Impairment of alternative splice sites defining a novel gammaretroviral exon within gagmodifies the oncogenic properties of Akv murine leukemia virus

Sørensen, Annette Balle; Lund, Anders H; Kunder, Sandra; Quintanilla-Martinez, Leticia; Schmidt, Jörg; Wang, Bruce; Wabl, Matthias; Pedersen, Finn Skou

doi:10.1186/1742-4690-4-46

Table 3 Positions of integrated proviruses in tumor DNA

From: Impairment of alternative splice sites defining a novel gammaretroviral exon within gagmodifies the oncogenic properties of Akv murine leukemia virus

#	Virus	Diagnosis	Chromosome	Position (mm8)	Gene/RefSeq^a	No. of hits in RTCGD (mm8)	Novel RISs^b	Novel CISs^c
1	Akv-EH	DLBCL (from FBL)	1	24641886	Lmbrd1	0	1	-
2	Akv-EH	DLBCL (from FBL)	1	36406157	Cnnm4	0	1	-
3	Akv wt	DLBCL (from FBL)	1	78743292	Kcne4	0	1	-
4	Akv-EH	PCT	1	82855932	Slc19a3	0	1	-
5	Akv wt	FBL	1	93014894	Ramp1	5	-	-
6	Akv-CD	n.d.	1	93022552
7	Akv-EH	Lymphoma, NOS	1	120226476	AK080782	0	1	-
8	Akv-CD	DLBCL (from FBL)	1	130341056	Cxcr4	3	-	-
9	Akv wt	PCT	1	135878316	Fmod/Btg2	8	-	-
10	Akv wt	DLBCL (from FBL)	1	135882183
11	Akv-CD	Abscess	1	139604557	---	1	-	1
12	Akv wt	PCT	1	144940508	---	0	1	-
13	Akv wt	PCT	1	163725782	AK029097	0	1	-
14	Akv wt	FBL	1	173476364	Slamf7	0	1	-
15	Akv wt	PCT	1	174350588	Tagln2/AK006449	2	-	-
16	Akv wt	DLBCL (from FBL)	1	182219328	MGC68323/AK038867	2	-	-
17	Akv-CD	SMZL	2	11542293	Il2ra	4	-	-
18	Akv-CDH	DLBCL (from FBL)	2	13133178	Rsu1	0	1	-
19	Akv-CDH	PCT	2	35270244	Ggta1	5	-	-
20	Akv wt	DLBCL (from FBL)	2	44741201	Gtdc1	0	1	-
21	Akv wt	DLBCL (from FBL)	2	46263959	---	0	1	-
22	Akv wt	DLBCL (from FBL)	2	71667822	Itga6/Pdk1	0	1	-
23	Akv wt	DLBCL (from FBL)	2	90883313	Slc39a13/Sfpi1	6	-	-
24	Akv wt	SMZL	2	90883476
25	Akv wt	PCT	2	102668507	Cd44	0	1	-
26	Akv wt	DLBCL (from FBL)	2	102782324	Pdhx	0	1	-
27	Akv wt	FBL	2	118352393	Pak6	0	1	-
28	Akv wt	FBL	2	119028536	Spint1	0	1	-
29	Akv-CDH	Lymphoma, NOS	2	120301032	Zfp106	1	-	1*
30	Akv-CDH	PTLL	2	128875013	Slc20a1	0	1	-
31	Akv-CDH	Lymphoma, NOS	2	129283153	Ptpns1	1	-	1
32	Akv-EH	PCT	2	131711284	Rassf2	0	1	-
33	Akv-CDH	DLBCL (from FBL)	2	158379688	Ppp1r16b	4	-	-
34	Akv wt	SMZL	2	164051325	Slpi	0	1	-
35	Akv wt	DLBCL (from FBL)	2	169860192	Zfp217	5	-	-
36	Akv wt	FBL	3	22265638	Tbl1xr1	0	1	-
37	Akv-CDH	PCT	3	27464311	Aadacl1	0	1	-
38	Akv-CDH	DLBCL (from FBL)	3	30203814	Evi1	5	-	-
39	Akv-CDH	PCT	3	30203870
40	Akv-CDH	Lymphoma, NOS	3	76043446	Golph4	0	1	-
