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Transfer RNA, well-studied as the key adapter molecule in protein translation, is now recognized as having a plethora of additional regulatory functions when further processed into shorter RNAs. Many groups have contributed to this rapidly advancing field, inevitably leading to a constellation of diverse yet often overlapping names attributed to tRNA-derived fragments (e.g., tRFs, tsRNAs, tiRNAs, SHOT-RNAs, tRNA halves, etc.). In order to promote the growth of the research community and aid the recognition of structural/processing/functional relationships among the many forms of tRNA-derived RNAs (tDRs), the tRNA community proposes a consistent, uniform naming system integrating three main parts: (i) the prefix "tDR" (tRNA-Derived RNA), (ii) the portion of the mature tRNA from which the fragment is derived (using standardized Sprinzl tRNA base numbering), and (iii) the Genomic tRNA Database Identifier (GtRNAdb ID) of the tRNA gene(s) or transcript(s).

tDRnamer provides a consistent, stable name with annotations for submitted tDR sequences based on the naming system described below. The web server at is a point-and-click environment that does not require any software installation. Researchers who have a large data set including pre-processed small RNA-seq reads (FASTQ file format) and tDR sequences (FASTA file format) can utilize the standalone version on a Linux/Unix platform. Both versions provide additional annotations for each submitted tDR sequence including length, location of tDRs relative to source tRNAs, and sequence alignments. In addition, users can submit tDR names that are formatted according to this naming system and obtain the corresponding sequences with related annotations. More details are available in this user guide.

Standardized tDR naming system

tDR name

The standardized tDR name for tRNA-derived RNAs consists of five parts as shown in the figure above.

  1. Prefix - All tDR names start with the prefix "tDR" that stands for "tRNA Derived RNA".

  2. Position - The second part includes the start and end positions of the tDR relative to the source tRNA. The two positions are separated by a colon. The standard Sprinzl tRNA position numbering is used. If the position is located at the leader or trailer sequence of the precursor tRNA gene, the numbering will be preceded with a letter "L" or "T" respectively. For example, L3 stands for position -3 and T5 stands for position +5 of the source tRNA gene.

  3. Source tRNA - This is the name of the tRNA from which the tDR is derived. tRNA names from Genomic tRNA Database are used. If the tDR is derived from a mature tRNA transcript, only the isotype, anticodon, and transcript ID will be included as in the figure above. If the tDR is derived from a pre-tRNA gene that has unique leader or trailer sequence, the gene copy number will also be included, for example, Val-AAC-1-2.

  4. Matching tRNA transcripts - A tDR may be derived from multiple tRNAs due to identical sequence in some parts of different tRNA transcripts. If this occurs, an optional component with prefix "M" and the number of matching tRNAs will be added to the tDR name.

  5. Variations (optional) - A tDR may have sequence variations to the source tRNA due to mutations or RNA editing. If a variant is found based on sequence alignment, an annotation can be optionally added to the tDR name. If more than one variant exists, multiple annotations will be appended to the name.

    For a substitution, the annotation will include the base in tDR, the position of the substitution relative to the tDR, and the substituted base in the source tRNA. For example, U10A means that U at position 10 of the tDR is substituted by A.

    For an insertion, the annotation will include a prefix "I", followed by the position of the insertion relative to the tDR, and the inserted base. For example, I3G stands for an insertion of G at position 3 of the tDR.

    For a deletion, the annotation will include a prefix "D", followed by the position before the deletion relative to the tDR, and the deleted base from the source tRNA. For example, D16C stands for a deletion of C after position 16 of the tDR.