Repbase Reports |
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| 2009, Volume 9, Issue 3 |
| March 31, 2009 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 726 |
AsDRF1 |
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A non-autonomous DNA transposon inserted in the first and third intron of the AsDRF1 gene. |
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Submitted: 31-Mar-2009 |
Accepted: 31-Mar-2009 |
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Key Words: DNA transposon; Transposable Element; Nonautonomous; AsDRF1 |
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Source: Aegilops speltoides |
Organism: Aegilops speltoides |
Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Aegilops |
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| [1] |
Authors: Karthikeyan,T., Latini.A,., Galeffi.P,. and Porceddu.E.,. |
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Title: A non-autonomous DNA transposon is inserted in the first and third intron of the AsDRF1 gene. |
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Journal: Repbase Reports 9(3), 726-726 (2009) |
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Abstract: An AsDRF1 non-autonomous DNA transposon is inserted in the first and third intron of the AsDRF1 gene. Terminal inverted repeats (TIR) approximately 32bp long were observed with 3 mismatches and a single deletion. Target site duplications (TSD) approximately 4bp long were observed with a single mismatch. The ~32bp TIR are 90% identical to each other. Apart from the ~32bp TIR, we also observed the presence of 18bp (88% identical each other) TIR with 2 mismatches. 2bp-long TSDs were observed for this 18bp TIR. The 18bp TIR is flanked by the ~32bp TIR. The 18bp TIR shares 100% homology with 18bp of the ~32bp TIR. Between the 18bp TIR and ~32bp TIR, a fragment approximately 93bp long was observed at the 5? end. At the 3? end, the 18bp TIR shares 88% homology with 18bp of the ~32bp TIR (exactly 31bp) TIR, since the 18bp TIR has 2bp mismatches with 18bp of the ~32bp TIR. Between the 18bp and ~32bp (exactly 31bp) TIRs, there is a fragment approximately 89bp long. These 18bp and ~32bp TIRs are nested terminal inverted repeats of this non-autonomous DNA transposon. It?s clearly evident that transposase carried the 18bp from some other part of the genome and recognized the ~32bp TIR, since it has the homology with the 18bp. Then, this 18bp either inserted at the region after 93bp from the ~32bp TIR or the 18bp enlarged up to ~32bp upon the selective insertion of this 18bp TIR+2bpTSD on 12bp TIR, which leads to the formation of ~32bp TIR with 4bp TSD. Other than the usual TSD formation, we also observed that 4bp (TGTT) is an internally duplicated region (Internal target site duplication, ITSD), flanked by 18bp TIR. The ITSD was possibly generated upon the sequence insertion in the 18bp inverted repeat, anchoring 4bp to become a transposon. The TSD is generally formed due to transposon insertion. On the other hand, during the sequence insertion in an 18bp inverted repeat anchoring, 4bp become a cohesive end, perhaps due to transposase (type II restriction enzyme?). Subsequent gap filling of overhanging 4bp leads to the formation of ITSDs. Generally, the palindromic sequence becomes a transposon and it is also possible, due to this ITSD formation, for the inverted repeat (anchoring few base pairs) to become a transposon as a palindromic sequence. This inverted repeat (or palindromic sequence) derived DNA transposon could move from one part to another part of the genome. After several generations, hybridizations and transpositions in various regions of the genome, the TIR or TSD or ITSD or any region of the DNA might be gradually altered due to spontaneous mutation. Conclusion: According to our analysis, the transposase possibly carried a 1191bp transposon from some other part of the genome and recognized the 32bp TIR site (which is possibly another transposon of 253bp with 4bp TSD) due to the homology of the 18bp, then inserted after ~90bp internally on TC(a target site), which leads to the formation of 2bp TSD. Finally, it became a nested non-autonomous DNA transposon upon the insertion of the 1191bp non-autonomous DNA transposopable element on the already existing 253bp non-autonomous DNA transposable element and the final length became 1448bp including newly formed TSD of 2bp at both terminals. Link to supplemental materials: ( http://www.girinst.org/server/publ/AsDRF1/ ).
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Derived: Positions 599 2046 Accession No FJ843102 EMBL/GenBank/DDBJ |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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