41	Akv-EH	DLBCL (from FBL)	3	79339620	---	0	1	-
42	Akv wt	FBL	3	90334704	Slc39a1	0	1	-
43	Akv-CD	DLBCL (from FBL)	3	96900321	Cd160	0	1	-
44	Akv wt	SMZL	3	98031475	LOC433632	13	-	-
45	Akv-EH	PCT	3	98041399
46	Akv-CD	SMZL	3	98043109
47	Akv-CDH	DLBCL (from FBL)	3	98043150
48	Akv wt	PCT	3	98043377
49	Akv wt	DLBCL (from FBL)	3	98043659
50	Akv-CD	SMZL	3	98064421
51	Akv-CDH	DLBCL (from FBL)	3	98127957	Notch2	8	-	-
52	Akv-EH	PCT	3	108214198	Ampd2	0	1	-
53	Akv-CD	SMZL	3	115828351	Dph5	1	-	1
54	Akv wt	DLBCL (from FBL)	3	131582947	Papss1	1	-	-
55	Akv wt	SBL	3	145870070	Bcl10	3	-	-
56	Akv wt	DLBCL (from FBL)	3	146091393	Mcoln2	0	1	-
57	Akv-EH	DLBCL (from FBL)	3	157996860	Lrrc40	0	1	-
58	Akv wt	SBL	4	8842182	BC034239	1	-	1
59	Akv-CDH	PCT	4	11915327	AK132816	0	1	-
60	Akv-CD	DLBCL (from FBL)	4	32560128	Bach2	14	-	-
61	Akv wt	FBL	4	32611866
62	Akv-CD	n.d.	4	32619341
63	Akv wt	PCT	4	32702311
64	Akv-CD	Histiocytic sarcoma	4	44734542	Pax5	4	-	-
65	Akv wt	SMZL	4	55369934	Rad23b	1	-	1
66	Akv-CDH	Plasma cell prolif.	4	57933461	Akap2	0	1	-
67	Akv-CD	DLBCL (from FBL)	4	97386196	Nfia/D90173	2	-	-
68	Akv-EH	DLBCL (from FBL)	4	132220004	Fgr	3	-	-
69	Akv wt	SMZL	4	134699599	Dscr1l2	0	1	-
70	Akv-CDH	PCT	4	138050107	Pla2g2d	0	1	-
71	Akv wt	FBL	5	39921672	Hs3st1	0	1	-
72	Akv-CDH	Lymphoma, NOS	5	65179064	Tlr1	1	-	1
73	Akv-CD	Histiocytic sarcoma	5	75074642	---	0	1	-
74	Akv-CDH	PTLL	5	107966364	Gfi1	78	-	-
75	Akv-CDH	PCT	5	121838640	Aldh2	0	1	-
76	Akv-CDH	DLBCL (from FBL)	5	141077075	Gna12	4	-	-
77	Akv wt	DLBCL (from FBL)	6	29717975	4631427C17Rik	0	1	-
78	Akv-EH	de novo DLBCL	6	40821642	BC048599	0	1	-
79	Akv-CDH	Lymphoma, NOS	6	40955151	2210010C04Rik	0	1	-
80	Akv-CDH	PCT	6	54425558	Scrn1	0	1	-
81	Akv wt	FBL	6	72441620	BC100525	2	-	-
82	Akv wt	PCT	6	84016089	Dysf	0	1	-
83	Akv-CDH	Lymphoma, NOS	6	88923549	Gpr175	0	1	-
84	Akv-EH	DLBCL (from SMZL)	6	99153396	Foxp1	1	-	1*
85	Akv-CDH	Lymphoma, NOS	6	113010477	Thumpd3	1	-	1
86	Akv-CD	DLBCL (from FBL)	6	120535110	Cecr5	3	-	-
87	Akv-CD	Histiocytic sarcoma	6	136905161	Arhgdib	0	1	-
88	Akv-CD	PCT	6	145079282	Lrmp	4	-	-
89	Akv-CDH	Plasma cell prolif.	7	18841894	Apoc4	0	1	-
90	Akv wt	FBL	7	24263292	Xrcc1	0	1	-
91	Akv wt	PCT	7	28498093	5830482F20Rik	0	1	-
92	Akv-EH	de novo DLBCL	7	28691963	Map4k1	1	-	1
93	Akv-EH	PCT	7	29760852	Zfp14	0	1	-
94	Akv-CD	Histiocytic sarcoma	7	30746023	Fxyd5	0	1	-
95	Akv wt	PCT	7	45003648	Flt3l	0	1	-
96	Akv wt	DLBCL (from FBL)	7	66812108	Adamts17	0	1	-
97	Akv wt	DLBCL (from FBL)	7	73481277	---	7	-	-
98	Akv-CD	SMZL	7	76335733	D430020F16	0	1	-
99	Akv-EH	DLBCL (from FBL)	7	79083435	Mfge8	0	1	-
100	Akv-EH	PCT	7	80764333	AK034740	0	1	-
101	Akv wt	PCT	7	82574727	Eftud1	1	-	1*
102	Akv-EH	de novo DLBCL	7	99422958	Arrb1/mmu-mir-326	0	1	-
103	Akv wt	SBL	7	113972740	Rras2/Copb1	32	-	-
104	Akv-CDH	DLBCL (from FBL)	7	121248057	AK043969	0	1	-
105	Akv-EH	de novo DLBCL	7	126957227	Cd2bp2	2	-	-
106	Akv wt	DLBCL (from FBL)	7	132147451	4631426J05Rik	0	1	-
107	Akv-CD	DLBCL (from FBL)	7	144741729	Ccnd1	21	-	-
108	Akv-CD	SMZL	8	8401964	---	0	1	-
109	Akv-EH	DLBCL (from FBL)	8	10980425	---	4	-	-
110	Akv wt	FBL	8	35575516	Dctn6	0	1	-
111	Akv wt	PCT	8	37098099	---	0	1	-
112	Akv-CD	SMZL	8	74527100	Pgls	3	-	-
113	Akv wt	DLBCL (from FBL)	8	98522228	Gins3	0	1	-
114	Akv wt	SBL	8	112753504	BC027816	0	1	-
115	Akv-EH	de novo DLBCL	8	118119184	Wwox	1	-	1
116	Akv-EH	Lymphoma, NOS	8	123611854	Irf8	1	-	-
117	Akv-EH	DLBCL (from FBL)	8	126312417	Tubb3/Mela	1	-	1
118	Akv wt	DLBCL (from FBL)	8	126312418
119	Akv wt	PCT	9	46235263	---	0	1	-
120	Akv-CD	Abscess	9	86514607	A330041J22Rik	0	1	-
121	Akv-CDH	PCT	9	104103363	Acpp	1	-	1
122	Akv-EH	FBL	9	115327386	---	0	1	-
123	Akv wt	PCT	9	117143474	Rbms3	0	1	-
124	Akv-EH	PCT	10	5056902	Syne1	1	-	-
125	Akv wt	SBL	10	7626524	Map3k7ip2	1	-	1
126	Akv wt	FBL	10	19681745	Map3k5	2	-	-
127	Akv wt	PCT	10	43100419	Pdss2	0	1	-
128	Akv-EH	PCT	10	59295561	Dnajb12	2	-	-
129	Akv-CD	Histiocytic sarcoma	10	75678805	Prmt2	0	1	-
130	Akv wt	FBL	10	77412375	Pfkl	0	1	-
131	Akv wt	DLBCL (from FBL)	10	8009951	BC058238	2	-	-
132	Akv wt	DLBCL (from FBL)	10	84366577	Ric8b	0	1	-
133	Akv-EH	de novo DLBCL	10	87574719	BC070476	0	1	-
134	Akv-EH	de novo DLBCL	10	92501677	Pctk2	1	-	-
135	Akv-CD	n.d.	10	123752010	---	0	1	-
136	Akv-CDH	PCT	11	3236433	1500004A08Rik	0	1	-
137	Akv wt	PCT	11	5331124	AK133342	0	1	-
138	Akv wt	DLBCL (from FBL)	11	23587218	4933435A13Rik	4	-	-
139	Akv-CD	DLBCL (from FBL)	11	23587651
140	Akv wt	PCT	11	32443618	Stk10	1	-	1
141	Akv wt	PCT	11	46693128	Timd4	0	1	-
142	Akv-CD	PCT	11	51687729	Phf15	0	1	-
143	Akv-EH	de novo DLBCL	11	62648918	Trim16	0	1	-
144	Akv wt	PCT	11	67380781	Gas7	0	1	-
145	Akv-EH	de novo DLBCL	11	74962635	Smg6	9	-	-
146	Akv-EH	de novo DLBCL	11	78821537	Ksr1	0	1	-
147	Akv-EH	PCT	11	86862765	Gdpd1	0	1	-
148	Akv wt	DLBCL (from FBL)	11	95031687	Tac4	0	1	-
149	Akv-EH	de novo DLBCL	11	102249514	Grn	0	1	-
150	Akv wt	DLBCL (from FBL)	11	102990732	Fmnl1	2	-	-
151	Akv wt	DLBCL (from FBL)	11	106946907	Nol11	0	1	-
152	Akv-CD	Abscess	11	107232889	Pitpnc1	1	-	1
153	Akv-EH	PCT	11	116126666	Exoc7	0	1	-
154	Akv-CDH	Lymphoma, NOS	11	118058083	Pscd1	1	-	1*
155	Akv-CD	SMZL	12	3288080	Rab10	0	1	-
156	Akv wt	PCT	12	13172238	Ddx1	0	1	-
157	Akv-CD	Abscess	12	56600484	Garnl1	0	1	-
158	Akv-EH	de novo DLBCL	12	77286036	Zbtb25	1	-	1
159	Akv wt	DLBCL (from FBL)	12	80214408	AK132344	1	-	1
160	Akv wt	DLBCL (from FBL)	12	86569587	Batf	2	-	-
161	Akv-CD	DLBCL (from FBL)	12	113688885	BC004786	5	-	-
162	Akv wt	PCT	13	24453563	Cmah	1	-	1*
163	Akv-CDH	DLBCL (from FBL)	13	28624333	---	0	1	-
164	Akv wt	PCT	13	28727388	---	3	-	-
165	Akv-CDH	DLBCL (from FBL)	13	28764182
166	Akv-CDH	DLBCL (from FBL)	13	28950798	Sox4	79	-	-
167	Akv-CD	DLBCL (from FBL)	13	28950905
168	Akv-EH	de novo DLBCL	13	28955972
169	Akv wt	DLBCL (from FBL)	13	28958981
170	Akv-EH	DLBCL (from FBL)	13	30695323	Dusp22	4	-	-
171	Akv-CD	Histiocytic sarcoma	13	30727958
172	Akv wt	PCT	13	31914670	Gmds	1	-	1
173	Akv-CD	SMZL	13	36214883	Fars2	0	1	-
174	Akv wt	PCT	13	37804150	Rreb1	8	-	-
175	Akv-CD	Histiocytic sarcoma	13	38701503	Eef1e1	1	-	-
176	Akv-CD	DLBCL (from FBL)	13	43205444	Gfod1	1	-	1*
177	Akv-CD	SMZL	13	63488458	Fancc	4	-	-
178	Akv wt	DLBCL (from FBL)	13	84050271	Mef2c	11	-	-
179	Akv-CDH	DLBCL (from FBL)	14	6779744	Dnase1l3	1	-	1
180	Akv-CDH	Lymphoma, NOS	14	24439077	Rai17	10	-	-
181	Akv-CDH	PCT	14	25348097	Slmap	1	-	1
182	Akv-EH	Lymphoma, NOS	14	29013598	Cacna1d	0	1	-
183	Akv wt	SBL	14	30491074	Btd	0	1	-
184	Akv wt	DLBCL (from FBL)	14	59481891	---	0	1	-
185	Akv wt	FBL	14	59637396	AK151394	3	-	-
186	Akv-EH	de novo DLBCL	14	63115780	Msra	1	-	1*
187	Akv wt	PCT	14	72420139	Sucla2	0	1	-
188	Akv wt	SMZL	14	113921088	microRNA cluster	2	-	-
189	Akv wt	FBL	15	57752356	BC066830	0	1	-
190	Akv-CD	SMZL	15	58238320	15Ertd621e	0	1	-
191	Akv wt	PCT	15	61240727	---	0	1	1
192	Akv wt	PCT	15	61240729
193	Akv wt	FBL	15	73548838	Gpr20/Ptp4a3	6	-	-
194	Akv-EH	DLBCL (from FBL)	15	79567673	Unc84b	4	-	-
195	Akv wt	DLBCL (from FBL)	15	79728346	Apobec3	0	1	-
196	Akv-EH	Plasma cell prolif.	15	90445122	Cpne8	1	-	-
197	Akv wt	FBL	16	23906462	Bcl6	5	-	-
198	Akv-EH	de novo DLBCL	16	24049008	---	5	-	-
199	Akv-CD	DLBCL (from FBL)	16	24086635
200	Akv-EH	DLBCL (from FBL)	16	24101470
201	Akv-EH	Lymphoma, NOS	16	24152772
