Table of all Cytochrome P450 genes and pseudogenes in rice, Arabidopsis and Populus

D. Nelson April 4, 2005, revised Dec. 23, 2005

 

Rice is shown in red, Arabidopsis in black, Populus in blue

Subfamilies present in Arab. and rice are highlighted in yellow.

Families absent in rice or Arab. are highlighted in cyan.

The Populus pseudogenes (203 sequences) are highlighted cyan.  The pseudogenes

end in several conventions –de for detritus exon near the parent gene,

-se for solo exon not associated with a parent gene.  –un for pseudogenes

unassigned to a specific subfamily.  The capital P on the end of a gene indicates

a more complete pseudogene, not just one or two exons.

 

There are 310 unique named cottonwood P450s.  In addition to these there are

52 probable alleles with slightly different sequences to these 310.  The alleles

are marked as v1, v2, v3 etc. on the end of the names.  Some of these might be due to

sequence errors on duplicated contigs.  13 of the 310 sequences are incomplete,

with part of the sequence in a sequence gap or split into non-overlapping contigs.

[71D27, 71D44, 71D28, 76T4, 80C2, 81B10, 81S2, 82C8, 89A25, 98A26, 72D2, 714E2, 716C3]

 

13 sequences have a duplicate seq on another contig that is 100% identical

or has just one or two aa differences.  These 13 are

[71B40v1, 71B40v2, 71D22v1, 71D22v2, 71D29v1, 71D29v2, 71D38v1, 71D38v2,

71D40Pv1, 71D40Pv2, 74C6v1, 74C6v2, 74C7v1, 74C7v1, 85A1, 85A1P, 98A25v1,

98A25v2, 704A12, 704A12P, 705B4Pv1, 705B4Pv2, 711A7v1, 711A7v2, 715A2v1, 715A2v2]

many of these have one partner on a high numbered scaffold.  These scaffolds

are less reliable and may be haplotypic to the genome assembly i.e. alleles.

 

CYP72D2 has two entries because one entry has exon 1 and the other has exons 2-5.

We believe this is one gene, but cannot prove it yet.

 

The sum of 310 genes + 203 pseudogene sequences + 52 possible alleles +

One extra entry for 72D2 = 566 P450 Sequences found in the Populus genome data.

 

Sequences thought to derive from the recent genome duplication will be shaded

gray, but this is still in progress.

 

Arabidopsis                              Rice                        Populus

        synonyms           ATG number

 

