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Anne Brown Josh Fitzgerald Jieqing Ping

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Presentation on theme: "Anne Brown Josh Fitzgerald Jieqing Ping"— Presentation transcript:

1 Anne Brown Josh Fitzgerald Jieqing Ping
Seq3 Annotation Group 3 Anne Brown Josh Fitzgerald Jieqing Ping

2 Preliminary Search

3 CpG Plot

4 Repeat Sequence analysis

5 Comparing Masked to Unmasked in FGENESH
FGENESH-Repeat masked sequences FGENESH-Unmasked sequences ID Start (TSS) Initial Exon Final Exon End (PolyA) Strand # Exons 1 60 2790 2930 + 3 2 3085 3397 3810 4024 4081 4420 4641 5587 4 16327 15387 8156 7793 - 7 17349 18027 34855 35176 29 5 6 35494 36140 38902 39492 44937 44930 39888 39650 45067 8 52023 51599 49168 49113 9 52359 52471 58267 58900 10 64066 63961 60517 60231 67117 67195 71111 71983 11 66623 74026 74159 76479 77421 12 73329 79123 78855 78112 77741 80394 80191 79739 79196 13 80548 14 81229 81871 87473 87867 92776 92759 91788 90825 15 124690 107781 101003 100648 16 104667 104210 17 107805 105556 105477 18 108456 109104 114706 115682 19 124223 119481 119082 124782 124931 125621 126518 20 21 129502 130738 132574 133748 22 136712 135706 134108 133830 23 136865 139107 140522 140757 149522 149161 145907 145469 24 *Repeat masked sequences *Unmasked sequences ex Match Difference Retrotransposon Bad E-Values

6 Comparing Masked to Unmasked in GeneMark
GeneMark-Repeat masked sequences GeneMark-Unmasked sequences ID Start (TSS) Initial Exon Final Exon End (PolyA) Strand # Exons 1 60 2790 + 3 2 3397 4687 5 5080 5881 4 14092 8113 - 11 21548 23650 32158 34808 7 6 40083 40424 36140 38986 9 8 44930 41718 10 51063 50433 52471 53519 12 55152 59671 13 60918 60517 14 61615 60940 15 63200 61706 16 63961 63277 17 64297 65671 67195 71270 18 74333 76479 19 78855 78112 20 78030 80191 79739 21 22 81871 88603 23 90404 89881 92759 91788 24 25 98541 99955 101389 101003 26 27 109104 114336 28 124073 119851 124934 125621 29 124931 30 131323 132695 31 135706 134108 149113 145907 32 149160 149247 33 ex Match Difference Retrotransposon Bad E-Values

7 Gene Prediction FGENESH GeneMark ID Start (TSS) Initial Exon
Final Exon End (PolyA) Strand # Exons 1 17349 18027 34855 35176 + 29 21548 23650 5 2 32158 34808 7 3 40083 40424 44937 44930 39888 39650 - 6 4 41718 67117 67195 71111 71983 71270 74026 74159 76479 77421 74333 79123 78855 78112 77741 80394 80191 79739 79196 8 92776 92759 91788 90825 9 124690 107781 101003 100648 10 101389 124782 124931 125621 126518 11 124934 149522 149161 145907 145469 12 149113 13 149160 149247 *Repeat masked sequences ex Match Difference Retrotransposon Bad E-Values

8 Go Terms

9 Gene Models Gene10-6 Locus names: GRMZM2G Map Position: [139,939, ,940,191]; (79.6 centisomes) on Chr.8 Length: 453 bp / 150 aa PFAM ID: PF00125: Core histone H2A/H2B/H3/H4 , PF00808: Histone-like transcription factor (CBF/NF-Y) and archaeal histone Biological Process GO: nucleosome assembly Molecular Function GO: DNA binding Cellular Component GO: chromatin GO: nucleosome GO: nucleus Top 4 Models Predicted by I-TASSER

10 GRMZM2G470292

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