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Figures: Ancient Nature of AS and function of introns

Figures: Ancient Nature of AS and function of introns. Kemin Zhou Nov 24, 2011. 0.06. 0.05. 0.04. NAG/EST Coverage. 0.03. 0.02. 0.01. 0. 0. 100. 200. 300. 400. 500. 600. 700. 800. 900. EST Coverage. Fig 1. Count. NAG. Fig 2. Aspac1: 3.6. 0.8. 0.6. NAG per Exon.

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Figures: Ancient Nature of AS and function of introns

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  1. Figures: Ancient Nature of AS and function of introns Kemin Zhou Nov 24, 2011

  2. 0.06 0.05 0.04 NAG/EST Coverage 0.03 0.02 0.01 0 0 100 200 300 400 500 600 700 800 900 EST Coverage Fig 1

  3. Count NAG Fig 2

  4. Aspac1: 3.6 0.8 0.6 NAG per Exon Aspca3: 3.6 Spoth2: 3.1 0.4 Lacbi2: 4.7 0.2 Agabi2: 6.8 0 200 400 600 800 EST Coverage Figure 3

  5. 0.14 0.12 0.1 0.08 No AS AS 0.06 0.04 0.02 0 Agabi2 Aspca3 Aspac1 Lacbi2 Spoth2 AS Ancient Fraction of proteins with homologs in all three kingdoms Figure 4

  6. 0.7 observe 0.6 expect 0.5 0.4 0.3 0.2 0.1 0.0 N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y 2000 1800 1600 1400 1200 1000 800 600 400 200 0 N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y Spoth2 Aspac1 Agabi2 Aspac1 Aspca1 Aspca3 Lacbi2 Lacbi2 Perfect Near perfect Indel Partial None A. Fraction B. Count Figure 5

  7. 0.35 3.34E-06 5.19E-09 2.60E-05 0.0017 0.3261 0.34 0.33 0.32 3.43E-12 3.38E-10 9.74E-03 1.27E-12 0.0422 0.0155 0.9277 0.1000 0.7692 0.3000 0.3148 0.1966 0.0668 0.2068 0.576 0.10 0.31 0.08 0.06 0.04 0.36 0.30 0.02 2.25E-02 0.34 9.85E-05 0.06376 1.94E-02 0.00 1.45e-02 8.15E-08 0.58455 3.23E-08 0.00025 0.78046 -0.02 0.32 -0.04 -0.06 0.30 Agabi2 Aspca3 Lacbi2 Spoth2 Aspac1 No Mi Ma No Mi Ma No Mi Ma No Mi Ma No Mi Ma 0.40 Agabi2 Aspca3 Lacbi2 Spoth2 Aspac1 0.28 N Y N Y N Y N Y N Y 0.35 Agabi2 Aspca3 Lacbi2 Spoth2 Aspac1 0.30 2.03E-54 4.20E-08 6.71E-34 4.83E-52 2.15E-05 1.62E-09 7.09E-03 0.0123 0.0113 0.25 0.681 1.7E-62 8.2E-07 1.4E-84 7.3E-07 1.0E-46 2.6E-30 2.6E-22 0.8562 1.8E-07 6.0E-35 0.0012 3.7E-07 0.0099 9.1E-10 0.9484 0.0605 0.0209 0.1136 1.5E-12 8.4E-40 0.2687 0.6857 0.0112 0.3054 0.0143 0.0746 0.0062 0.2227 0.6142 0.2806 3n 0.20 3n+1 N Y N Y N Y N Y N Y 0.5 3n+2 Agabi2 Aspca3 Lacbi2 Spoth2 Aspac1 0.4 0.3 0.2 0.1 N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y N Y 0.5 0.6 0.3 0.7 0.5 0.6 0.5 0.4 0.4 0.7 0.7 0.6 0.4 0.6 0.4 0.5 0.3 0.4 0.3 0.4 0.8 0.6 0.5 0.5 0.4 0.6 0.6 0.2 0.7 0.3 No Mi Ma No Ma Mi Ma No Mi Ma Mi No Ma No Mi 0.850 0.045 0.804 0.080 0.860 0.923 0.032 0.068 0.070 0.098 0.042 0.127 0.034 0.011 0.955 Lacbi2 Aspac1 Agabi2 Aspca3 Spoth2 A. Intron 3n length distribution C. Stop Codon Fraction of total Fraction of total D. RI type B. Coding region Fraction of total Diff. against coding E. Stop and RI type Fraction of total Fig 6

