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 I LARGE INSERTION 2/1

CYP76H11 J I 1/1

CYP76H12P I/J PSEUDOGENE

CYP76H13P J I PSEUDOGENE

CYP76H14P J I PSEUDOGENE

CYP76H15P I/J PSEUDOGENE

CYP76H16P J I PSEUDOGENE

CYP76K1 I/J 1/1

CYP76K2P I/J PSEUDOGENE

CYP76L1 I/J 1/1

CYP76M1 I J no introns

CYP76M2 J I no introns

CYP76M3P I J PSEUDOGENE?

CYP76M4P I/J PSEUDOGENE

CYP76M5 I J no introns

CYP76M6 J I no introns

CYP76M7 I/J no introns

CYP76M8 I/J no introns

CYP76M9 I/J no introns

CYP76M10 J I no introns

CYP76M11P I/J PSEUDOGENE

CYP76M12P I J PSEUDOGENE

CYP76M13 J I no introns

CYP76M14 J I no introns

CYP76N1 I/J 1/1

CYP76N2 I J 1/1

CYP76N3 J I 16KB INSERT 2/0

CYP76N4P I J PSEUDOGENE

CYP76P1 J I 1/0

CYP76P2 J I 1/0

CYP76P3 I/J 1/0

CYP76P4P I/J PSEUDOGENE

CYP76P5 J I 1/0

CYP76P6 J I 1/0

CYP76Q1 I 1/1

CYP76Q2 I J 1/1

CYP77A9 J I no introns

CYP77B2 I/J 1/1

CYP78A11 J I 1/1

CYP78B4 I J no whole seq. known

CYP78B5 I/J 1/0

CYP78B6 I J 1/0

CYP78C5 J I 1/1

CYP78C6 I J 1/1

CYP78C7 J I 1/1

CYP78D1 I J 1/1

CYP79A7 J I 1/0

CYP79A9 I J 1/1

CYP79A10 I J 1/0

CYP79A11 I J no whole seq known

CYP81A5 I/J 1/1

CYP81A6 I/J FUSION GENE? 1/0

CYP81A7 I/J ANNOTATED IN GB 1/1

CYP81A8 I/J ANNOTATED IN GB 1/1

CYP81L2 J I 3?/2

CYP81L3 I J 3/3

CYP81L4 I/J 3/3

CYP81L5 J I

CYP81L6X = 81L5 I/J

CYP81M1 J I 1/1

CYP81N1 I/J 1/1

CYP81N2 I/J ?/0

CYP81N3P I/J PSEUDOGENE

CYP81P1 I/J 1/1

Summary of CYP72 to CYP81 families

99 sequences, 19 are pseudogenes

not counting the pseudogenes, 3/80 sequences are partial and might be

from intact genes, but may also be pseudogenes.

96% of non-pseudogene sequences are complete in indica or japonica

summary for CYP51 to CYP81

229 sequences

49 pseudogenes (21%)

8 partial sequences from the non-pseudogene sequences

96% of non-pseudogene sequences are complete in indica or japonica

only 48 intron exon boundaries are not checked in this set.

