AetLTR: LTR retrotransposons in _Aegilops tauschii_
In TE: Insertion/Deletion Dynamics for Transposable Elements
Description
This data file contains the LTR retrotransposons in Ae. tauschii.
Format
A data frame with 18024 rows and 12 columns. Each row corresponds to a unique LTR retrotransposon, and each column corresponds to a feature of the LTR-RT. The columns are:
- SeqID
LTR retrotransposon sequence ID
- UngapedLen
Length of each LTR
- Mismatch
Number of mismatches
- Distance
Divergence, as defined by (# of mismatches) / (LTR length)
- Chr
Chromosome number
- Start
Start location in bp
- Stop
Ending location in bp
- GroupID
LTR retrotransposon Family ID
- sup
Super family membership
- recRt5
Recombination rate
- nearOld
Whether the LTR-RT is near a gene that is colinear with wild emmer (TRUE) or not (FALSE)
- cCodon
Whether the LTR-RT is near the start codon (1) or not (-1)
- logDist
Log distance to the nearest gene in bp
- distToGene
Distance to the nearest gene in bp
References
Luo, Ming-Cheng, et al. (2017) "Genome sequence of the progenitor of the wheat D genome Aegilops tauschii." Nature 551.7681.
Dvorak, J., L. Wang, T. Zhu, C. M. Jorgensen, K. R. Deal et al., (2018) "Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size". The Plant Journal 95: 487-503.
Dai, X., Wang, H., Dvorak, J., Bennetzen, J., Mueller, H.-G. (2018). "Birth and Death of LTR Retrotransposons in Aegilops tauschii". Genetics
TE documentation built on May 1, 2019, 10:13 p.m.
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Description
This data file contains the LTR retrotransposons in Ae. tauschii.
Format
A data frame with 18024 rows and 12 columns. Each row corresponds to a unique LTR retrotransposon, and each column corresponds to a feature of the LTR-RT. The columns are:
- SeqID
LTR retrotransposon sequence ID
- UngapedLen
Length of each LTR
- Mismatch
Number of mismatches
- Distance
Divergence, as defined by (# of mismatches) / (LTR length)
- Chr
Chromosome number
- Start
Start location in bp
- Stop
Ending location in bp
- GroupID
LTR retrotransposon Family ID
- sup
Super family membership
- recRt5
Recombination rate
- nearOld
Whether the LTR-RT is near a gene that is colinear with wild emmer (TRUE) or not (FALSE)
- cCodon
Whether the LTR-RT is near the start codon (1) or not (-1)
- logDist
Log distance to the nearest gene in bp
- distToGene
Distance to the nearest gene in bp
References
Luo, Ming-Cheng, et al. (2017) "Genome sequence of the progenitor of the wheat D genome Aegilops tauschii." Nature 551.7681.
Dvorak, J., L. Wang, T. Zhu, C. M. Jorgensen, K. R. Deal et al., (2018) "Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size". The Plant Journal 95: 487-503.
Dai, X., Wang, H., Dvorak, J., Bennetzen, J., Mueller, H.-G. (2018). "Birth and Death of LTR Retrotransposons in Aegilops tauschii". Genetics
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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