80	207	107	111	LHCNE	479	640	486
10	VmPyV3	NC_025898.1	12	75	192	131	135	LFCSE	462	622	483
11	EidolonPyV	NC_020068.1	–	–	–	236	240	LRCDE	588	752	495
12	GgorgPyV1	NC_025380.1	–	–	–	200	204	LFCDE	554	714	483
13	HPyV9	NC_015150.1	12	86	225	123	127	LFCSE	446	606	483
14	HPyV12	NC_020890.1	–	–	–	–	–	–	473	635	489
15	MfasPyV1	NC_019851.1	12	86	225	125	129	LFCTE	465	665	603
16	MCPyV	NC_010277.2	–	–	–	212	216	LFCDE	567	727	483
17	HaPyV	NC_001663.2	–	–	–	130	134	LTCQE	522	682	483
18	BatPyV3b	NC_028123.1	–	–	–	107	111	LYCDE	467	630	492
19	MPyV	NC_001515.2	–	–	–	142	146	LFCYE	549	709	483
20	NJPyV	NC_024118.1	12	80	207	107	111	LHCDE	476	636	483
21	OtomopsPyV	NC_020066.1	12	92	243	107	111	LYCDE	483	643	483
22	OtomopsPyV1	NC_020071.1	–	–	–	185	189	LRCDE	520	680	483
23	PtrovPyV2a	NC_025370.1	–	–	–	200	204	LFCDE	556	716	483
24	PtrovPyV3	NC_019855.1	12	75	192	–	–	–	486	646	483
25	PtrovPyV4	NC_019856.1	12	75	192	–	–	–	489	646	474
26	PtrovPyV5	NC_019857.1	12	86	225	123	127	LFCSE	439	599	483
27	PtrosPyV2	NC_019858.1	12	85	222	108	112	LYCSE	432	632	603
28	PtrovPyV1a	NC_025368.1	–	–	–	203	207	LYCDE	558	718	483
29	PbadPyV2	NC_039051.1	12	92	243	107	111	LHCNE	476	637	486
30	PrufPyV1	NC_019850.1	12	93	246	107	111	LHCNE	476	637	486
31	RacPyV	NC_023845.1	–	–	–	167	171	LFCEE	504	685	546
32	RnorPyV1	NC_027531.1	–	–	–	128	132	LYCSE	535	698	492
33	BatPyV3a-B0454	NC_038557.1	–	–	–	107	111	LHCHE	477	637	483
34	OraPyV-Sum	NC_028127.1	12	75	192	–	–	–	489	649	483
35	TSPyV	NC_014361.1	12	77	198	122	126	LFCHE	445	605	483
36	YbPyV1	NC_025894.1	12	75	192	131	135	LFCSE	463	663	603
37	AelPyV1	NC_022519.1	–	–	–	–	–	–	400	564	495
38	BatPyV2c	NC_038558.1	–	–	–	223	227	LLCEE	559	719	483
39	BVPyV	NC_028117.1	12	67	168	146	150	LTCHE	383	574	576
40	BatPyV6a	NC_026762.1	–	–	–	84	88	LFCHE	395	557	489
41	BatPyV6b	NC_026770.1	–	–	–	98	102	LFCHE	407	570	492
42	BatPyV6c	NC_026769.1	–	–	–	100	104	LFCRE	426	587	486
43	SLPyV	NC_013796.1	12	77	198	113	117	LHCHE	397	556	480
44	CalbPyV1	NC_019854.2	–	–	–	100	104	LFCNE	410	570	483
45	CeryPyV1	NC_025892.1	12	75	192	105	109	LFCHE	402	562	483
46	VmPyV2	NC_025896.1	12	75	192	105	109	LFCHE	402	562	483
47	CVPyV	NC_028119.1	12	67	168	145	149	LSCNE	382	573	576
48	BatPyV2a	NC_028122.1	12	80	207	–	–	–	406	565	480
49	EPyV	NC_017982.1	12	86	225	105	109	LRCDE	402	562	483
50	BKPyV	NC_001538.1	12	75	192	105	109	LFCHE	402	562	483