Many of these are at locations of known introns in related genes

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

CYP84A5 J I 1/0

CYP84A6 J I 1/1

CYP84A7 I J 1/1

CYP84A8P I/J PSEUDOGENE

CYP85A1 J I 8/3

CYP86A9 J I no introns

CYP86A10 J I no introns

CYP86A11 J I no introns

CYP86A12P I/J PSEUDOGENE

CYP86A13P I/J PSEUDOGENE

CYP86A14P I J PSEUDOGENE

CYP86A15P I/J PSEUDOGENE

CYP86A16P I J PSEUDOGENE

CYP86A17P I/J PSEUDOGENE

CYP86B3 J I 1/1

CYP86E1 J I no introns

CYP87A4 J I 8/7

CYP87A5 I J MADE FROM PIECES 8/0

CYP87A6 J I 8/6

CYP87B1 I J 8/8

CYP87B2 J I 8/4

CYP87B3 I J 8/8

CYP87B4 J I 8/6

CYP87B5 I/J 8/8 2FS in J

CYP87C1P I J PSEUDOGENE 8/1

CYP87C2 I J 8/8

CYP87C3 J I 8/2

CYP87C4 J I 8/8

CYP87C5P I J PSEUDOGENE 8/2

CYP88A5 J I 5/0

CYP89B1 I/J no introns

CYP89B2 J I no introns

CYP89B3 I/J no introns

CYP89B4 I/J MIGHT BE TWO GENES no introns

CYP89B5 J I no introns

CYP89B6 J I no introns

CYP89B7P I/J PSEUDOGENE

CYP89B8P J I PSEUDOGENE no introns

CYP89B9 I/J no introns

CYP89B10 I/J no introns

CYP89B11 J I no introns

CYP899B12P I/J PSEUDOGENE

CYP89B13P I J PSEUDOGENE

CYP89B14P I/J PSEUDOGENE

CYP89B15P I/J PSEUDOGENE

CYP89C1 I/J no introns

CYP89C2 I J no introns

CYP89D1 I/J no introns

CYP89E1 I/J no introns

CYP89F1 J I ?/0

CYP89G1 I/J no introns

CYP90A3 J I 6?/1

CYP90A4 I J no whole seq. known

CYP90B2 J I 7/7

CYP90D2 J ANNOTATED IN GB 7/7

CYP90D3 J I 7/1

CYP90D4P I/J PSEUDOGENE

CYP92A7 J I 1/0

CYP92A8 J I 1/0

CYP92A9 I/J 1/0

CYP92A10P I/J PSEUDOGENE

CYP92A11 J I 1/0

CYP92A12 I/J no introns

CYP92A13 I J 1/0

CYP92A14 I/J 1/0

CYP92A15 J I 2/2

CYP92A16P I J PSEUDOGENE

CYP92C1 I J no introns

CYP92C2P I/J PSEUDOGENE

CYP92C3P I/J PSEUDOGENE

CYP92C4P I/J PSEUDOGENE

CYP93F1 J I 1/1

CYP93F2P I/J PSEUDOGENE

CYP93F3P I/J PSEUDOGENE

CYP93F4P I/J PSEUDOGENE

CYP93F5P I/J PSEUDOGENE

CYP93G1 I/J 1/1

CYP93G2 J I 1/1

CYP94B4 I/J no introns

CYP94B5 J I no introns

CYP94C2 J I no introns

CYP94C3 J I no introns

CYP94C4 I J no introns

CYP94D4 J I no introns

CYP94D5 I/J no introns

CYP94D6 J I no introns

CYP94D7 J I no introns

CYP94D8P J I PSEUDOGENE

CYP94D9 J I no introns

CYP94D10 J I no introns

CYP94D11 J I no introns

CYP94D12 J I no introns

CYP94D13 J I no introns

CYP94D14P I J PSEUDOGENE

CYP94D15 J I no introns

CYP94D16P I J PSEUDOGENE

CYP94D17P I J PSEUDOGENE

CYP94D18P I/J PSEUDOGENE

CYP94D19P I/J PSEUDOGENE

CYP94D20P J I PSEUDOGENE

CYP94D21P I/J PSEUDOGENE

CYP94E1 I/J no introns

CYP94E2 J I no introns

CYP94E3 I J no introns

CYP96B2 I J no introns

CYP96B3 I J no introns

CYP96B4 I J no introns

CYP96B5 I/J no introns

CYP96B6 I/J no introns

CYP96B7 J I no introns 2FS

CYP96B8 I J no introns

CYP96B9 I J no introns

CYP96B10 J I no introns 1FS

CYP96D1 J I 1/0

CYP96D2 I J no introns

CYP96E1 J I no introns

CYP97A4 J I 14/14

CYP97B4 I/J 14/14

CYP97C2 J I 7/7

CYP98A4 I/J 2/2

CYP98A15P I/J PSEUDOGENE

CYP98A16P J I PSEUDOGENE

CYP98A17 I J no whole seq. known

CYP98A18 I J no whole seq. known

CYP99A2 J I 1/1

CYP99A3 J I 1/0

CYP701A6 I/J 9/9

CYP701A7 I/J 9/9

CYP701A8 I/J 6/2

CYP701A9 J I 5/2

CYP703A3 J I 1/0

CYP704A3 J I 3/3

CYP704A4 J I 5?/0

CYP704A5 J I 4?/0

CYP704A6 J I 4?/0

CYP704A7 J I 4?/0

CYP704A8 I J no whole seq. known

CYP704B2 J I 3?/0

CYP706C1 J I 1/1

CYP706C2 J I 1/1

CYP706C3 I J 1/1

CYP706C4 I J 1/1

CYP707A5 J I 4/4

CYP707A6 J I 8/8

CYP709C4 J I 4/4

CYP709C5 J I 1/1

CYP709C6 I/J 1/1

CYP709C7P I/J PSEUDOGENE

