Data Statistics
Genome Facts:
Gene Prediction
Gene set Number Average transcript length (bp, UTR excluded) Average CDS length (bp) Average exons per gene Average exon length (bp) Average intron length (bp)
De novo prediction Augustus 49,091 1,790 1,004 4.73 213 211
GlimmerHMM 49,301 1,583 892 4.08 219 224
Homolog prediction A.thaliana 48,183 2,092 1,075 4.32 249 307
O.sativa 44,649 2,376 1,251 3.63 345 428
C.papaya 58,051 1,368 805 3.03 266 278
V.vinifera 52,174 2,016 991 3.52 282 407
P.trchocarpa 61,622 1,476 849 3.15 270 291
Brassica_FLcDNA 7,428 3,165 622 3.46 180 1,035
B_rapa_unigene 16,378 5,570 808 4.18 193 1,499
B_rapa_EST 30,266 6,935 761 4.2 181 1,927
B_oleracea_EST 30,043 2,167 617 3.1 199 738
Brassica_95k_EST 55,772 4,587 648 2.9 223 2,075
Final Gene sets 45,758 1,761 1,037 4.55 228 204
Non-coding RNA Annotation
Type Copy Average length (bp) Total length (bp) % of genome
miRNA 336 118.76 39904 0.0072
tRNA 1425 74.86 106678 0.0192
rRNA rRNA 553 165.63 91596 0.0165
18S 85 458.88 39005 0.0070
28S 103 123.51 12722 0.0023
5.8S 57 177.12 10096 0.0018
5S 308 96.67 29773 0.0054
snRNA snRNA 1442 110.29 159042 0.0287
CD-box 1219 104.76 127703 0.0230
HACA-box 62 123.47 7655 0.0014
splicing 161 147.11 23684 0.0043
Repeat Sequence Annotation
Categories Intact copies Copy number* Length (bp) % 259.6M
Class I:Retrotransposon LTR/Copia 1,482 25,978 25,406,064 9.79
LTR/Gypsy 607 13,658 14,052,529 5.41
LTR/Unclassified 144 5,712 3,517,450 1.35
LINE 71 2,722 1,965,467 0.76
SINE 238 1,198 325,132 0.13
Subtotal   2,542 49,268 45,266,642 17.44
Class II:DNA transposon Tc1/Mariner 42 9,325 3,411,306 1.31
hAT 338 7,141 1,901,076 0.73
Mutator 301 8,372 3,771,624 1.45
PIF/Harbinger 39 1,559 861,363 0.33
Pong 585 13,794 7,045,593 2.71
CACTA 1,312 16,536 14,002,269 5.39
MITE/Stowaway 930 6,325 1,206,199 0.46
MITE/Tourist 350 2,384 527,663 0.2
Helitron 820 26,159 10,406,906 4.01
Subtotal   4,717 91,595 43,133,999 16.59
Total   7,259 140,863 88,400,641 34.03

 

Last modified at: 2014-07-28
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.
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