Description

These tracks contain pseudogene predictions and their parents as identified by PseudoPipe.

Display Conventions

Pseudogene track

By default pseudogenes are labeled by parent Hugo ID and type of pseudogene. The Hugo IDs are based on the Ensembl gene IDs provided by the Gerstein lab after dataset creation; not all PseudoPipe IDs could be mapped back to their original Ensembl IDs. In these cases the gene ID is listed as NA.
Pseudogenes are colored by type.

Mouseover on items shows the PseudoPipe ID and Ensembl gene ID. Clicking on the gene ID opens the parent track in that location.

Parent track

Each parent gene is shown with their pseudogenes represented as grey blocks. Each block has a mouseover with a link to the pseudogene track.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API.
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Methods

Annotations were filtered to remove duplicates and non standard chromosomes, and overlapping exons merged if they belonged to the same transcript.

Credits

Thanks to Cristina Sisu for providing data in GTF format with parents annotated. Track created by Jeltje van Baren.

References

Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 2006 Jun 15;22(12):1437-9. PMID: 16574694