Supplementary Table: Annotation Comparison between the GenBank, TIGR and Reannotation of the RM5 Region in japonica Genome and O. rufipogon Genome
GenBank annotation of the japonica genome / TIGR annotation of the japonica genome / Reannotation of the japonica in this paper / Annotation of theO. rufipogon
Gene ID / OSJNBa0090K04.10 / Os01g42190 / OsJap01 / Oruf01
cDNA Size (bp) / 591 / 594 / >420
(incomplete) / >426
(incomplete)
No. of Exons / 5 / 5 / 4 / 4
Supported bya / AK065697 / AK065697 / AK065697 / AK065697
Putative Function / heat shock-like protein / DnaJ-like protein / heat shock-like protein / DnaJ-like protein / DnaJ-like protein / DnaJ-like protein
Gene ID / OSJNBa0090K04.11 / Os01g42200
cDNA Size (bp) / 501 / 504
No. of Exons / 1 / 1
Supported by / AK105136 / AK105136
Putative Function / unknown protein / unknown protein
Gene ID / OSJNBa0090K04.12 / Os01g42210
cDNA Size (bp) / -- / 1772
No. of Exons / -- / 3
Supported by / -- / --
Putative Function / pseudogene, far-red impaired response protein / hypothetical protein
Gene ID / OSJNBa0090K04.13 / Os01g42220 / OsJap02 / Oruf02
cDNA Size (bp) / 1395 / 519 / 666 / 672
No. of Exons / 4 / 1 / 3 / 3
Supported by / -- / -- / AK062506 / AK062506
Putative Function / hypothetical protein / hypothetical protein / hypothetical protein / hypothetical protein
Gene ID / OSJNBa0090K04.14-2 / Os01g42234.2 / OsJap03 / Oruf03
cDNA Size (bp) / -- / 1999 / 1599 / 1599
No. of Exons / -- / 8 / 8 / 8
Supported by / AK105656 / AK105656 / AK105656 / AK105656
Putative Function / probably inactive due to including stop codon(s) in CDS / Putative Amino Acid permease / Putative amino acid or GABA permease / Putative amino acid or GABA permease
Gene ID / OSJNBa0090K04.14-1 / Os01g42234.1 / OsJap03B / Oruf03B
cDNA Size (bp) / -- / 2005 / 1563 / 1563
No. of Exons / -- / 8 / 8 / 8
Supported by / AK071623 / AK071623 / AK071623 / AK071623
Putative Function / probably inactive due to no termination codon in CDS / Putative Amino Acid permease / Putative amino acid or GABA permease / Putative amino acid or GABA permease
Gene ID / OSJNBa0090K04.15 / Os01g42250 / OsJap04 / Oruf04
cDNA Size (bp) / 708 / 1272 / 633 / 633
No. of Exons / 6 / 6 / 5 / 5
Supported by / AK109289 / AK109289 / AK109289 / AK109289
Putative Function / unknown protein / unknown protein / unknown protein / unknown protein
Gene ID / OSJNBa0090K04.16-2
cDNA Size (bp) / --
No. of Exons / --
Supported by / AK105049
Putative Function / --
Gene ID / OSJNBa0090K04.16-1 / Os01g42260 / OsJap05 / Oruf05
cDNA Size (bp) / 2628 / 3185 / 2631 / 2634
No. of Exons / 18 / 18 / 18 / 18
Supported by / AK101152 / AK105049 / AK101152 / AK101152
Putative Function / putative LEUNIG / Putative Transcriptional co-repressor LEUNIG / Putative Transcriptional co-repressor LEUNIG / Putative Transcriptional co-repressor LEUNIG
Gene ID / OSJNBa0090K04.17 / Os01g42270 / OsJap06 / Oruf06
cDNA Size (bp) / 2322 / 2325 / 2325 / 2264
No. of Exons / 18 / 18 / 18 / 18
Supported by / -- / -- / AK101152 / AK101152
Putative Function / putative LEUNIG / Putative Transcriptional co-repressor LEUNIG / Putative Transcriptional co-repressor LEUNIG / Putative Transcriptional co-repressor LEUNIG
Gene ID / OSJNBa0090K04.18
cDNA Size (bp) / 459
No. of Exons / 3
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.19 / Os01g42280 / OsJap07 / Oruf07
cDNA Size (bp) / -- / 2554 / 1851 / 1851
No. of Exons / -- / 1 / 1 / 1
Supported by / -- / -- / AK062372 / AK062372
Putative Function / pseudogene, pentatricopeptide (PPR) repeat-containing protein / unknown protein; pentatricopeptide (PPR) repeat-containing protein / Putative selenium-binding protein-like / Putative selenium-binding protein-like
Gene ID / OSJNBa0090K04.20
cDNA Size (bp)
No. of Exons / 4
Supported by / --
Putative Function / hypothetical ORF
Gene ID / OSJNBa0090K04.21 / Os01g42294 / OsJap08 / Oruf08
cDNA Size (bp) / 2052 / 2055 / 855 / 855
No. of Exons / 2 / 2 / 4 / 4
Supported by / -- / -- / AK060360 / AK060360
Putative Function / receptor-like protein kinase 1-like / protein kinase / Putative receptor-like protein kinase / Putative receptor-like protein kinase
