How are RNA genes annotated?


A large proportion of the RNA genes in VectorBase are annotated in a completely automated way. There are some exceptions to this rule, where we import genes from other sources, or have been supplied with manual annotations for particular classes of RNA.

VectorBase automated annotation

VectorBase uses three sources for RNA gene annotation:

  • miRBase provide genomic locations of precursor microRNA genes for a small subset of species (Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis).
  • tRNAscan-SE is used to predict tRNA genes (with a score threshold of 65). Lowe, T. M., & Eddy, S. R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5), 955–964.
  • Rfam covariance model alignments are used to annotate RNA genes of all classes except tRNA. Models are restricted to those that are taxonomically appropriate, and are filtered to prevent overlapping genes (on either strand). Nawrocki, E. P., Burge, S. W., Bateman, A., Daub, J., Eberhardt, R. Y., Eddy, S. R., … Finn, R. D. (2015). Rfam 12.0: updates to the RNA families database. Nucleic Acids Research, 43(Database issue), D130–D137.

RNA genes from other sources

The following classes of RNA genes have not been annotated automatically by VectorBase:

  • Aedes albopictus: precursor microRNA (pre_miRNA)
  • Anopheles darlingi: ribosomal and transfer RNA (rRNA, tRNA)
  • Musca domestica: transfer RNA (tRNA)
  • Rhodnius prolixus: precursor microRNA (pre_miRNA)
  • Sarcoptes scabiei: ribosomal and transfer RNA (rRNA, tRNA)
  • Stomoxys calcitrans: transfer RNA (tRNA)


This a gene page (click on the image to enlarge), notice the following information:

  • the transcript table links in the Biotype column that provide the full name of the gene acronyms
  • the Summary section links to the Rfam page/wikipedia page
  • the secondary structure image in the gene-based displays

Gene set table;r=supercont1.131:1212365-1212706;t=AAEL018514-RA

Two other FAQs have related information that may also be of your interest: