Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice.

Basic Info

Gene ID		OGI # \| Score			Accession \| Assembly \| Annotation			Location		Links
OsNip_03g0730400		OGI:03083480 \| 16/16			Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)			Chr03:29858907-29864432		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		SCP19, OsSCP19
DNA seq		TGATTATAAGCTTGAGCTTTACTTAGTTCCACAAAAAAAAAAACTGTTGACAAAAAAAACTCAGATCTTCAAGCTGCCAGAGCACTGAAAAAGGAAGCAAAGCAATGGTCTTGGAGCTTCTCACAATGGCTGCTCACCGCGTGGGGCGATGCATGCTCCTGCAACCACCGCGCCTCGCCACCTGCGTCCTCTTCCTCCTGCTACCGCTGCTGCTGCCGTGCTCGGCGTCGTCGTCGGTGATCACCCACCTCCCGGGCTTCCACGGCCGCTTGCCGTTCCACCTTGAGACCGGGTAAGGGGCTCCCTGTATGTTTTCTTTTCTCCAGCTGTTACATATGACTTTTAATCGAAGGGAAATTGGAAACTCAAACGCAAAAGGGAATCGAATCCCAGGGGAATTAGGAGTAGAGCAGACGACTCGTTTTGCTTGATTTGGTTGGTTTCTGACTTTCTGCAGAGAGAATGGTATGGGATGCCACTACGTATTTACACTATTCTCTGTTGAAAAATAAATTTATTTTGTCAGTGAATCTGGGACAGTGGGACTGAGGGTGTACATGGCTTAGGCTGTGTTTGGAACTCCAAGTTCCCAACCCCTCTCCCTCGTTTTCCGCGCGCACGCTTTTCAAACTGCTAAACGGTGTATTTTTTTTAAAAAGTTTCTATACAAAAGTTGCTTAAAAAATTCAAATTAATCCATTTTTTAAAAATAAATTAGCCGATTCTTAATTAATCACGCGCTAATGGACCGCTCCGTTTTCCGTGCGGGGAGATTGGGTTCCCATCCCTGCTATCCAAACACAGCCTTAGGGAGACGCTGATCCGCGGCTGCAGGCGCGTGGTCAGTTTCCACCCTTTCGTCCTCCCCCATATACTACTGTATGTACTCTCTCCGTCCAAAATATAGCAACCTAGAACCGAACGGGATGTATCCTAGTACTACGAATCTAGACATGTCCCTGTTCAGATTCGTAGTACTAAGATACGTCCCATCCGGTTTTAGGTTGCTATATTCTGGAACGGAGGGAGTATGTATATATAACCATATACGCATATACTTCCTCTGTTTCACAATGTAAGTTATTCTAGTATTTTTCACATTCATATTGATATATGTCTAGATTTATTAACATCAATATAAAAGTGAAAAATGCTAAAAATGCTAGAATGACTTACATTGTGAAACGGAGAAAATACTTAGAATTTATACATAAACTATATAGGTATAGAGTTTATAGGTATACATGTAAAGTTATAAAGTTTGCATGTATAGGGTAGAAAAAATATATATTTGGTGGGTCCGAAACTGATAGCCGGTGCCACCCTGCTAACGACTGATTGCTAATTAGCGATTCGAAATGGTTTGGATTAAGTAATTACCTTATTATAGTGTATAGCAATTCTAATATTTTAAGTTATTTCTCGGTTCCTAATATTAAAAAAACGTATTTACCCGTTACAATACACGGATATTTTTTCTAGCTGGACCTTAATTGAGAAATAACCTTGCAGGTATGTTGGTGTGGACGAGGAGACGGGCACTGAGCTCTTCTACTACTTCGTTGAATCGGAGAGGAGCCCAAGTACAGGCCCTGTGATCCTCTGGTTGACAGGCGGGCCTGGCTGCTCCGGATTCAGCGGTGTCGTCTTTGAAGTAGGTTAGTAGTAGTGATTGGGATTTGATGATGAGAAAAAGATTTGTAGAACTGACAGAGACTATGCTTTCATTGCTCTAAGGTTAATACTATTCTCATGTTGGCTCAATCGAATATAAATTATGCATGATTTTTTTGAGTTAATAAATTATGCATGATTATACATATTTTTGAGTAAATTGCATCATCGGTGAACAAACTTGTCATGTGGGTGCAATCTAGTGCACGAATTTGTAAAATGCTTGTTTTGGTACATGAATTTGTCTGGTGTGTGTGTGGGGAAAAACCAAAAATACGCTACGTAGCTAATCTTGTTGATTTAGAGGTTGATTAGCATACTAGGTAAACACACACACACATGAGAAGATTGTTGTTAGATATACACCTCTTCATAAAAAGATAGAATATGATATAGTGATCGTAAAAAGATATGAAAAACCAAACAATGATCGATATAAGGGTTAGAAATATATGAAATTCATCATTACCATAATAAAGGATAAAATAGAAACCAAAATTATAAATATAATATGTCTTATGCATACTCATTACACATATACACGTTACGTCCTGATAAACATCAACTTCGTAAAATTAACATTGATAAGCCATTTTAGTCATGGTTTGCACGAACTGGAAACGAGCACTTTACAGGTTGATATACTAAATTACACCCACCTAACACATATTCGTGCATGATTATATGGTGGCCAAGATTGTACAGTTTGCCATGGTTTTGGACTACTGGGGAGCAATTGGGTCTGCTCCTACGCTCTGTGCTCTCTACACTCACACATATTTTACATTGCACGTGTTAACCTTCTGATATCCATAGGTGACGATTATGTACAGGACCTATGAAATACGTGTTGGAGCCTTATAATGGTAGTTTGCCACGATTGGTTTATAATCAGTATTCATGGACACAGGTGATATGCTCCTCTAAAACACACAGGATATTTCTCTCTACCTCATTTTACTTATTTGTGGTTCTGTTACTATGATCAGATGGCAAGCATCCTCTTCTTGGACACTCCTGTTGGTTCTGGTTTCTCATACGCTCATGATCCTAAAGGTTATAATGTCGGGGACATATCATCGTCTTTGCAAGTCGTAACATTTCTGAAGAAGGTGACCTGAAAGCACATCTGGTTTTCTACTACAGTAAAAATGGAAGAACAACTTCTATATTTATTACTTACCATCTTGTACGTACTAGTGTAGTGGTTCAATGATCACCCACGCTATCTCTCAAATCATTTCTATGTTGGAGGAAGCTCATACGCTGGAAAGGTGATTCCAATTATCATGAAGTTCATTTCAGAAGGTAATCAACTATATATTTCACATATTCTGTGATGAATTAGATGAGAATATTTTTTTAGATAATGGAATATAATCCCGACCTTTGCTCAAAGAGTTACAGCCAATTATTACACCAACTCAACAAAAATTCACACCTGAATAAACAAAAACACAGACAAACTAATAAAAACTCACACAGCATAAAAAGACCATAAAAATTATTGAATTTTATTTGTGAATCTCCATCGAAAGTTGGCGAACAGCTGCATAACCAATGACTCAAGATTACGACATGCACCTTTCACTGACTTGATTTCTTCATGTAGCTGAGCCCAAGATCAGAGCCAGTATGTTGCCCTGAAAAGATTTTTTATTAACTCCCACAAGCCAATTCTCAAAAATATAAGATATACTATGAGGAGATAATTTCGGAAATCATCTAATGTATATGTTTTAGAACCTCTGTTGTGTTATATAAAAGATGCAAAAAGTGTTCAGCGGAAAGTTCAAACTAATCTCAAAAGACAAATGGTGCATTTGTTTGTTAATTTCTTCAGAGTGATAAGCTCACTATGTTTTCAACCTTTGAACTTCAATTCGCCACAAACCAATTAATGTTTGCATCTACTTATGTTTAATCATTACCTCCAATCAAATAACTAATTCCTTACCTCGTTTGGTTTATGCCTGCTCTCCAGGAATTGAACAAAGGCAGCAGCCATTGGTTAATCTTAAGGCATGGCATTCTGTATCCTTCAAACAACTAGTGACCTTTGCATAGTTAATAATGTGGCATCATGTTTCTTATATTCTTTTTGGTGCTTATATATGAAATCAGTTACAGGGGTATATAGTTGGCAACCCCATTACAGGCTCGAAGATTGATGATAATTTCAAAATTCCATATTCTCATGGTGTTGGGATCATATCTGATCAATTATACGAGGTAATTTCACATCCATACAATTAGAATATGGTGATACAACTCTGTAGCATTTTCCTTTCCCTGTTTGTAGGCTGCAGTAGCAAACTGCAATGGAGATTATGTGACCACAACAAATGAATTATGTGCTAAGGCCCTAAATGCTATTGATAATGTAAGATTCTTGTCTAACCTAGTTTAGAAGTTTACTAATATCCAACTACTATCAAACTTATGCATATCCCTTTTGTTTCAGCTCATGTCTGAAGTTGATTATGGAAATATCTTGGATGATAAATGTGTTCGTGCTACACCAAAACCCATAAATGAAGTTTCAAGAAGTAGGAGTCTGCAAGAAGATTACATTCGGCTAAGTGAGCCGACTGTTCGACCTACTATCAATTGTTTTGTAAGTTATTATCATTCATCGATCCCATTGTGTTAGTTTGATTGAAGATTGTAGTTTTTTTTTAAAGAAGCAGTATAAAGAGATTGTAATGATACATTATATCACAACTCTGTTTTTTCCTAATGTTAATCTGCCTCCTGTTTTTCTTCTTAAATGCAGTCATACCGTTACTATCTATCATTCTTGTGGATGAACAACAATTTGACTAGAGAAGCTCTTAAGATCAAGAAGGTAACCATTCGTTATCTTTTGCCTGTATAATTAGGACCCTACAATGTGTTTCCCTTCTAAGATTTCTTGCGAAGCTTAAATGAGAAGAGTATAAGATGCCATCTATACAAAGTATGATTTGCTAGCTAGGAAAAGCTTCCATTATTTTGTTAAAAAAGTTGGCTAAATATAACAAATCCAATAATGGCGCAAATATGACAATAGGGAACAGTCGGCGAATGGATAAGATGCAAGACAGGGCTACCCTATGTTCAAGATGTCGCAAGCAGCATCAAGTATCATTTTGACCTCACCACAGGAGGTTACCGGGCACTTGTGTTCAGGTGAAATCATCAGAGGAAAATTCATTTATCTGCTTCCTGCAGGTTAAATCCATATTCCATGTCTTAAAAATTATTATGACATTTATGAATGCAGTGGTGACCATGATCTCATATTGCCATTTCTGAGCACCCAGGCATGGATAAGATCCTTGAACTTCTCCATAGTTGATGAGTGGAGAGCATGGCATGTGGATGGCCAGGCTGCAGGGTTAAGCCATCTGTTTCTGCTCACAAATTGTGCATTTCAATTGATGTTTTTTCCATGTTTGCCTGATCTGATATTAATATTATGTGTCATCTTCTTTTATGCAGATTTACAATTTTGTACGCCAACAACTTGACCTTTGCCACAGTAAAGGTGTTACTTTTTCTTTCTTGACCTTTTCTCGTTAAACTGGTATTTGTGTCTATAGTGTCCAGCCCTTCACAATTCACATACTGGCTTTCTGAAGAATCCTAAACAAGGTTTATGATGTGCAGGGTGGTGGCCATACCTCTATAGAAACCAATCCTAAACAAGGTTTTGCCATGGGCAAACGTTGGCTAGATAATAAGCCTCTGTGATGTTCACCTGCTTTGACCCAACCTGTATACTCGTGCAACTGGTATTGTTTGTATGAAGAACTACTTTATCTCCCATGTTTTCCAACAACGAATAGAAGACAAGATAAATACTCCGCC More
CDS seq		ATGGTCTTGGAGCTTCTCACAATGGCTGCTCACCGCGTGGGGCGATGCATGCTCCTGCAACCACCGCGCCTCGCCACCTGCGTCCTCTTCCTCCTGCTACCGCTGCTGCTGCCGTGCTCGGCGTCGTCGTCGGTGATCACCCACCTCCCGGGCTTCCACGGCCGCTTGCCGTTCCACCTTGAGACCGGGTATGTTGGTGTGGACGAGGAGACGGGCACTGAGCTCTTCTACTACTTCGTTGAATCGGAGAGGAGCCCAAGTACAGGCCCTGTGATCCTCTGGTTGACAGGCGGGCCTGGCTGCTCCGGATTCAGCGGTGTCGTCTTTGAAGTAGGACCTATGAAATACGTGTTGGAGCCTTATAATGGTAGTTTGCCACGATTGGTTTATAATCAGTATTCATGGACACAGATGGCAAGCATCCTCTTCTTGGACACTCCTGTTGGTTCTGGTTTCTCATACGCTCATGATCCTAAAGGTTATAATGTCGGGGACATATCATCGTCTTTGCAAGTCGTAACATTTCTGAAGAAGTGGTTCAATGATCACCCACGCTATCTCTCAAATCATTTCTATGTTGGAGGAAGCTCATACGCTGGAAAGGTGATTCCAATTATCATGAAGTTCATTTCAGAAGGAATTGAACAAAGGCAGCAGCCATTGGTTAATCTTAAGTTACAGGGGTATATAGTTGGCAACCCCATTACAGGCTCGAAGATTGATGATAATTTCAAAATTCCATATTCTCATGGTGTTGGGATCATATCTGATCAATTATACGAGGCTGCAGTAGCAAACTGCAATGGAGATTATGTGACCACAACAAATGAATTATGTGCTAAGGCCCTAAATGCTATTGATAATCTCATGTCTGAAGTTGATTATGGAAATATCTTGGATGATAAATGTGTTCGTGCTACACCAAAACCCATAAATGAAGTTTCAAGAAGTAGGAGTCTGCAAGAAGATTACATTCGGCTAAGTGAGCCGACTGTTCGACCTACTATCAATTGTTTTTCATACCGTTACTATCTATCATTCTTGTGGATGAACAACAATTTGACTAGAGAAGCTCTTAAGATCAAGAAGGGAACAGTCGGCGAATGGATAAGATGCAAGACAGGGCTACCCTATGTTCAAGATGTCGCAAGCAGCATCAAGTATCATTTTGACCTCACCACAGGAGGTTACCGGGCACTTGTGTTCAGGTGA More
