Hi everyone,

I was wondering if anyone if familiar of any annotation term in the human genes annotation e.g. from gencode or ensembl to be able to extract **pseudogenes** and separate them from non-pseudogenes.

Any thoughts?

Thanks in advance,
Sergio
You can use Ensembl BioMart with the following query:

[very long BioMart query..... Modify parameters as you like][1]

There are many sub-types of pseudo genes, the query outputs the gene type in the last column. 

  [1]: http://www.ensembl.org/biomart/martview/d5e8623bf33a920fd3fdf6149c374e2a?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id%7Chsapiens_gene_ensembl.default.feature_page.ensembl_gene_id_version%7Chsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id%7Chsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id_version%7Chsapiens_gene_ensembl.default.feature_page.start_position%7Chsapiens_gene_ensembl.default.feature_page.end_position%7Chsapiens_gene_ensembl.default.feature_page.strand%7Chsapiens_gene_ensembl.default.feature_page.chromosome_name%7Chsapiens_gene_ensembl.default.feature_page.description%7Chsapiens_gene_ensembl.default.feature_page.gene_biotype&FILTERS=hsapiens_gene_ensembl.default.filters.biotype.%22IG_C_pseudogene,IG_J_pseudogene,IG_V_pseudogene,polymorphic_pseudogene,processed_pseudogene,rRNA_pseudogene,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,translated_unprocessed_pseudogene,TR_J_pseudogene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene%22&VISIBLEPANEL=resultspanel