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.
- orange - unspecified pseudogene
- blue - processed pseudogene
- olive green - unprocessed pseudogene
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.
- purple - parent gene
- grey - pseudogene indicators
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