202	Akv wt	FBL	16	24178252
203	Akv wt	DLBCL (from FBL)	16	32049420	Lrrc33	3	-	-
204	Akv-CD	n.d.	16	52388367	Alcam	1	-	1
205	Akv wt	PCT	17	6624877	Vil2	3	-	-
206	Akv wt	PCT	17	11630998	Park2	1	-	1*
207	Akv wt	DLBCL (from FBL)	17	36597927	2410137M14Rik	0	1	-
208	Akv wt	FBL	17	49537999	2310015N21Rik	1	-	1*
209	Akv-EH	DLBCL (from FBL)	17	63705275	Fert2	0	1	-
210	Akv-CD	SMZL	17	71389894	Kntc2	0	1	-
211	Akv-CDH	PTLL	17	74614066	Birc6	1	-	-
212	Akv wt	PCT	18	11242422	---	0	1	-
213	Akv-CD	SMZL	18	12368360	Npc1	1	-	1
214	Akv-CD	SMZL	18	36016553	Cxxc5	3	-	-
215	Akv-CDH	DLBCL (from FBL)	18	39790170	---	0	1	-
216	Akv wt	FBL	18	42916219	Ppp2r2b	0	1	-
217	Akv-EH	de novo DLBCL	18	60930595	Ii/Cd74	0	1	1
218	Akv-EH	DLBCL (from FBL)	18	60930793
219	Akv-CD	DLBCL (from FBL)	18	60930833
220	Akv wt	PCT	18	60931233
221	Akv-CDH	PCT	18	60934151
222	Akv wt	DLBCL (from FBL)	18	61103722	Camk2a	0	1	-
223	Akv-EH	PCT	18	65601468	Malt1	1	-	-
224	Akv wt	DLBCL (from FBL)	18	67824697	Ptpn2	0	1	-
225	Akv wt	FBL	19	11607493	Ms4a4d	0	1	-
226	Akv wt	DLBCL (from FBL)	19	34362400	Fas	2	-	-
227	Akv-EH	de novo DLBCL	19	37505125	Hhex/Exoc6	44	-	-
228	Akv-CD	DLBCL (from FBL)	19	37532944
229	Akv-EH	de novo DLBCL	19	37537038
230	Akv-CD	SMZL	19	37560104
231	Akv-CD	Histiocytic sarcoma	19	37560104
232	Akv-EH	PCT	19	43474871	Cnnm1	0	1	-
233	Akv-CDH	PCT	19	47583866	Obfc1	0	1	-
234	Akv wt	DLBCL (from FBL)	19	47963460	AK014581	0	1	-
235	Akv wt	PCT	19	53994934	Shoc2	0	1	-
236	Akv wt	FBL	19	55633727	Vti1a	1	-	1*
237	Akv wt	FBL	X	103293531	P2ry10	0	1	-
238	Akv-CDH	Lymphoma, NOS	X	109985132	Dach2	1	-	1
239	Akv-EH	DLBCL (from FBL)	X	129928954	Btk	0	1	-
240	Akv wt	DLBCL (from FBL)	X	162452646	Tmsb4x	1	-	1

^aThe gene (or RefSeq) closest to the integrated provirus is given (UCSC, mouse mm8 assembly). --- indicates that the distance to the closest gene/RefSeq is more than 100 kb.
^bFor each insertion, it is indicated, based on RTCGD (mm8), whether a novel RIS has been defined.
^cFor each insertion, it is indicated, based on RTCGD (mm8), whether a novel CIS has been defined. The definition follows the recommendations from RTCGD with a window size of 100 kb, 50 kb, and 30 kb for CISs with 4 (or more), 3, or 2 insertions, respectively. * indicates an exception from this rule, if two integration sites are found within the same gene/RefSeq.
n.d., not determined.

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