MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments

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2,282,606 requests 04/04/2019 stats: 28,824 expressed tRFs | 12,023 datasets | 125,285 genomic instances

MINTbase glossary

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Term Definition
tRF We report tRNA fragments (tRFs) with lengths 16-50 nt that originate from mature tRNAs (true tRNA, pseudo tRNA, exact tRNA-lookalikes, and MT-tRNA) (see also tRNA-space).
tRNA fragment see tRF definition.
type of tRF Letting XYZ be the anticodon and abXYZcd indicate the immediate vicinity of it, then:
  • 5'-half: any fragment that begins at the 5' end "+1 position" or at the "-1" position of a tRNA and ends in one of 'a,' 'b,' 'X' or 'Y.'
  • 3'-half: any fragment that begins at one of 'b,' 'X,' 'Y' or 'Z' and ends in either the first 'C,' the second 'C,' or the 'A' of the non-templated 'CCA' addition.
  • 5'-tRF: any fragment that begins at the 5' end "+1 position" of the tRNA or at the "-1" position and ends in a position other than 'a,' 'b,' 'X,' or 'Y.' In other words, a 5-tRF ends either before 'a' or after 'Y' (including potentially positions to the right of d).
  • 3'-tRF: any fragment that begins at a position other than 'b,' 'X,' 'Y' or 'Z' and ends in either the first 'C,' the second 'C,' or the 'A' of the non-templated 'CCA' addition. In other words, a 3-tRF begins either after 'Z' or before 'b' (including potentially positions to the left of a).
  • i-tRF: any fragment that both does not begin at the 5' end "+1 position" or the "-1" position, and does not end at the first 'C,' the second 'C,' or the 'A' of the non-templated 'CCA' addition.
For more information on i-tRFs visit here.
RPM Reads per million (RPM) is a measure of abundance of a tRF among the primary raw reads of a dataset. To calculate the RPM two values are required, a) the total number of sequenced reads and b) the number of times the tRF was encountered after mapping.
To ensure uniformity among the submitted datasets, MINTbase, requires that both numbers are submitted via MINTsubmit and calculates the RPM automatically as (b*106) ⁄ a.
Dataset number (with RPM ≥ x) The total number of datasets that were submitted in MINTbase and reported the tRF with an RPM value of more than or equal to x. If no RPM requirement is stated then x equals 1. MINTbase and MINTsubmit automatically discard tRFs with an RPM value of RPM < 1.
Expressed tRF MINTbase generates all possible potential tRFs and does not wait for them to be reported. Some of those tRFs have not yet (or may never be) found in any dataset.
A tRF is characterized as expressed if it is included in at least one dataset that has been submitted in MINTbase with RPM ≥ 1 (see also dataset number). Otherwise it is considered not-expressed.
A user can select to view all possible tRFs or expressed tRFs only.
tRNA space A tRF is marked as being exclusive to tRNA space if there is no genomic location that contains the tRF's sequence which is not located within the confounds of a true tRNA, a pseudo tRNA, an exact tRNA-lookalike, a true MT-tRNA, a pseudo MT-tRNA or an exact MT-tRNA-lookalike.
Fragments that are not exclusive to tRF space have a greater likelihood of not being a bona-fide tRF.
Unique ID (sequence derived) License plates or tRF license plates or Sequence derived MINTbase unique IDs, are a tRNA fragment ID that depends solely on the tRF's genomic sequence which transcends assemblies and species. Find out more or generate convert your own by using MINTplates.
License Plate See "Unique ID (sequence derived)" definition.
Alternative IDs (assembly-derived) Assembly specific ID that consists of the tRNA ID (see "tRNA name"), the start and end position of the tRF with respect to the mature tRNA and the tRF's length. A tRF tRF sequence may contain multiple values for this ID if it could come from multiple locations in tRNA space.
tRNA name Includes reference tRNA number (if from gtRNAdb2009), unspliced coordinates, and the amino acid and anticodon of the tRNA. Other tRNA names are shown and can be used interchangeably with MINTbase's. See more.
Candidate mature tRNA sources Candidate mature tRNA sources or Parental tRNAs are the tRNAs from which the tRF can be derived. Those are the tRNAs whose mature sequence (or their post-modifications) contains the tRFs.
Parental tRNAs See "Candidate mature tRNA sources" definition.
MINTsubmit Use this tool to upload your tRF expression dataset to MINTbase. You can access it here.