Nuclear and mitochondrial tRNA-lookalikes in the human genome

An extended discussion on the potential functions of tRNA lookalikes as well as mitochondrial tRNA-lookalikes for several species can be found here.

If you use any of the below please cite: Telonis AG, Loher P, Kirino Y, Rigoutsos I (2014) Nuclear and mitochondrial tRNA-lookalikes in the human genome. Frontiers in Genetics doi: 10.3389/fgene.2014.00344

In this page you will find the genomic coordinates of tRNA-lookalikes of Homo Sapiens as described in ¹. tRNA-lookalikes were found by using the Blastn algorithm in search of additional instances of the known tRNA genes (632 genes, refered as ‘tRNA-Reference’). Click the buttons below to download the tRNA-Lookalikes and tRNA-Reference.

.txt format 2963 Downloads

.xlsx format 2709 Downloads

File structure

The list of tRNA-Reference and tRNA-lookalike genomic loci are listed in tab-delimited format. The columns are as follows:

• Column 1: Description of the genomic locus (tRNA-Reference genes contain the label ‘KnowntRNAgene’, while lookalikes that are contained wholly in annotated transcripts are labeled as ‘LOOKALIKEWhollyInKnownTranscript’).
• Column 2: Percentage identity with the best-matched tRNA-Reference gene.
• Column 3: Number of mismatches as compared with the best-matched tRNA-Reference gene.
• Column 4: Presence or absence in RepeatMasker (RM).
• Column 5: Presence or Absence in Nuclear Mitochodrial DNA (NUMT) as defined in ².
• Column 6: Chromosome.
• Column 7: Strand.
• Column 8: “from” coordinate (inclusive).
• Column 9: “to” coordinate (inclusive).
• Column 10: Best-matched tRNA-Reference gene (if line describes lookalike) or tRNA-Reference gene at this genomic location.
• Column 11: Upstream (5’) sequence (50 nts long, always in 5’ -> 3’ orientation).
• Column 12: sequence of the tRNA-lookalike or tRNA-Reference gene (always in 5’ -> 3’ orientation).
• Column 13:  Downstream (3’) sequence (50nts long, always in 5’ -> 3’ orientation).

Notes

1. Protein-coding unspliced pre-mRNAs, non-protein-coding unspliced transcripts and lincRNAs from ENSEMBL 75 along with lncRNAs from GENCODE v.19 were used as ‘annotated transcripts’. For details see ¹.
2. In the case of known tRNA genes (tRNA-Reference) columns 2 and 3 contain values of ‘100.00’ and ‘0.mismatches’, respectively.

 

References

1. Telonis AG, Loher P, Kirino Y, Rigoutsos I (2014) Nuclear and mitochondrial tRNA-lookalikes in the human genome. Frontiers in Genetics doi: 10.3389/fgene.2014.00344
2. Ramos A, Barbena E, Mateiu L, Del Mar Gonzalez M, Mairal Q, Lima M, Montiel R, Aluja MP Santos C (2011) Nuclear insertions of mitochondrial origin: Database updating and usefulness in cancer studies. Mitochondrion 11, 946-953. doi: 10.1016/j.mito.2011.08.009

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We gratefully acknowledge support of this work by the William M. Keck Foundation.