Protein seq		MVLELLTMAAHRVGRCMLLQPPRLATCVLFLLLPLLLPCSASSSVITHLPGFHGRLPFHLETGYVGVDEETGTELFYYFVESERSPSTGPVILWLTGGPGCSGFSGVVFEVGPMKYVLEPYNGSLPRLVYNQYSWTQMASILFLDTPVGSGFSYAHDPKGYNVGDISSSLQVVTFLKKWFNDHPRYLSNHFYVGGSSYAGKVIPIIMKFISEGIEQRQQPLVNLKLQGYIVGNPITGSKIDDNFKIPYSHGVGIISDQLYEAAVANCNGDYVTTTNELCAKALNAIDNLMSEVDYGNILDDKCVRATPKPINEVSRSRSLQEDYIRLSEPTVRPTINCFSYRYYLSFLWMNNNLTREALKIKKGTVGEWIRCKTGLPYVQDVASSIKYHFDLTTGGYRALVFR
Function		Serine carboxypeptidase-like 18 [UniProtKB/Swiss-Prot:Q9C7Z9]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_03g0730400	OsNip_03t0730400-01	Chr03	29858907	29864431	+	RAP2018-11-26
CDS seq	ATGGTCTTGGAGCTTCTCACAATGGCTGCTCACCGCGTGGGGCGATGCATGCTCCTGCAACCACCGCGCCTCGCCACCTGCGTCCTCTTCCTCCTGCTACCGCTGCTGCTGCCGTGCTCGGCGTCGTCGTCGGTGATCACCCACCTCCCGGGCTTCCACGGCCGCTTGCCGTTCCACCTTGAGACCGGGTATGTTGGTGTGGACGAGGAGACGGGCACTGAGCTCTTCTACTACTTCGTTGAATCGGAGAGGAGCCCAAGTACAGGCCCTGTGATCCTCTGGTTGACAGGCGGGCCTGGCTGCTCCGGATTCAGCGGTGTCGTCTTTGAAGTAGGACCTATGAAATACGTGTTGGAGCCTTATAATGGTAGTTTGCCACGATTGGTTTATAATCAGTATTCATGGACACAGATGGCAAGCATCCTCTTCTTGGACACTCCTGTTGGTTCTGGTTTCTCATACGCTCATGATCCTAAAGGTTATAATGTCGGGGACATATCATCGTCTTTGCAAGTCGTAACATTTCTGAAGAAGTGGTTCAATGATCACCCACGCTATCTCTCAAATCATTTCTATGTTGGAGGAAGCTCATACGCTGGAAAGGTGATTCCAATTATCATGAAGTTCATTTCAGAAGGAATTGAACAAAGGCAGCAGCCATTGGTTAATCTTAAGTTACAGGGGTATATAGTTGGCAACCCCATTACAGGCTCGAAGATTGATGATAATTTCAAAATTCCATATTCTCATGGTGTTGGGATCATATCTGATCAATTATACGAGGCTGCAGTAGCAAACTGCAATGGAGATTATGTGACCACAACAAATGAATTATGTGCTAAGGCCCTAAATGCTATTGATAATCTCATGTCTGAAGTTGATTATGGAAATATCTTGGATGATAAATGTGTTCGTGCTACACCAAAACCCATAAATGAAGTTTCAAGAAGTAGGAGTCTGCAAGAAGATTACATTCGGCTAAGTGAGCCGACTGTTCGACCTACTATCAATTGTTTTTCATACCGTTACTATCTATCATTCTTGTGGATGAACAACAATTTGACTAGAGAAGCTCTTAAGATCAAGAAGGGAACAGTCGGCGAATGGATAAGATGCAAGACAGGGCTACCCTATGTTCAAGATGTCGCAAGCAGCATCAAGTATCATTTTGACCTCACCACAGGAGGTTACCGGGCACTTGTGTTCAGGTGA More
Protein seq	MVLELLTMAAHRVGRCMLLQPPRLATCVLFLLLPLLLPCSASSSVITHLPGFHGRLPFHLETGYVGVDEETGTELFYYFVESERSPSTGPVILWLTGGPGCSGFSGVVFEVGPMKYVLEPYNGSLPRLVYNQYSWTQMASILFLDTPVGSGFSYAHDPKGYNVGDISSSLQVVTFLKKWFNDHPRYLSNHFYVGGSSYAGKVIPIIMKFISEGIEQRQQPLVNLKLQGYIVGNPITGSKIDDNFKIPYSHGVGIISDQLYEAAVANCNGDYVTTTNELCAKALNAIDNLMSEVDYGNILDDKCVRATPKPINEVSRSRSLQEDYIRLSEPTVRPTINCFSYRYYLSFLWMNNNLTREALKIKKGTVGEWIRCKTGLPYVQDVASSIKYHFDLTTGGYRALVFR More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_03g0730400	OsNip_03t0730400-02	Chr03	29858939	29860668	+	RAP2018-11-26
