Nicole colonfall2012researchproposalv4 final

ANNOTATION OF THE KIF3C GENE OF DROSOPHILA

BIARMIPES FROM FOSMID 66

Nicole Colon Carrion

Dr. Michael Rubin

Department of Biology

University of Puerto Rico, Cayey

DROSOPHILA MELANOGASTER

small fly belonging to the Drosophilidae family.

Drosophila genus contains around 1,500 species.

They are usually found around spoiled or ripe fruits.

D. MELANOGASTER AS A MODEL ORGANISM

Many studies have used Drosophila melanogaster as a model system for understanding human biology and diseases.

It has 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).

DROSOPHILA BIARMIPES 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 portion of each wing.  From: FlyBase

data/phylogeny/Drosophilidae-Tree/suzukiisubgroup.htmhttp://flybase.org/static_pages/allied-l

YELLOW GENE

Yellow-like genes have only been identified in insect species and a number of bacteria.

Dmel\y also known as the yellow gene that encodes a protein that functions in melanization and behavior in Drosophila.

Propotionated by: Science Directhttp://www.sciencedirect.com/science/article/pii/S006526600700003X

EXPRESSION OF THE YELLOW GENE

KIF3C Protein coding gene in charge of controlling

molecular functions. In D. melanogater is referred by the symbol

Dmel\Kif3C It is involved in controlling microtubule motor

activity. Studding and annotating Kif3c can led to a better

understanding of the gene function and pathway.

EXPRESSION OF THE KIF3C

Number of published studies where the KIF3C gene is over/under expressed.

From: EMBL-EBIhttp://www.ebi.ac.uk/gxa/gene/AI107317http://www.ebi.ac.uk/gxa/experiment/E-GEOD-27927/FBgn0039925?ef=

Figure 1

OBJECTIVE It is 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.

PROBLEM AND HYPOTHESIS

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

METHODOLOGY

FlyBaseIdentify possible orthologs in

D. biarmipes.

Gene Record FinderIsoforms and exons sequences were identified and collected using the Gene Record Finder

BLASTXEach exon was analyzed based on their

position and gene sequence using BLASTx.

Based on the alignments chosen, the start and stop codon of the possible gene model will

be identified using BLASTx.

METHODOLOGY

Genome BrowswerThe process of joining exons was

begun.

The donor site as GT.

The acceptor site was identified as AG.

Gene Model CheckerConfirm your gene model using the

Gene Model Checker.

ALIGNMENT OF KIF3C VS. SUBMITTED SEQUENCE

Identity 233/678 (34.4%),

Similarity 266/678 (39.2%)

Gaps 371/678 (54.7%)

DOT PLOT OF ALIGNMENT OF KIF3C VS. SUBMITTED SEQUENCE

GENE MODEL

Approximate location in project covered by gene (from 5’ end to 3’ end): from base 17,150 to base

23,800

Gene model contains 5 exons

Gene model contains 23 amino

acids

GENE MODEL

Start and Termination Codons of the model gene from the Kif3C gene were identify as ATG and TAA.

Start Codon Termination Codon

CONCLUSIONS 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.

ACKNOWLEDGEMENTS Dr. Rubin

Joseph Perez

GEP

QUESTIONS