DNA Marker Primer Information

Primer Information

Primer. f/r sequence Taget Type of markers Reference
5P2 f GTAGCCGTTGTTAAACCAGG
TCGAATACTTTATGAAATG		 PS-ID (rpl116-rpl14 linker sequence) sub-species unique sequence Nakamura et al. 1997
This primer was used to sequence nucleotide from a stop codon of rpl16. SNPs at three sites were recorded as (4-16nt)-(31-36nt)-(61-64t) known as SNP-composition for PS-ID.
3P r ATCTGCAGCATTTAAAA
GGGTCTGAGGTTGAATCAT		 PS-ID (rpl116-rpl14 linker sequence) sub-species unique sequence  
This primer was used to sequence nucleotide from a stop codon of rpl16. SNPs at three sites were recorded as (4-16nt)-(31-36nt)-(61-64t) known as SNP-composition for PS-ID.
RCt１ f catccttttcaatccaaaatca Rct1, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt１ r tgcctgatgtagggaaaagc Rct1, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt2 f ctgggggggattatacctgt Rct2, Nipponbare=A11 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt2 r atatctctcatttccgacgca Rct2, Nipponbare=A11 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt3 f taggcataattcccaaccca Rct3, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt3 r cttatccatttggagcataggg Rct3, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt4 f acggaattggaacttctttgg Rct4, Nipponbare=T12 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt4 r aaaaggagccttggaatggt Rct4, Nipponbare=T12 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt5 f atttggaatttggacattttcg Rct5, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt5 r actgattcgtaggcgtggac Rct5, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt6 f gaattttagaactttgaattttttaccc Rct6, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt6 r aagcgtaccgaagactcgaa Rct6, Nipponbare=A10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt7 f gtgtcattctctaggcgaac Rct7, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt7 r aaatatgacagaaaagaaaaatagg Rct7, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt8 f atagtcaagaaagaggatctagaat Rct8, Nipponbare=T17 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt8 r accgcgattcaataagagta Rct8, Nipponbare=T17 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt9 f ataaggttattccccgcttacc Rct9, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt9 r aaattgggggaattcgtacc Rct9, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt10 f tcttcatttggaatctgggc Rct10, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
RCt10 r ctattgatgcaaacgctgtacc Rct10, Nipponbare=T10 Simple nucleoide repeats Ishii and McCouch 2000
Simple sequence was recorded by 6% sequencing gel
Reference Ishi, T. and S.R. McCouch Theor. Appl. Genet. (2000) 100:1257-1266 Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight Gramineas spesies

Nakamura, I., N. Kameya, Y. Kato, S. Yamanaka, H. Jomori and Y-I. Sato (1997)Breeding Science
47:385-388. A proposal for the short ID sequence which addressed the plastid subtype of higher plants.
/rice/oryzabase