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Nicole colonfall2012researchproposalv4 final


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Nicole colonfall2012researchproposalv4 final

  1. 1. Nicole Colon CarrionDr. Michael RubinDepartment of BiologyUniversity of Puerto Rico, Cayey
  2. 2.  small fly belonging to the Drosophilidae family. Drosophila genus contains around 1,500 species. They are usually found around spoiled or ripe fruits.
  3. 3.  Many studies have used Drosophila melanogaster as a model system for understanding human biology and diseases. Ithas been estimated that nearly 75% of disease- related genes in humans have functional orthologs in the fly (Udai Bhan Pandey and Charles D. Nichols, 2011; Reiter et al., 2001; Lloyd and Taylor, 2010).
  4. 4.  native to South-East Asia belonging to the suzukii subgroup. Adults of this fruit fly are almost identical to Drosophila melanogaster, with the exception that the males have one black spot on the back From: FlyBase portion of each wing. data/phylogeny/Drosophilidae- Tree/suzukiisubgroup.htmhttp://
  5. 5.  Yellow-like genes have only been identified in insect species and a number of bacteria. Dmely also known as the yellow gene that encodes a protein that functions in melanization and behavior in Drosophila. Propotionated by: Science Direct rticle/pii/S006526600700003X
  6. 6.  Protein coding gene in charge of controlling molecular functions. In D. melanogater is referred by the symbol DmelKif3C It is involved in controlling microtubule motor activity. Studding and annotating Kif3c can led to a better understanding of the gene function and pathway.
  7. 7. Number of published studies where the KIF3C gene is over/under expressed. Figure 1From: EMBL-EBI
  8. 8.  Itis our objective to annotate the Kif3c gene present in the Fosmid 66 of Drosophila biarmipes using different Bioinformatics tools. Compare the gene annotation results of Drosophila biarmipes with Drosophila melanogaster.
  9. 9.  Problem: whether D. melanogaster will be helpful for the annotation of Kif3c gene of D. biarmipes. Hypotesis:D. melanogaster will be helpful for the annotation of Kif3c gene of D. biarmipes
  10. 10. FlyBase Gene Record Finder Identify possible orthologs in Isoforms and exons sequences were identified D. biarmipes. and collected using the Gene Record Finder BLASTX Based on the alignments chosen, the start and stop Each exon was analyzed based on their codon of the possible gene model willposition and gene sequence using BLASTx. be identified using BLASTx.
  11. 11. Genome Browswer Gene Model CheckerThe process of joining exons was begun. Confirm your gene model using the Gene Model Checker. The donor site as GT.The acceptor site was identified as AG.
  12. 12. Identity 233/678 (34.4%),Similarity 266/678 (39.2%)Gaps 371/678 (54.7%)
  13. 13. Approximatelocation in project covered by gene(from 5’ end to 3’ end): from base 17,150 to base 23,800Gene model contains 5 exons Gene modelcontains 23 amino acids
  14. 14. Start and Termination Codons of the model gene from the Kif3C gene were identify as ATG and TAA. Start Codon Termination Codon
  15. 15.  The Kif3C gene From Fosmid 66 of Drosophila biarmipes containing 5 exons was annotated successfully using different Bioinformatics tools. The gene models were confirmed using the Gene Model Checker. Start and Termination Codons of the model gene from the Kif3C gene were identify as TGA and TAA. The gene annotation results of Drosophila biarmipes were compared with Drosophila melanogaster showing a 34.4% identity.
  16. 16.  Dr. Rubin Joseph Perez GEP