Gene ID / OSJNBa0090K04.21 / Os01g42294 / OsJap09 / Oruf09
cDNA Size (bp) / 1533 / 1479
No. of Exons / 1 / 1
Supported by / AK065199 / AK065199
Putative Function / Putative receptor-kinase isolog / Putative receptor-kinase isolog
Gene ID / OSJNBa0090K04.22
cDNA Size (bp) / --
No. of Exons / --
Supported by / --
Putative Function / hypothetical ORF
Gene ID / OSJNBa0090K04.23 / OsJap10 / Oruf10
cDNA Size (bp) / -- / 270 / 264
No. of Exons / -- / 2 / 2
Supported by / -- / AK110441 / AK110441
Putative Function / hypothetical ORF / Putative Nitrite transporter / Putative Nitrite transporter
Gene ID / OSJNBa0090K04.24
cDNA Size (bp) / 267
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.25
cDNA Size (bp) / 189
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.26 / Os01g42310
cDNA Size (bp) / 354 / 357
No. of Exons / -- / 3
Supported by / -- / --
Putative Function / hypothetical protein / hypothetical protein
Gene ID / OSJNBa0090K04.27
cDNA Size (bp) / 435
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.28
cDNA Size (bp) / 198
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.29
cDNA Size (bp) / 702
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.30
cDNA Size (bp) / 414
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.31 / Os01g42320 / OsJap11 / Oruf11
cDNA Size (bp) / 1356 / 1479 / 1413 / 1425
No. of Exons / 2 / 3 / 3 / 2
Supported by / -- / -- / AK105989 / AK105989
Putative Function / nucleoid DNA-binding protein cnd41-like / Eukaryotic aspartyl protease family protein / Putative chloroplast nucleoid DNA-binding protein cnd41-like / Putative chloroplast nucleoid DNA-binding protein cnd41-like
Gene ID / OSJNBa0090K04.32
cDNA Size (bp) / --
No. of Exons / --
Supported by / --
Putative Function / hypothetical ORF
Gene ID / Part of OSJNBa0090K04.33 / Os01g42330
cDNA Size (bp) / 3783
No. of Exons / 6
Supported by / --
Putative Function / retrotransposon protein
Gene ID / OSJNBa0090K04.33 / OsJap12 / Oruf12
cDNA Size (bp) / 4122 / 3192 / 3150
No. of Exons / 4 / 3 / 3
Supported by / -- / AK068412 / AK068412
Putative Function / rust resistance protein Rp1-dp8-like / Putative rust-resistance protein Lr21
[pseudogene] / Putative rust-resistance protein Lr21
[pseudogene]
Gene ID / Os01g42340
cDNA Size (bp) / 2109
No. of Exons / 1
Supported by / --
Putative Function / hypothetical protein
Gene ID / OSJNBa0090K04.34 / P0410E03.1
cDNA Size (bp) / --
No. of Exons / --
Supported by / --
Putative Function / hypothetical ORF
Gene ID / P0410E03.2
cDNA Size (bp) / 2808
No. of Exons / --
Supported by / --
Putative Function / hypothetical protein
Gene ID / P0410E03.3
cDNA Size (bp) / --
No. of Exons / --
Supported by / --
Putative Function / hypothetical ORF
Gene ID / P0410E03.4
cDNA Size (bp) / --
No. of Exons / --
Supported by / AK103201
Putative Function / non-coding transcript probably inactive due to including stop codon(s) in CDS
Gene ID / P0410E03.5 / Os01g42350 / OsJap13 / Oruf13
cDNA Size (bp) / -- / 4440 / 4440 / 4440
No. of Exons / -- / 21 / 21 / 21
Supported by / -- / AK103201 / AK100135 / AK100135
Putative Function / pseudogene, ABC1 protein / PDR5-like ABC transporter / PDR5-like ABC transporter / PDR5-like ABC transporter
Gene ID / P0410E03.6 / Os01g42360
cDNA Size (bp) / 363 / 297
No. of Exons / 1 / 1
Supported by / -- / --
Putative Function / hypothetical protein / hypothetical protein
Gene ID / P0410E03.7 / Os01g42370 / OsJap14 / Oruf14
cDNA Size (bp) / -- / 4335 / 4335 / 4335
No. of Exons / -- / 22 / 22 / 22
Supported by / -- / -- / AK100135 / AK100135
Putative Function / pseudogene, PDR5-like ABC transporter / PDR5-like ABC transporter / Putative PDR12 ABC transporter / Putative PDR12 ABC transporter
Total Genes / 6 putative,
19 unknown/ hypothetical genes & 6 pseudogenes / 8 putative and
8 unknown/ hypothetical genes / 12 putative and
2 unknown/ hypothetical genes / 12 putative and
2 unknown/ hypothetical genes
aKOME, Knowledge-based Oryza Molecular Biological Encyclopedia (Kikuchi et al. 2003)