Automated Genome Project Investigation Environment

Zebra Finch EST Project

Organization of the MAGPIE database

The MAGPIE zebra finch EST database contains sequences for 9845 cDNA clones, drawn from four cDNA libraries, made from total brain tissue of zebra finches from different developmental stages. cDNAs were cloned into the pBluescript plasmid vector, and sequenced from the 3'-end using the T3 primer.

Sequences from each library are organized into groups, with each group representing a single 96-well plate. The detail page for each plate-group includes NCBI Genbank accession numbers for all component sequences, along with predicted protein functions, if available, and a plate-ID number, indicating clone position in the original 96-well plate. Each Genbank ID number is linked to a detail page containing additional information about that individual clone, including sequence similarity to zebra finch cDNAs from other sources, as well as evidence supporting functional annotation assignments based on BLAST searches against NCBI's protein and nucleotide databases. The following table describes the libraries, RNA sources and clone naming conventions.

Library type RNA source Library name prefix
Embryonic library embryonic zebra finch brains zf_eli
Developmental I library brains from 1 to 20 day old male zebra finches. zf_0, zf_yg
Developmental II library brains from 30-50 day old male zebra finches. zf_30D
Developmental III library brains from 60-90 day old male zebra finches. zf_60d

All cDNA clones are available upon request.
Please direct clone inquiries to Dr. Xiao-Ching Li (
For MAGPIE web-interface questions, contact  


This work is described in the following manuscript, currently submitted for publication:

Genomic Resources for Birdsong Research and Their Use in Characterization of Gene Expression During Songbird Brain Development.

Xiao-Ching Li1*, XiuJie Wang2*, Jonathan Tannenhauser1, Sheila Podell3, Piali Mukherjee1, Moritz Hertel1, Jeremy Biane1, Shoko Musuda1, Fernando Nottebohm1 and Terry Gaasterland3. (2006).

1 The Rockefeller University, 1230 York Ave. NY, NY 10021;
2 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
3 University of California, San Diego, La Jolla CA 92093-0202.
*These two authors contributed equally to the paper.

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