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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/RefSeqa No. of hits in RTCGD (mm8) Novel RISsb Novel CISsc
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
  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.
  2. bFor each insertion, it is indicated, based on RTCGD (mm8), whether a novel RIS has been defined.
  3. 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.
  4. n.d., not determined.