51	KIPyV	NC_009238.1	–	–	–	108	112	LRCNE	410	572	489
52	JCPyV	NC_001699.1	12	75	192	105	109	LFCHE	401	561	483
53	WsPyV	NC_032120.1	12	77	198	113	117	LHCNE	400	561	486
54	SV40	NC_001669.1	12	75	192	103	107	LFCSE	400	560	483
55	MasPyV	NC_025895.1	–	–	–	101	105	LFCNE	414	576	489
56	MmelPyV1	NC_026473.1	12	80	207	111	115	LRCDE	365	559	585
57	MiniopterusPyV	NC_020069.1	12	75	192	103	107	LHCHE	369	560	576
58	MPtV	NC_001505.2	–	–	–	103	107	LFCNE	418	573	468
59	MyPyV	NC_011310.1	–	–	–	–	–	–	441	603	489
60	PtrovPyV8	NC_028635.1	12	75	192	105	109	LFCHE	402	562	483
61	PteronotusPyV	NC_020070.1	12	80	207	108	112	LRCDE	405	564	480
62	BatPyV2b	NC_028121.1	12	80	207	108	112	LRCDE	406	617	636
63	RatPyV2	NC_032005.1	12	79	204	178	182	LHCDE	474	634	483
64	SsciPyV1	NC_038559.1	–	–	–	101	105	LFCHE	410	572	489
65	SquiPyV	NC_009951.1	–	–	–	101	105	LFCHE	411	570	480
66	AlPyV	NC_034251.1	12	67	168	107	111	LYCNE	407	567	483
67	WUPyV	NC_009539.1	12	89	234	108	112	LRCNE	417	579	489
68	YbPyV2	AB767295.2	12	75	192	105	109	LFCHE	402	562	483
69	HPyV6	NC_014406.1	–	–	–	109	113	LYCDE	393	571	537
70	HPyV7	NC_014407.1	–	–	–	109	113	LYCTE	416	576	483
71	MWPyV	NC_018102.1	–	–	–	105	109	LSCNE	421	580	480
72	STLPyV	NC_020106.1	12	83	216	105	109	LTCNE	406	566	483
73	ADPyV	NC_026141.2	8	61	162	69	73	LYCEE	408	582	525
74	BFDV	NC_004764.2	6	82	231	–	–	–	372	532	483
75	Butcherbird PyV	NC_023008.1	8	67	180	70	74	LFCDE	410	572	489
76	CaPyV	NC_017085.1	8	61	162	67	71	LSCNE	390	550	483
77	CpyV	NC_007922.1	11	80	210	69	73	LQCEE	405	569	495
78	EgouPyV1	NC_039052.1	8	75	204	70	74	LYCEE	374	572	597
79	FPyV	NC_007923.1	6	70	195	60	64	LFCDE	382	543	486
80	GHPV	NC_004800.1	8	81	222	65	69	LFCDE	404	599	588
81	HunFPyV	NC_039053.1	6	77	216	60	64	LFCDE	382	543	486
82	BassPyV1	NC_025790.1	–	–	–	105	109	LMCGE	338	495	474
83	BPyV	NC_001442.1	10	73	192	93	97	LHCDE	391	586	588
84	DPyV	NC_025899.1	11	77	201	82	86	LYCDE	357	536	540
85	GfPyV1	NC_026244.1	–	–	–	–	–	–	348	517	510
86	SspPyV	NC_026944.1	–	–	–	–	–	–	372	529	474

ScanProsite results together with ProRule-based predicted intra-domain features were used for functional domains retained in LT-Ag of PyVs. LXCXE motifs and their encoding sequences were extracted through the JAVA programming

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ISSN: 1743-422X

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