CYP51G1 CYP51A2             At1g11680    CYP51G1                     51G1

CYP51G2 CYP51A1             At2g17330    CYP51G3                     51G5

                                         CYP51G4P

                                         CYP51H1 

                                         CYP51H2P

                                         CYP51H3 

                                         CYP51H4 

                                         CYP51H5 

                                         CYP51H6  

                                         CYP51H7 

                                         CYP51H8 

                                         CYP51H9 

CYP71A12                    At2g30750            

CYP71A13                    At2g30770            

CYP71A14                    At5g24960            

CYP71A15                    At5g24950            

CYP71A16                    At5g42590            

CYP71A17P                                        

CYP71A18                    At1g11610            

CYP71A19                    At4g13290            

CYP71A20                    At4g13310            

CYP71A21                    At3g48320            

CYP71A22                    At3g48310            

CYP71A23                    At3g48300            

CYP71A24                    At3g48290            

CYP71A25                    At3g48280            

CYP71A26                    At3g48270            

CYP71A27P                   At4g20240a           

CYP71A28                    At4g20240b           

CYP71B2                     At1g13080            

CYP71B3                     At3g26220            

CYP71B4                     At3g26280            

CYP71B5                     At3g53280                                71B38

CYP71B6                     At2g24180                                71B39P

CYP71B7                     At1g13110                                71B40v1

CYP71B8                     At5g35715                                71B40v2

CYP71B9                     At2g02580                                71B41

CYP71B10                    At5g57260                                71B41-de1b

CYP71B11                    At5g25120                                71B42P

CYP71B12                    At5g25130                                71B43P

CYP71B13                    At5g25140                                71B44P

CYP71B14                    At5g25180                                71B45P

CYP71B15 PAD3               At3g26830            

CYP71B16                    At3g26150            

CYP71B17                    At3g26160            

CYP71B18                                         

CYP71B19                    At3g26170            

CYP71B20                    At3g26180            

CYP71B21                    At3g26190            

CYP71B22                    At3g26200            

CYP71B23                    At3g26210            

CYP71B24                    At3g26230            

CYP71B25                    At3g26270            

CYP71B26                    At3g26290            

CYP71B27                    At1g13070            

CYP71B28                    At1g13090            

CYP71B29                    At1g13100            

CYP71B30P                   At3g53290            

CYP71B31                    At3g53300            

CYP71B32                    At3g53305            

CYP71B33                                         

CYP71B34                    At3g26300            

CYP71B35                    At3g26310            

CYP71B36                    At3g26320            

CYP71B37                    At3g26330            

CYP71B38                    At3g44250            

                                         CYP71C12

                                         CYP71C13P

                                         CYP71C14

                                         CYP71C1 

                                         CYP71C16

                                         CYP71C17

                                         CYP71C18

                                         CYP71C19

                                         CYP71C20

                                         CYP71C21

                                         CYP71C22P

                                         CYP71C23P

                                                                     71D22

                                                                     71D22P

                                                                     71D23P

                                                                     71D24P

                                                                     71D25Pv1

                                                                     71D25Pv2

                                                                     71D26

                                                                     71D27

                                                                     71D28v1

                                                                     71D28v2

                                                                     71D29v1

                                                                     71D29v2

                                                                     71D29-se1[1]

                                                                     71D29-se2[1]

                                                                     71D29-se3[1]

                                                                     71D30P

                                                                     71D31P

                                                                     71D32P

                                                                     71D33P

                                                                     71D34

                                                                     71D35P

                                                                     71D36Pv1

                                                                     71D36Pv2

                                                                     71D36Pv3

                                                                     71D37P

                                                                     71D38v1

                                                                     71D38v2

                                                                     71D38v2-de2b

                                                                     71D38v2-de2c

                                                                     71D39

                                                                     71D40Pv1

                                                                     71D40Pv2

                                                                     71D41

                                                                     71D42

                                                                     71D43

                                                                     71D44

                                                                     71D45P

                                                                     71D46P

                                                                     71D53P

                                         CYP71E4 

                                         CYP71E5  

                                         CYP71E6 

                                         CYP71K2P

                                         CYP71K3 

                                         CYP71K4 

                                         CYP71K5 

                                         CYP71K6 

                                         CYP71K7P

                                         CYP71K8 

                                         CYP71K9 

                                         CYP71K10

                                         CYP71K11

                                         CYP71K12

                                         CYP71K13P

                                         CYP71P1 

                                         CYP71P2P

                                         CYP71Q1 

                                         CYP71Q2 

                                         CYP71Q3P

                                         CYP71Q4P

                                         CYP71R1 

                                         CYP71R2P

                                         CYP71R3 

                                         CYP71S1 

                                         CYP71S2 

                                         CYP71T1 

                                         CYP71T2 

                                         CYP71T3 

                                         CYP71T4 

                                         CYP71T5 

                                         CYP71T6 

                                         CYP71T7 

                                         CYP71T10P

                                         CYP71U1P

                                         CYP71U2 

                                         CYP71U3 

                                         CYP71V1 

                                         CYP71V2 

                                         CYP71V3 

                                         CYP71V4 

                                         CYP71V5 

                                         CYP71V6P

                                         CYP71W1 

                                         CYP71W2P

                                         CYP71W3 

                                         CYP71W4 

                                         CYP71W5P

                                         CYP71W6P

                                         CYP71X1P

                                         CYP71X2 

                                         CYP71X3 

                                         CYP71X4 

                                         CYP71X5 

                                         CYP71X6 

                                         CYP71X7 

                                         CYP71X8 

                                         CYP71X9P

                                         CYP71X10

                                         CYP71X11

                                         CYP71X12

                                         CYP71X13P

                                         CYP71X14

                                         CYP71X15

                                         CYP71X16

                                         CYP71X17P

                                         CYP71Y1 

                                         CYP71Y2P

                                         CYP71Y3 

                                         CYP71Y4