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Scarlet Runner Bean Genome Sequence: Contig232576 By Elaine Chiu.

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Presentation on theme: "Scarlet Runner Bean Genome Sequence: Contig232576 By Elaine Chiu."— Presentation transcript:

1 Scarlet Runner Bean Genome Sequence: Contig By Elaine Chiu

2 What is Contig232576? -A 15.1KB sequence in the SRB genome -Found 4 predicted genes that are supported by ESTs -1 predicted gene from Soybean -Contains 1 repetitive sequence: TY1/Copia about 240bp

3 FGENESH GENSCAN GENEMARK BLASTn entire scaffold KB Repeated sequence (n ) How many predicted sequences are there and where are they located? 3

4 How do we determine if the predicted genes are likely to be real? ESTs -A predicted gene is likely to be a real gene if there are many ESTs supporting it -If the E-value is very Low, not likely to match by chance (significance cut-off is E-10) E-value of 4e-113

5 FGENESHBLASTnBLASTptBLASTnDescription Gene 1n/a1.41.8Not significant (NS) Gene 22e-445.5e-5 454PCS Scarlet Runner Bean globular stage suspensor Gene 34e-1135e-27e-30 ALF-R-11_ /ALF(R)-11_N09_018_1 Alfalfa (Medicago sativa) Trichome S13dNF77C04GS034_ Germiniating Seed Medicago truncatula Gene 43e-651.7e-15VBL1_32_G04_E001.g1 Cotyledon and young leaves of peanut Arachis hypogaea GENSCANBLASTnBLASTptBLASTnDescription Gene 13e-143.8n/aCT Eucalyptus gunnii Gene 24e NS Gene 3e-754e-246e-25 KN0AAQ7YB22RM1 IVIA1 Citrus clementina ALF-R-11_ /ALF(R)- 11_N09_018_1 Alfalfa (Medicago sativa) S13dNF77C04GS034_ Germiniating Seed Medicago truncatula Gene 4n/a2.1n/aNS

6 GENEMARKBLASTnBLASTptBLASTnDescription Gene 1n/a1.45e-8NS Gene 2n/ae-262e-25 ATP synthase CF1 beta subunit [Populus trichocarpa] VVB168G01_ An EST database for abiotic stressed leaves of Vitis vinifera Gene 3n/a Gene 4n/a1.41.8NS Gene 5n/a0.465e-30 IC0AA39AB01RM2 CitNFL Citrus clementina CT Eucalyptus gunni Gene 6n/a6e-264e-34 S13dNF77C04GS034_ Germiniating Seed Medicago truncatula Gene 7n/a0.674e GmaGlobSeed Soybean Seeds Containing Globular Stage Gene 8n/a NS Gene 9n/a3.02e-12 VBL1_32_G04_E001.g1 Cotyledon and young leaves of peanut Arachis hypogaea Gene 10n/a0.85e-20MOOE277TF MOO Vigna unguiculata Gene 11n/a NS

7 Thank You Sorry Daisy, Kristin and Anhthu for spamming you. LOL Thanks Brandon, Min, Chen, Tomo, Kelli for behind the scenes help. So many photos to upload. Thanks Ingrid for Monday night dinners to everyone was always late for. Thanks Anhthu for making funny jokes and for lunch. And teaching me about Alaska. Thanks Daisy and Kristin for Always being in the lab when we need you. Thanks Dr. Goldberg for making this lab possible. I never imagined I could do something like this in my freshman year (and enjoy it).


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