GEP Annotation Report for fosmid 2392K12

Student name:Candice Cooper 
Student email:cfcooper@unm.edu 
Faculty advisor:Dr. Paul Szauter 
College/University:University of New Mexico 

Project Details

 
Project name:dananassae_3Lcontrol_Jan2013_fosmid_2392K12
Project species:Drosophila ananassae 
Date of submission: 
Size of project in base pairs:38,496
Number of genes in project:2

Does this report cover all genes and all isoforms or is it a partial report?
All genes and isoforms

Complete the following Gene Report Form for each gene in your project. Copy and paste the sections below to create as many copies as needed. Be sure to create enough Isoform Report Forms within your Gene Report Form for all isoforms.

Gene report form

Gene name (i.e. D. mojavensis eyeless):Thioredoxin reductase 2
Gene symbol (i.e. dmoj_ey):dana_Trxr-2
Approximate location in project (from 5' end to 3' end):25,142-23,601
Number of isoforms in D. melanogaster:1
Number of isoforms in this project:1

Name of unique isoform
based on coding sequence		List of isoforms with identical coding sequences
Trxr-2-PA  
   
   

Gene-isoform name (i.e. dmoj_ey-PA):    dana_Trxr-2-PA
Names of the isoforms with identical coding sequences as this isoform:    none

Is the 5' end of this isoform missing from the end of project:    no
    If so, how many exons are missing from the 5' end:    N/A
Is the 3' end of this isoform missing from the end of the project:    no
    If so, how many exons are missing from the 3' end:    N/A

1. Gene Model Checker checklist

Enter the coordinates of your final gene model for this isoform into the Gene Model Checker and paste a screenshot of the checklist results below:

Trxr-2

2. View the gene model on the Genome Browser

Trxr-2

Trxr-2 has had a microinversion in D. ananassae from D. melanogaster. It is on the (-) strand in D. ananassae and the (+) strand in D. melanogaster.

3. Alignment between the submitted model and the D. melanogaster ortholog

Show an alignment between the protein sequence for your gene model and the protein sequence from the putative D. melanogaster ortholog. You can use the protein alignment generated by the Gene Model Checker or you can generate a new alignment using BLAST 2 Sequences (bl2seq). Copy and paste the alignment below:

Trxr-2

4. Dot plot between the submitted model and the D. melanogaster ortholog

Paste a copy of the dot plot of your submitted model against the putative D. melanogaster ortholog (generated by the Gene Model Checker). Provide an explanation for any anomalies on the dot plot (e.g. large gaps, regions with no sequence similarity).

Trxr-2

Gene report form

Gene name (i.e. D. mojavensis eyeless):CG11404
Gene symbol (i.e. dmoj_ey):dana_CG11404
Approximate location in project (from 5' end to 3' end):21671-22338
Number of isoforms in D. melanogaster:2
Number of isoforms in this project:2

Name of unique isoform
based on coding sequence		List of isoforms with identical coding sequences
CG11404-PA CG11404-PB
   
   

Gene-isoform name (i.e. dmoj_ey-PA):    dana_CG11404-PA
Names of the isoforms with identical coding sequences as this isoform:    CG11404-PB

Is the 5' end of this isoform missing from the end of project:    no
    If so, how many exons are missing from the 5' end:    N/A
Is the 3' end of this isoform missing from the end of the project:    no
    If so, how many exons are missing from the 3' end:    N/A

1. Gene Model Checker checklist

Enter the coordinates of your final gene model for this isoform into the Gene Model Checker and paste a screenshot of the checklist results below:

CG11404

2. View the gene model on the Genome Browser

CG11404

3. Alignment between the submitted model and the D. melanogaster ortholog

Show an alignment between the protein sequence for your gene model and the protein sequence from the putative D. melanogaster ortholog. You can use the protein alignment generated by the Gene Model Checker or you can generate a new alignment using BLAST 2 Sequences (bl2seq). Copy and paste the alignment below:

CG11404

CG11404

4. Dot plot between the submitted model and the D. melanogaster ortholog

Paste a copy of the dot plot of your submitted model against the putative D. melanogaster ortholog (generated by the Gene Model Checker). Provide an explanation for any anomalies on the dot plot (e.g. large gaps, regions with no sequence similarity).

CG11404

CG11404

Preparing the project for submission

For each project, you should prepare the project GFF, transcripts and peptide sequence files (for ALL isoforms) along with this report. You can combine the individual files generated by the Gene Model Checker into a single file using the Annotation Files Merger.

The Annotation Files Merger also allows you to view all the gene models in the combined GFF file within the Genome Browser. Please refer to the Annotation Files Merger User Guide for detail instructions on how to view the combined GFF file on the Genome Browser (you can find the user guide under “Help” -> “Documentations” -> “Web Framework” on the GEP website at http://gep.wustl.edu).

Paste a screenshot (generated by the Annotation Files Merger) with all the gene models you have annotated in this project.

merged gbrowse

Have you annotated all the genes?

For each region of the project with gene predictions that do not overlap with putative orthologs identified in the BLASTX track, perform a BLASTP search using the predicted amino acid sequence against the non-redundant protein database (nr). Provide a screenshot of the search results. Provide an explanation for any significant (E-value < 1e-5) hits to known genes in the nr database and why you believe these hits do not correspond to real genes in your project.

3 genscan gene predictions, 1 invalid

merged gbrowse

no significant hits against entire nr database, invalid gene prediction

Repeats

Wolbachia repeats seen around 4967-5194, 30078-30129, 19501-19615, 34435-3511

Wolbachia

retroviral repeats seen around ***35,000***

BLASTX