| Supplementary Information 13 |
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| A.
Masked repeat elements in the FANTOM2 clone set. |
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| Repeat
Class |
No. of masked
repeats |
Repeat length
[bp] |
% of total clone
sequence |
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| SINE |
45,125 |
5,829,996 |
4.86% |
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| LINE |
8,846 |
2,837,240 |
2.37% |
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| LTR |
10,064 |
2,960,662 |
2.47% |
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| RNA |
548 |
40,937 |
0.03% |
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| DNA |
2,843 |
474,385 |
0.40% |
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| Satellite |
66 |
14,863 |
0.01% |
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| Simple repeat |
23,128 |
1,077,170 |
0.90% |
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| Unknown/Others |
312 |
90,194 |
0.08% |
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| Low complexity |
14,929 |
624,385 |
0.52% |
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| Total |
105,861 |
13,949,832 |
11.64% |
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| Numbers
are based on the RepeatMasker outputs of 60,770 cDNA clones |
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| B. TU (RTPS) based repeat element analysis for FANTOM2 cDNA
clones |
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| Summary of repeat
containing FANTOM2 RTPS Tus |
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| Total No. of repeats |
51,372 |
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| FANTOM2 RTPS representatives |
25,438 |
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| FANTOM2 RTPS representatives with one or
more repeats (incl. low complexity) |
16,473 (64.76%) |
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| FANTOM2 RTPS representatives with CDS start
and end positions |
8,692 (34.17%) |
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| FANTOM2 RTPS representatives
with CDS overlap in one or more repeats |
* 1,232 (14.17%) |
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| Total
length of FANTOM2 RTPS representative [bp] |
50,911,383 |
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| Total repeat length [bp] |
8,401,011 |
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| % repeat length of FANTOM2 RTPS
representative length |
16.50% |
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| *
% is based on the 8,692 CDS containing FANTOM2 RTPS members |
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| Summary of repeat
classes occuring in FANTOM2 RTPS TUs |
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| REPEAT CLASS |
No. of repeats
in FANTOM2 RTPS members |
Repeat-containing
FANTOM2 RTPS members |
FANTOM2 RTPS
members with CDS overlap in one or more repeats |
Repeat length [bp] and % FANTOM2
RTPS members |
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| LINE |
6,955 (13.54%) |
4,387 |
254 |
2,083,083 (4.09%) |
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| LTR |
7,754 (15.09%) |
5,020 |
246 |
2,055,818 (4.04%) |
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| SINE |
25,830 (50.28%) |
11,005 |
412 |
3,368,332 (6.62%) |
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| RNA |
281 (0.55%) |
270 |
8 |
21,604 (0.04%) |
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| DNA |
1,746 (3.40%) |
1,507 |
23 |
287,105 (0.56%) |
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| Satellite |
40 (0.08%) |
36 |
2 |
12,538 (0.02%) |
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| Simple repeat |
7,581 (14.76%) |
5,820
|
378 |
426,784 (0.84%) |
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| Others |
6 (0.01%) |
3 |
2 |
904 (0.00%) |
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| Unknown |
242 (0.47%) |
199 |
2 |
63,929 (0.13%) |
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| Low complexity |
930 (1.81%) |
866 |
113 |
80,914 (0.16%) |
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| Total |
51,372 |
* n/a |
*n/a |
8,401,011 |
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| *
Numbers were calculated per repeat class. Since one FANTOM2 RTPS member can
contain multiple repeats of different classes the numbers were not summed
up. |
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| Summary
of repeat families occuring in FANTOM2 RTPS TUs |
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| REPEAT
FAMILY |
No. of repeats in FANTOM2 RTPS
members |
Repeat-containing FANTOM2 RTPS
members |
FANTOM2 RTPS members with
repeat-CDS overlap |
Repeat length [bp] |
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| LINE/CR1 |
22 |
22 |
1 |
3,176 |
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| LINE/L1 |
6,674 |
4,191 |
299 |
2,036,757 |
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| LINE/L2 |
259 |
236 |
7 |
43,150 |
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| LTR |
816 |
671 |
17 |
233,342 |
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| LTR/ERV |
3 |
2 |
1 |
1,278 |
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| LTR/ERV1 |
413 |
303 |
24 |
137,496 |
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| LTR/ERVK |
1,259 |
822 |
85 |
438,021 |
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| (LTR/ERVK) |
38 |
35 |
1 |
9,153 |
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| LTR/ERVL |
354 |
312 |
21 |
88,747 |
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| LTR/MaLR |
4,869 |
3,533 |
141 |
1,147,781 |
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| SINE/Alu |
11,249 |
6,911 |
224 |
1,277,948 |
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| SINE/B2 |
6,495 |
4,626 |
116 |
1,040,736 |
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| SINE/B4 |
6,453 |
4,700 |
142 |
898,904 |
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| SINE/ID |
1,018 |
966 |
9 |
73,347 |
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| SINE/MIR |
607 |
569 |
10 |
77,397 |
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| RNA |
6 |
6 |
0 |
758 |
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| rRNA |
13 |
13 |
1 |
1,052 |
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| scRNA |
114 |
112 |
3 |
9,006 |
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| snRNA |
50 |
49 |
3 |
4,266 |
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| srpRNA |
4 |
4 |
0 |
438 |
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| tRNA |
95 |
93 |
1 |
6,084 |
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| DNA |
50 |
46 |
0 |
6,462 |
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| DNA/AcHobo |
62 |
51 |
1 |
11,252 |
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| DNA/MER1
type |
1,218 |
1,090 |
18 |
192,344 |
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| (DNA/MER1
type) |
15 |
14 |
0 |
2,140 |
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| DNA/MER2
type |
358 |
309 |
5 |
67,577 |
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| DNA/Mariner |
27 |
23 |
0 |
4,737 |
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| DNA/T2
type |
6 |
4 |
0 |
935 |
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| DNA/Tc2 |
10 |
10 |
0 |
1,658 |
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| Satellite |
40 |
36 |
2 |
12,538 |
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| Simple
repeat |
7,581 |
5,820 |
378 |
426,784 |
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| Low
complexity |
930 |
866 |
113 |
80,914 |
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| Other |
5 |
2 |
0 |
848 |
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| Other/Y
chr. |
1 |
1 |
0 |
56 |
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| Unknown |
207 |
171 |
2 |
61,704 |
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| Unknown/Y
chr. |
35 |
28 |
0 |
2,225 |
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| TOTAL |
51,356 |
* n/a |
* n/a |
8,401,011 |
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102712 |
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| *
Numbers were calculated per repeat family. Since one FANTOM2 RTPS member can
contain multiple repeats of different classes the numbers were not summed
up. |
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| The
statistics for the FANTOM2 RTPS members was derived from the RepeatMasker
outputs of all FANTOM2 clones. For the analysis repeats were counted if their
Smith-Waterman score exceeded 225. The CDS overlap (>1bp) was determined from the CDS start and end positions. The
repeat family assignments in parenthesis are tentative. |
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