Nucleic databases - Hoppsigen
Hoppsigen is a nucleic database of homologous processed pseudogenes.
Processed pseudogenes are retroelements (like SINE and LINE). They are generated by two ways:
Reverse transcription of RNA messenger in germ line cells.
Duplication of an existing processed pseudogene in germ line cells.
So if we compare processed pseudogenes to their functional homologs, they have lost introns and they have no promoter (except for processed pseudogenes which are inserted near an existing promoter).
Genes giving rise to processed pseudogenes have to be expressed in germ line cells. Their identification could help us to identify precisely genes expressed in these cells. Since they lack promoters, generally they are no longer transcribed so they quickly accumulate mutations. That’s the reason why we consider that these sequences are non functional. They are no longer subjected to selection constraints. So they could be used to estimate silent substitution rates along genomes in relation with the local GC content.