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