• gokhan.karakulah@ibg.edu.tr


What is PetMbase?

PeTMbase is an online resource for endogenous miRNA target mimics for plants. Our database provides 2728 eTM sequences identified computationally from 11 different plant species. The number of deposited eTM records are being increased as the new species are dissected for target mimicry and all eTM sequences are available for download.

How do we identify eTM sequences?

We systematically collect long non-coding RNA (lncRNA) species from the following online data sources: (i) Sequence Read Archive (To discover novel lncRNA transcripts of 11 plant species, we utilize our custom STAR Cufflinks analysis pipeline), (ii) Plant Non-coding RNA Database , and (iii) GreenNC database . MicroRNA sequences are retrieved from Mirbase, and searched within the lncRNA sequences as described by Wu et al, 2013 : (i) the 2 nd to 8 th positions at the 5’ end of a microRNA sequence must perfectly match to target eTM sequence, (ii) three nucleotides bulges are allowed between the 9th to 12th positions at the 5’ end of the microRNA sequence, and (iii) maximum 3 nucleotide mismatch (excluding bulge region) can be between microRNA and eTM sequences. Below is an example of pairing a microRNA sequence and its corresponding potential eTM transcript.

Which genome sources do we utilize for identification of plant eTMs?

We use the following assemblies for the identification of eTMs:

  • Arabidopsis thaliana - TAIR10
  • Brachypodium distachyon - v1.0
  • Glycine max (soybean) - V1.0
  • Hordeum vulgare (barley) - ASM32608v1
  • Medicago truncatula - MedtrA17_4.0
  • Oryza sativa (rice) - IRGSP-1.0
  • Populus trichocarpa (poplar) - JGI2.0
  • Sorghum bicolor - Sorbi1
  • Solanum lycopersicum (tomato) - SL2.50
  • Triticum aestivum (wheat) - IWGSC1+popseq
  • Zea mays (maize) - AGPv3

How to search?

You can simply search by microRNA name e.g. “miR827-3p” or “zma-miR827- 3p”, or select a species name to list all available eTMs regarding the species of interest. The below shows how to search and to see results in PetMbase database.

How can I download eTM data?

You can freely download all available sequence, microRNA and binding site information in .csv format per species. Please select and click the corresponding link of each species in the download section.