CYP709C8 I/J 1/1

CYP709C9 I/J 2/2

CYP709C10 J I 2?/0

CYP709C11 J I 2?/0

CYP709C12P I/J PSEUDOGENE

CYP709C13P I/J PSEUDOGENE

CYP709D1 J I 4/4

CYP709E1 J I 4/0

CYP709E2 J I 4/2

CYP709E3 J I 4/4

CYP710A5 J I no introns

CYP710A6 J I no introns

CYP710A7 J I no introns

CYP710A8 J I no introns

CYP710A9P I J PSEUDOGENE

CYP710A10P I/J PSEUDOGENE

CYP711A2 J GB ANNOTATION I 3/0

CYP711A3 J GB ANNOTATION I 4/0

CYP711A4 J I 4/4

CYP711A5 I/J 3/0

CYP711A6 I/J no whole seq. known

CYP714B1 I/J 3/3

CYP714B2P I/J PSEUDOGENE

CYP714C1 I J 3/0

CYP714C2 I/J 4/4

CYP714C3 I J 2/0

CYP714D1 J I 1/1

CYP714D2 I J no whole seq. known

CYP715B1 I/J no introns

CYP715B2P I/J PSEUDOGENE

CYP715B3P I/J PSEUDOGENE

CYP715B4P I/J PSEUDOGENE

CYP721B1 J I 3/3

CYP721B2 J I 3/3

CYP722B1 J I 4/0

CYP723A2 J I no introns

CYP723A3 J I no introns

CYP723A4P I/J PSEUDOGENE

CYP724B1 J I 8/8

CYP727A1 I/J 6/6

CYP728A1 I J no introns

CYP728A2P I/J PSEUDOGENE

CYP728B1 I/J 1/1

CYP728B2 I/J 1/0

CYP728B3 I/J 1/0

CYP728C1 J I 3/3

CYP728C2P J I PSEUDOGENE

CYP728C3 J I 3/3

CYP728C4 J I 3/3

CYP728C5 J I 3/3

CYP728C6P J I PSEUDOGENE

CYP728C7 J I 3/3

CYP728C8P J I PSEUDOGENE

CYP728C9 J I 3/0

CYP728C10 I/J 3/1

CYP729A1 I J 7/7

CYP729A2 I/J 7/7

CYP730A1 I J no whole seq. known

CYP730A2 I J no whole seq. known

CYP730A3 I J no whole seq. known

CYP730A4 I J no whole seq. known

CYP730A5 I J no whole seq. known

CYP730A6 I J no whole seq. known

CYP730B1 I J no whole seq. known

CYP730B2 I J no whole seq. known

CYP730C1 I J no whole seq. known

CYP730? I J no whole seq. known #454

CYP730?? I J no whole seq. known #458

CYP731A1 I J no whole seq. known

CYP732A1 I J no whole seq. known

CYP733A1 J I 8/8

CYP734A2 I/J 4/1

CYP734A3P I J PSEUDOGENE

CYP734A4 J I 4/4

CYP734A5 J I 2/1

CYP734A6 J I 3/3

CYP735A3 I/J 3/3

CYP735A4 J I 4/4

226 SEQUENCES

CYP730A3, 730A4, 730A5, 730A6, CYP730? and CYP730?? are C-terminals

CYP730B1, 730B2, 730C1 and 732A1 are unmatched N-terminals

These are probably different parts of 6 genes, so the gene count may drop by 4.

There may be 222 DIFFERENT SEQUENCES

50 PSEUDOGENES

176 NON-PSEUDOGENES

19 INCOMPLETE, CHECKED FOR MORE SEQ., none found

157 COMPLETE IN INDICA OR JAPONICA

summary for CYP51 to CYP81

229 sequences

49 pseudogenes (21%)

180 non-pseudogenes

8 partial sequences from the non-pseudogene sequences

172 (96%) of non-pseudogene sequences are complete in indica or japonica

summary for all rice P450s

455 unique sequences

99 are probable pseudogenes (22%)

356 are probable real genes

28 of these are partial, checked for more seq., found none

4 of the 28 partials are probably parts of other incomplete seqs.

this would reduce the gene count by 4 to 451 genes + pseudogenes

25/28 partials are only known in indica

2/28 are incomplete in both indica and japonica

328 are full length

Note concerning Indica sequences without japonica orthologs.

IRGSP Interim Meeting Highlights

November 22, 2003

Shanghai Institute for Biological Research

Shanghai, PRC

1277 JAPONICA clones remain to be finished by a deadline of Dec. 2004

as of November 16, 2003.

There are 56 physical gaps in the japonica genome covering 24.5 Mb

About 30% of the total length of remaining gaps are in centromeres (7.4MB).

there are 80 unanchored contigs on the AGI map covering about 12 Mb.

http://demeter.bio.bnl.gov/Shanghai_summary.html

The CYP730 sequences are probably in a cluster that exists in one of these gaps