  8. Lacbi2 10 Agabi2 15 Aspca3 4 Intron Length Comparison Spoth2 Aspac1 3 Fig 7

  9. 0.0037 8.84E-05 0.7346 0.8827 0.0063 0.7741 0.0101 0.6887 0.9135 0.1062 0.4289 0.3131 0.9612 0.0031 0.5572 0.12 0.08 0.04 Fraction of total 0.00 -0.04 -0.08 No Mi Ma No Mi Ma No Mi Ma No Mi Ma No Mi Ma 7.28E-300 4.75E-174 4.09E-133 2.06E-255 5.11E-25 9.18E-11 0.00E+00 3.32E-16 7.40E-03 1.02E-40 0.5 0.4 2.84E-87 4.81E-63 0.000169 5.67E-87 0.018908 7.14E-21 0.154472 3.91E-70 1.37E-08 9.36E-39 0.676498 0.003927 3.43E-26 0.045587 5.13E-55 0.4 0.3 0.3 Fraction of total 0.2 0.1 0.2 Phase 2 Phase 1 Phase 0 0.1 0.1 0.0 0.0 0 N N Y Y Y N Y Y N N Agabi2 Aspca3 Spoth2 Lacbi2 Aspac1 0.28 0.70 0.30 0.72 0.38 0.72 0.67 0.62 0.28 0.33 -0.1 Agabi2 Agabi2 Aspca3 Aspca3 Lacbi2 Lacbi2 Spoth2 Spoth2 Aspac1 Aspac1 -0.2 0 1 1 0 2 1 0 2 1 0 2 0 2 1 2 Agabi2 Aspca3 Lacbi2 Spoth2 Aspac1 A. Intron phase distribution C. Stopless Introns of different RI types Difference against stopless B. Introns with and without Stop Codon D. Stopless Introns of different 3n length Difference against stopless Fig 8.

  10. 4.9E-63 3.9E-37 1.6E-61 4.1E-04 3.9E-06 2.2E-05 3.7E-08 0.8825 0.4007 5.3E-24 1.6E-11 1.2E-21 9.0E-07 0.0237 8.1E-04 0.6276 4.3E-08 0.1937 5.8E-75 5.1E-59 1.9E-84 5.2E-05 0.0954 2.0E-05 1.4E-11 0.1149 8.6E-04 0.0022 0.2220 8.4E-05 0.1476 0.0049 0.0087 0.4174 0.0291 0.3106 0.6449 0.0117 0.0015 0.0156 0.3430 0.3442 0.0467 1.2E-10 0.0258 0.25 0.20 0.15 0.10 0.05 0.00 -0.05 -0.10 -0.15 -0.20 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Minor Minor Minor Minor Minor Major Major Major Major Major NRI NRI NRI NRI NRI ph0 ph1 ph2 Difference against stopless Aspac1 Lacbi2 Aspca3 Agabi2 Spoth2 Fig 9

  11. FLIMV Stopless Flexibility Phase Q * V S 13 aa * NNG|GTRAGTNN…NNTNYAG|NN 0 Limited 15/32 15/16 1/2 3/4 3/4 FLSYCW * LIVSPTA G KE VADEG 14 aa NNG|GTRAGTNN…NNTNYAG|NN 1 13/16 Best 13/16 7/8 7/8 SR V SFYC WRG * NNG|GTRAGTNN…NNTNYAG|NN 2 0 Limited 0/2 195/256 13/16 15/16 Fig 10.

  12. RI Evolution: Minor  Major  loss Evolution Gene NMD Stop Codon 3n+1, 3n+2 Splicing Error New Non-coding Function Minor RI NRI 3n, no stop New Protein Function Major RI Exonization Positive Selection A new Intron loss mechanism Fig 11.

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