Skip to main content

Table 4 Retrotransposon specific primers used in RT-PCR reactions.

From: Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

RT-PCR primers (Copia and Gypsy)

G13F

5'-TCAGACGGATGGGCAGTCTGAGCGA-3'

G13R

5'-ACTCTGGGCCACGACGGGAGTTCCA-3'

G22F

5'-ACGCGTTTGAACTTCAGTACGGCT-3'

G22R

5'-TCAGGACCTCTACGAGCATCC-3'

G30F

5'-GGTCTATCACCGGGTCTCAAC-3'

G30R

5'-TACCCGGAAATAATCGAAGTCGTG-3'

C211F

5'-GCTGGATGTCAGTTCTTAGG-3'

C211R

5'-GATTTCGATGTGTTTGGTCTT-3'

LTR isolation primers (Copia, Gypsy, and universal)

Copia ChWP3

5'-CGAGATGAGTGCGATGGGTGAAAT-3'

Gypsy ChWP4

5'-GCAGAGGTGGGAGATAGTCAGAT-3'

Anch. p

5'-ACCATCGTCCTCAGGTTAGTCAGG-3'

PBSmet

5'-TAGGTCGGAACAGGCTCTGATACCA-3'

P1FCo

5'-CTGGTGTCTGTAACTTGTCTGTATTCG-3'

P2FCo

5'-AAAGATATGCTTCGATTGATAGACCTC3'

P1FGy

5'-GTGAGTACGTACCAAATTTCGGGAC-3'

P2FGy

5'-TTTCAACTTGGGGATAATGTGACAAC -3'

IRAP primers (Copia)

FA C-LTR i-r

5'-AGAGCATTCTGTCCGAAACAC-3'

FC C-LTR-h

5'-TAGCTTGGATTCCGCACTCG-3'

FF C-LTR

5'-GGTTTAGGTTCGTAATCCTCCGCG-3'

C-LTR r-rt1

5'-CGATAGATGGTCCGAAGGATC-3'

C-LTR 1

5'-AGACACCAGTGGCACCAACA-3'

C-LTR 2

5'-ACAGACACCAGTGGCACCAAC-3'

IRAP primers (Gypsy)

1F G-LTR BO37

5'-GGACAATATCATGGTGCGGTTAC-3'

1F G-LTR DO48

5'-ACCCTTCTTGACGAGACCAGT-3'

G-LTR 1

5'-CTGGTTTTCCTGGGGTGTCA-3'

G-LTR 2

5'-GGGTTGTCACATTATCCCCAAG-3'

Polymorphic band analysis primers (Copia)

FF C-LTR

5'-GGTTTAGGTTCGTAATCCTCCGCG-3'

C-LTR 2

5'-ACAGACACCAGTGGCACCAAC-3'

EMB 1F

5'-TCTTGACATGGGTTGTGGGCT-3'

EMB 1R

5'-TCACATGAACACGGCTCACACA-3'

EMB 2F

5'-AGTCTAATGGGTCAGCATGG-3'

EMB 2R

5'-TCCCTGGTATGAGCCGAAGCTCT-3'