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.

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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.

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