Rice Transposon
Flanking Sequence Tag Database
Browse the rice genome for FSTs by clicking here

or

Search for FSTs within specific regions of the Rice Genome as follows:-

1) Enter a Rice Gene ID (MSU/TIGR or RAP)



(example: LOC_Os04g53720 for MSU or Os04g0629300 for RAP)


or
Return to Sundaresan Rice Genomics Page

Online Seed Ordering
Click Here

Retrieve flanking sequences by entering
the line number in the field below without spaces.

2) Paste a nucleotide sequence below to find matches to the Rice Genome


Transposable elements used in the insertion lines

These transposon insertion lines contain dSpm or Ds transposable elements. Each element carries the DsRed positive selection marker. The insertions are expected to be stable, because the transposase has been segregated away in the selection for the insertion lines.

RGT (Rice Gene Trap insertion line) Ds-gene trap element carrying a promoterless GUS reporter gene with the GPA1 intron and triple splice acceptor (SA) sequences upstream of ATG codon. This gene trap will reflect the expression pattern of the tagged endogenous rice gene if inserted in the right orientation, as previously demonstrated in Arabidopsis and Rice (Sundaresan et al., 1995, Kolesnik et al. 2003).
RDs (Rice Ds insertion line) Simple Ds element.
RdSpm (Rice dSpm insertion line) dSpm element.

The following transposon-specific nested primers were used to obtain transposon flanking sequence at the site of insertion. Verification of any sequenced insertion line is necessary, and can be performed using these primers.

Ds5’

Ds5'-1a : ACGGTCGGGAAACTAGCTCTAC

Ds5'-2a : TCCGTTCCGTTTTCGTTTTTTAC

Ds5'-3a : CGGTCGGTACGGGTTTTCC

Ds5'-4 : CTCGGGTTCGAAATCGATCGGGAT

Ds3’

Ds3'-1a : GGTTCCCGTCCGATTTCGACT

Ds3'-2a : CGATTACCGTATTTATCCCGTTC

Ds3'-3a : TCGTTTCCGTCCCGCAAGT

dSpm 5’

Spm5-1: 5’-GGT GTG GAA AAA CCC ACA CTC

Spm5-2: 5’-GCG TCG GTT TCA TCG GGA CC

Spm5-3: 5’-CTC TTT AAT TAA CTG ACA CTC C

dSpm 3’

Spm3-1: 5’-GTC GGT CCC CAC ACT TCT ATA CG

Spm3-2: 5’-GAG CGT CCA TTT TAG AGT GAC

Spm3-3: 5’-GTG TGG GGT TTT GGC CGA CAC

 

The starter lines for these insertion lines were created using Agrobacterium tumefaciens mediated transformation.

Please note that these lines are not T-DNA insertion lines. They are stable transposon insertion lines. The transposon
insertion has been segregated away from the T-DNA that was used in transformation.