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Populus trichocarpa Genome ?

View a sample region of chromosome 2 or select a region above:

Genome / Gene Models

The current genome assembly displayed at PtGDB is version . Annotated gene models are Ptr v2.2. For more information see Data & Methods. More about the genome...

Alignments to Genome

PtGDB displays high quality spliced alignments for EST, cDNA, PUT, and model species proteins. The current alignment database version is PtGDB179. For more information see Data & Methods. More about alignments...

Search / Download

Search or download any sequence from PtGDB using Search / Download links at left. Complete datasets can also be downloaded from the PtGDB Download page or by ftp. More about search / download...

Note: sequences displayed here may not reflect the latest Populus trichocarpa sequence count at PlantGDB, which can be viewed on our download page.


Sequence analysis tools accessed from the Genome Context View menu use the current genomic region as input. Or, to access the same tools without a genomic context, use PtGDB left menubar Tools links. More about tools...

Gene Structure Annotation

Help annotate the Populus trichocarpa genome using our yrGATE gene structure annotation tool (see Overview), aided by GAEVAL tables that flag problematic gene models. Video demo: QuickTime   Flash  

Custom Track Display

Distributed Annotation Service (DAS) (see Overview) is available for displaying remotely served genome alignments at PtGDB, as well as for displaying selected PtGDB tracks on a different genome browser (e.g. Ensembl, GBrowse). How to use DAS...

Additional custom track display features are under development.

Annotated Protein Alignments

A searchable table of splice-aligned, annotated protein models from one or more related species. Select from the left menu under Gene Annotations -> Splice-Aligned Proteins.


Genome browser video demo: QuickTime Flash
For help pages and tutorials focusing on genome browser features and gene annotation, see side bar.

PtGDB is being developed as a part of our NSF-funded project "Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB" (PI: Volker Brendel). The purpose of this resource is to provide a convenient sequence-centered genome view for Populus trichocarpa, with a narrow focus on gene structure annotation.

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