GENCODE Annotation

- Data: The current human manual annotation is available from GENCODE. .

- Description: The GENCODE annotation of pseudogenes contains models that have been created by the Human and Vertebrate Analysis and Annotation (HAVANA) team, an expert manual annotation team at the Wellcome Trust Sanger Institute. This is informed by, and checked against, computational pseudogene predictions by the PseudoPipe and RetroFinder pipelines.

PseudoPipe Output

- Data: The current PseudoPipe results are on Ensembl genome release 90. .

- Description: Genome-wide human pseudogene annotation predicted by PseudoPipe. PseudoPipe is a homology-based computational pipeline that searches a mammalian genome and identifies pseudogene sequences.

- Reference:

Other Human Pseudogene Sets

- Data: .

- Description: Archived pseudogene annotation on previous human genome releases from PseudoPipe. Genome-wide annotation or specific subset.

psiCube

- Data: Complete human, worm and fly pseudogene annotation and biochemical activity .

- Description: PsiCube consists of comparative analysis of pseudogene annotation, activity and evolution across human, worm and fly. In this analysis, we find the pseudogene complement has a strong lineage specificity which reflects each organims's evolution. However, we also find notable similarities in pseudogene activity among species. A majority of pseudogenes in each organism exhibit varying degree of partial activity, and in particular, a consistent fraction of pseudogenes are transcribed across all organisms.

- Reference:

psiDr

- Data: Pseudogene annotation from GENCODE version 7 and their activities in 5 ENCODE cell lines .

- Description: Genome-wide human pseudogene annotation from Gencode 7 and their biochemical activities in 5 ENCODE cell lines (GM12878, K562, H1-hESC, HeLa-S3 and HepG2). Pseudogene conservation has also been studied by comparing the annotion with the variation data from primate alignments and the 1000 Genomes project. An updated analysis on GENCODE version 10 pseudogenes is also included in psiCube.

- Reference:

• GENCODE
• Ensembl