Rice P450s status of annotation

 

In this table I = indica strain, J = japonica strain

 

Name     seq. is full  seq. is partial   no sequence    number of introns/phase checked

 

CYP51G1        I           J                                                          1/0

CYP51G3        I/J                                                                    1/1

CYP51G4P                 I/J        pseudogene with deletions, frameshifts

CYP51H1        J          I                                                           1/0

CYP51H2P                 I/J        Japonica seq is more complete no introns

CYP51H3        I/J                                                                    1/0    1 frameshift in both I/J

CYP51H4        J          I                                                           1/0

CYP51H5        J          I                                                           1/1

CYP51H6        J          I                                                           2/0

CYP51H7        J          I                                                           1/0

CYP51H8        J          I                                                           1/0

CYP51H9        J          I                                                           2/2

CYP71C12      I/J                                                                    no introns

CYP71C13P    J          I           numerous stop codons            no introns

CYP71C14      I/J                                                                    no introns

CYP71C15      J          I                                                           1/1

CYP71C16      J          I                                                           1/1

CYP71C17      I/J                                                                    1/1

CYP71C18      J                                  I                                   2/2

CYP71C19      J          I                                                           2/2

CYP71C20      I/J                                                                    no introns

CYP71C21      I                                   J                                  3/0

CYP71C22P                I/J        pseudogene fragment

CYP71C23P                I/J        pseudogene fragment

CYP71E4        I/J                                                                    2/2

CYP71E5        I/J                                                                    2/2

CYP71E6        J          I                                                           2/0

CYP71K1        J          I                                                           1/0

CYP71K2P                 I                       J          pseudogene fragment

CYP71K3        J          I                                                           1/1

CYP71K4        J          I                                                           1/1

CYP71K5        J          I                                                           1/1

CYP71K6        J          I           possible pseudogene               1/1 bad boundary

CYP71K7P     I/J                    pseudogene                             1/1 bad boundary

CYP71K8        J          I                                                           1/1

CYP71K9        I/J                                                                    1/1

CYP71K10      I/J                                                                    1/1

CYP71K11      I/J                                                                    2/2

CYP71K12      I/J                                                                    2/2

CYP71K13P               J                      I   pseudogene fragment

CYP71P1        I/J                                                                    1/1

CYP71P2P                  I/J        pseudogene fragment

CYP71Q1        J          I                                                           2/2

CYP71Q2        J          I                                                           2/2

CYP71Q3P                 I/J        pseudogene fragment

CYP71Q4P                 I/J        pseudogene fragment

CYP71R1        I/J                                                                    1/1

CYP71R2P      I/J                    pseudogene                             2/1??

CYP71R3                    I                       J          no whole seq known

CYP71S1        J          I                                                           1/1

CYP71S2        J          I                                                           1/1

CYP71T1        I/J                                                                    1/1

CYP71T2        J          I                                                           1/1

CYP71T3        J          I                                                           1/1

CYP71T4        I/J                                                                    1/1

CYP71T5        I                                   J                                  1/1

CYP71T6                    I                       J          no whole seq known

CYP71T7        I                                   J                                  1/0

CYP71T8X      J          I           55% to 71Z12X  = 71Z11X = 71AK1

CYP71T9X      J          I                                   = 71AK1 frag

CYP71T10P                I                       J          probable pseudogene

CYP71U1P                 I                       J          probable pseudogene

CYP71U2        I                                   J                                  1/1

CYP71U3        J                                  I                                   1/0

CYP71V1        J          I                                                           1/1

CYP71V2        I                                   J                                  1/0

CYP71V3        J          I                                                           1/0

CYP71V4        I                                   J                                  1/1

CYP71V5        I                                   J                                  1/1

CYP71V6P                  I                       J          pseudogene fragment

CYP71W1       I                                   J                                  1/1

CYP71W2P                I/J        pseudogene fragment

CYP71W3       I/J                                                                    1/1

CYP71W4       I/J                                                                    1/1

CYP71W5P                J                      I           pseudogene fragment

CYP71W6P                J                      I           pseudogene fragment

CYP71X1P                  I/J                               PSEUDOGENE

CYP71X2        J          I                                                           1/1

CYP71X3        J          I                                                           2/1??