CDS seq	ATGGTCTTGGAGCTTCTCACAATGGCTGCTCACCGCGTGGGGCGATGCATGCTCCTGCAACCACCGCGCCTCGCCACCTGCGTCCTCTTCCTCCTGCTACCGCTGCTGCTGCCGTGCTCGGCGTCGTCGTCGGTGATCACCCACCTCCCGGGCTTCCACGGCCGCTTGCCGTTCCACCTTGAGACCGGGTATGTTGGTGTGGACGAGGAGACGGGCACTGAGCTCTTCTACTACTTCGTTGAATCGGAGAGGAGCCCAAGTACAGGCCCTGTGATCCTCTGGTTGACAGGCGGGCCTGGCTGCTCCGGATTCAGCGGTGTCGTCTTTGAAGTAGGTTAG More
Protein seq	MVLELLTMAAHRVGRCMLLQPPRLATCVLFLLLPLLLPCSASSSVITHLPGFHGRLPFHLETGYVGVDEETGTELFYYFVESERSPSTGPVILWLTGGPGCSGFSGVVFEVG

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_03g0730400	OsNip_03t0730400-03	Chr03	29858952	29864432	+	IsoSeq
CDS seq	GTTGACAAAAAAAACTCAGATCTTCAAGCTGCCAGAGCACTGAAAAAGGAAGCAAAGCAATGGTCTTGGAGCTTCTCACAATGGCTGCTCACCGCGTGGGGCGATGCATGCTCCTGCAACCACCGCGCCTCGCCACCTGCGTCCTCTTCCTCCTGCTACCGCTGCTGCTGCCGTGCTCGGCGTCGTCGT
Protein seq	VDKKNSDLQAARALKKEAKQWSWSFSQWLLTAWGDACSCNHRASPPASSSSCYRCCCRARRRR

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.135461	4.649220

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g52040	RBH	0.000000	0.110022	1.170091
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0730400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0033460	RBH	0.0	26.226118	2.756449
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0033160	RBH	0.061128	5.233663	2.898850
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0033230	RBH	0.0	33.996284	5.481895
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0033550	RBH	0.0	0.558627	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0033160	SBH	4.530792	29.704414	38.734978
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_03G0509800	RBH	15.8599995	12.9050995	4.584564
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0032910	RBH	0.000000	0.657357	1.215913
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0510800	SBH	8.850739	7.067128	4.8354455
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_03g0033390	RBH	0.059732	0.035467	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0033380	RBH	0.000000	20.078350	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0033160	SBH	0.618060	47.915791	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0033110	RBH	0.911613	2.295577	5.892027
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0033100	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G032890	RBH	0.000000	2.657251	5.664279
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_03g0032730	RBH	0.395599	36.973579	21.343933

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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