Which are the gene biotype definitions?
This a Search query for all genes in VectorBase (click on the image to enlarge):
https://www.vectorbase.org/search/site/*?&site=%22Genome%22&bundle_name=%22Gene%22
All these terms are from the Sequence Ontology, http://www.sequenceontology.org, except for nontranslating_CDS. Below you will find each term link to SO, definitions are provided there and have also been included in VectorBase Glossary.
- protein_coding
- tRNA :
- ncRNA:
- pre_miRNA
- rRNA
- snRNA
- pseudogene
- snoRNA
- SRP_RNA
- lncRNA
- RNase_P_RNA
- RNase_MRP_RNA
- sense_intronic
- scaRNA
- ribozyme
In VectorBase we created the category nontranslating_CDS. This is for genes which have been annotated as 'protein_coding', but which have an invalid translation (i.e. internal stop codons). This means this category does not really reflect a biological fact like the other biotypes do, it's just a pragmatic way to represent our incomplete knowledge about a gene. This term is under review and its name it may changed in the future.
Two other FAQs have related information that may also be of your interest:
