Puerto Rican Parrot Project
The Puerto Rican Parrot Project is focused on annotating genes known to be expressed in the uterus during eggshell deposition with the aim of finding genetic differences between the Puerto Rican parrot and its sister species.
Resources & Tools
- APPRIS
- Assembly Hub for 2016 Assembly
- Assembly Hub for amaVitFlyeNextDenovo1
- Assembly Hub for AmaVitNtjoin2 Assembly
- Assembly Hub for Amazona ventralis (2018)
- Assembly Hub for Other Bird Genomes
- Clustal Omega
- Ensembl
- Gene Model Checker for Puerto Rican Parrot
- Gene Record Finder for Chicken (RefSeq)
- Gene Record Finder for Chicken (Ensembl)
- Isoform Information for Parrot Genes
- NCBI BLAST
- NCBI Gene
- Polyphen-2
- Report Mutations in Amazona vittata
- Scaffold Chicken Correspondence
- Sorting Intolerant from Tolerant (SIFT)
- UniProt
Faculty Resources
Help
Contacts
Project Leaders
Juan Carlos Martinez-Cruzado
Alondra Díaz Lameiro
Don Paetkau
Technical Support
Wilson Leung
The Puerto Rican parrot (Amazona vittata) is the last surviving species of parrots native to lands under the U.S. jurisdiction. It was listed as a critically endangered species in 1967 under the Endangered Species Preservation Act, being considered one of the ten most endangered bird species in the world. Reduced eggshell strength and the consequential loss of offspring is one of the main problems often found by conservationists. The Puerto Rican Parrot Project is focused on annotating genes known to be expressed in the uterus during eggshell deposition with the aim of finding genetic differences between the Puerto Rican parrot and its sister species.
PILOT Project Curriculum
Walkthrough Module 3
Finding amino acid changes candidates to be specific to A. vittata
(MS Word | PDF)
Walkthrough Module 4
Assessing the impact of amino acid changes on protein function and searching for those changes in other Amazona parrots
(MS Word | PDF)
Annotation Report Form
Submit Gene Report and .gff, .fasta, and .pep files to your instructor
(MS Word)
Annotation Report Example: ATP1B1
Example Annotation Report for the sodium/potassium-transporting ATPase subunit beta-1 (ATP1B1) gene
(MS Word | PDF)
Annotation Workflow
1 page annotation workflow outlining steps of the project protocol
(PDF)
- Page Last Updated: September 19, 2025