ID
|
Chromo-some
|
Transduced sequence start
|
Transduced sequence end
|
L1, Alu etc.
|
Start
|
End
|
+/−
|
Gene
|
Total Inserts
|
Tumours
|
Method
|
Max Transduced (bp)
|
Hot L1 list
|
Tubio list
|
---|
Reference L1s that transduce unique sequence
|
Chr 4
|
chr4
|
137213864
|
in L1
|
L1HS
|
137214650
|
137220701
|
-
|
none
|
3
|
2
|
L1
|
786
|
14
|
No
|
Chr 8
|
chr8
|
135082457
|
135082642
|
L1HS
|
135082987
|
135089016
|
-
|
none
|
6
|
3
|
L1
|
530
|
3
|
4
|
Chr 12_A
|
chr12
|
3606945
|
in L1
|
L1HS
|
3608362
|
3614394
|
-
|
PRMT8
|
5
|
3
|
L1
|
1417
|
35
|
6
|
Chr 20
|
chr20
|
23412922
|
23413624
|
L1HS
|
23406746
|
23412777
|
+
|
none
|
11
|
5
|
Cl
|
847
|
Not listed
|
8
|
Chr 22
|
chr22
|
29065365
|
29066424
|
L1HS
|
29059272
|
29065303
|
+
|
TTC28
|
129
|
36
|
Cl, L1
|
1121
|
7
|
137
|
Chr X_A
|
chrX
|
11731785
|
11732702
|
L1HS
|
11725369
|
11731399
|
+
|
none
|
80
|
19
|
Cl, L1
|
1303
|
19
|
7
|
Chr X_B
|
chrX
|
11952984
|
in L1
|
L1HS
|
11953208
|
11959433
|
-
|
none
|
23
|
6
|
L1
|
224
|
1
|
20
|
Non - reference L1s that transduce unique sequence
|
Chr 3
|
chr3
|
in L1
|
123595443
|
Polymorphic L1HS
|
123590726
|
123590724
|
+
|
MYLK
|
29
|
7
|
Cl
|
>4000
|
N/A
|
40
|
Chr 14
|
chr14
|
59220410
|
59221078
|
Polymorphic L1HS
|
59220404
|
59220404
|
+
|
none
|
179
|
11
|
Cl
| |
N/A
|
40
|
Reference genome elements that inserts align to
|
Chr 6
|
chr6
| | |
L1HS
|
24811907
|
24817934
|
-
|
FAM65B
|
3
|
3
|
L1
|
Nil
|
2
|
N/A
|
Chr 7
|
chr7
| | |
L1HS plus 4bp and polyA
|
30478859
|
30484914
|
+
|
NOD1
|
84
|
9
|
L1
|
Nil
|
18
|
N/A
|
Chr8
| |
see
|
footnote
|
L1HS
| | | | | | | | | | |
Chr 10
|
chr10
| | |
L1HS with polyA
|
111572121
|
111578215
|
-
|
none
|
6
|
6
|
L1
|
Nil
|
9
|
N/A
|
Chr 12_B
|
chr12
| | |
AluSx1 with polyA
|
66451373
|
66451739
|
-
|
none
|
98
|
21
|
Cl
|
Nil
|
N/A
|
N/A
|
Chr 15
|
chr15
| | |
AluYa5 with polyA
|
77910868
|
77911236
|
-
|
LINGO1
|
19
|
17
|
Cl
|
Nil
|
N/A
|
N/A
|
- Positions refer to reference genome GRCh37/hg19. The mobile ‘elements’ are identified by chromosome. At least two inserts were verified by PCR for each ‘element’ except the Chr 6 element (only one insert verified) and the Chr 3 element (not verified but described by Tubio et al. [13]). The Chr 3 and Chr 14 elements are polymorphic L1s that are not in the reference genome but were shown to transduce sequence by Tubio et al. [13]; their insertion point in the reference genome is given in italics. The polyA addition site for the Chr 14 element is at the end of a 36bp fragment of an L2a element. The Chr8 element showed both transduction and mapping to the native L1 insert—of the two inserts verified, one had 3’ unique sequence transduced and one was pure L1 3’ terminus
- Transduced sequence, maximum extent of unique sequence observed in inserts verified by PCR (Additional file 2), except for Chr 3 element where read map position is given. +/−, strand bearing polyA, which is same as orientation of L1 or Alu if present. Tumours, number of tumours with inserts. Method, method of identification: Cl, cluster of ‘translocation’ breakpoints from discordant reads; L1, cluster of breakpoints 3’ to a known active L1 (not exhaustive). Max transduced, maximum unique sequence transduced in cloned insert. Hot L1 list, rank in list of active L1s of Brouha et al. [24]. Tubio list, whether the elements that transduce 3’ sequence were listed by Tubio et al. [13] and how many inserts were reported; N/A, not applicable as were not transduction events