CYP71X4        J                                  I                                   1/1

CYP71X5        J          I                                                           1/1

CYP71X6        I/J                                                                    1/1

CYP71X7        I/J                                                                    1/1

CYP71X8        I/J                                                                    1/1

CYP71X9P                  I/J        pseudogene fragment

CYP71X10      J          I                                                           1/1

CYP71X11      I/J                                                                    1/1

CYP71X12      I/J                                                                    1/1

CYP71X13P    J          I           pseudogene

CYP71X14      I/J                                                                    1/1

CYP71X15      I                                   J                                  1/1

CYP71X16                  I                       J          no whole seq known

CYP71X17P                I                       J          probable pseudogene

CYP71Y1        J          I                                                           2/1

CYP71Y2P                  I/J        pseudogene fragment

CYP71Y3        J          I                                                           1/1

CYP71Y4        J          I                                                           1/1

CYP71Y5        J          I                                                           1/1

CYP71Y6        J          I                                                           1/1

CYP71Y7        J          I                                                           1/1

CYP71Y8        I                                   J                                  1/1

CYP71Y9P                  I                       J          probable pseudogene

CYP71Z1        J          I                                                           1/1

CYP71Z2        J          I                                                           1/1

CYP71Z3        I/J                                                                    1/1

CYP71Z4        I/J                                                                    1/1

CYP71Z5        I/J                                                                    1/1

CYP71Z6        I                                   J                                  1/1

CYP71Z7        I/J                                                                    1/1

CYP71Z8        J          I                                                           1/1

CYP71Z9/Z10             I                       J          no whole seq known two joined

CYP71Z11X    J          I           = 71T8X rename CYP71AK1

CYP71Z12X    J                                  I           NEW SUBFAM CYP71AK2

CYP71AA1P               I/J        pseudogene fragment

CYP71AA2     J          I                                                           1/1

CYP71AA3     I/J                                                                    1/1

CYP71AA4P               I/J        pseudogene fragment

CYP71AA5                 I                       J          no whole seq known

CYP71AB1     I/J                                                                    1/1

CYP71AB2     J          I                                                           1/1

CYP71AB3     I/J                                                                    1/1

CYP71AC1     I/J                                                                    1/1

CYP71AC2     I/J                                                                    1/1

CYP71AC3P               I                       J          pseudogene fragment

CYP71AC4X               I                       J          = 71AC3P END

CYP71AC5P               J                      I           pseudogene fragment

CYP71AC6P               J                      I           pseudogene fragment

CYP71AC7P               I                       J          pseudogene fragment

CYP71AD1     J          I                                                           no introns

CYP71AE1      I                                   J                                  2/2

CYP71AE2      J          I                                                           2/1

CYP71AF1      J          I                                                           1/1

CYP71AG1                 I                       J          no whole seq known

CYP71AK1     J          I           old 71T8 old 71Z11

CYP71AK2     J                                  I = old 71Z12

 

Summary of CYP51 and CYP71 families

 

130 sequences identified  (29% of total gene count)

approximately 30 are pseudogenes (23%) 

(in whole collection about 99 pseudogenes/454 total sequences = 22% pseudogenes

 

not counting the pseudogenes, 6/100 sequences are partial and might be

from intact genes, but some of these may also be pseudogenes.

 

Most non-pseudogene sequences (94/100) are complete in indica or japonica

and some are complete in both.

 

name    seq. is complete   seq incomplete     no seq.   number of introns/checked boundaries

 

CYP72A17      J                      I                                                           4/4

CYP72A18      J                      I                                                           4/4

CYP72A19      J                      I                                                           3/3

CYP72A20      J                      I                                                           4/4

CYP72A21      J                      I                                                           3/3

CYP72A22      J                      I                                                           3/3

CYP72A23      J                      I                                                           3/3

CYP72A24      J                      I                                                           4/4

CYP72A25      J                      I                                                           4/4

CYP72A31P                            I/J        pseudogene

CYP72A32      J                      I                                                           3/3

CYP72A33      J                      I                                                           3/3

CYP72A34      J                      I                                                           4/2

CYP72A35      J                      I                                                           4/0

CYP72A36P                            I/J        pseudogene

CYP72A37P                            I/J        pseudogene

CYP72A38P                            J                      I           pseudogene

CYP73A35P    I/J                                pseudogene

CYP73A38      I                       J                                                          2/2

CYP73A39      I/J                                                                                1/1

CYP73A40      I/J                                                                                1/1

CYP74A4        J                      I                                                           no introns

CYP74A5        J                      I                                                           no introns

CYP74E1        J                      I                                                           1?/0

CYP74E2        J                      I                                                           1?/0

CYP74E3P                              I                       J          pseudogene

CYP74F1        J                      I                                                           no introns

CYP75A11      J                      I                                                           2/0

CYP75B3        I/J                                                                                1/0

CYP75B4        J                      I                                                           1/1

CYP76H4        I/J                                                                                1/1

CYP76H5        J                      I                                                           1/1

CYP76H6        J                      I                                                           1/0

CYP76H7                                I/J                    no whole seq. known

CYP76H8        J                      I                                                           1/0

CYP76H9        J                      I                                                           1/1

CYP76H10      J                   &nbs