Plant Circular RNA Database

Detail information of Os10g0567400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os10g0567400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008059
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 22483668-22484492  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os10g0567400						
					
						Parent gene annotation
						
							Similar to Rieske. (Os10t0567400-01);Similar to Isoform 2 of Chl
orophyllide a oxygenase, chloroplastic. (Os10t0567400-02);Simila
r to Isoform 2 of Chlorophyllide a oxygenase, chloroplastic. (Os
10t0567400-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os10g0567200_circ_ag.1 EPlOSAG00000036674_circ_ig.1 Os10g0567300_circ_g.1 Os10g0567300_circ_g.2 Os10g0567300_circ_g.3 Os10g0567400_circ_g.1 Os10g0567400_circ_g.2 Os10g0567400_circ_g.4 Os10g0567400_circ_g.5 Os10g0567400_circ_g.6 Os10g0567400_circ_g.7 Os10g0567400_circ_g.8 Os10g0567400_circ_g.9 Os10g0567400_circ_g.10 Os10g0567400_circ_g.11 						
					
						Support reads
						2
					
						Tissues
						shoot, seed
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os10t0567400-02:3
Os10t0567400-03:3
Os10t0567400-01:3

General Information
CircRNA Name	Os10g0567400_circ_g.3
ID in PlantcircBase	osa_circ_008059
Alias	NA
Organism	Oryza sativa
Position	chr10: 22483668-22484492 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os10g0567400
Parent gene annotation	Similar to Rieske. (Os10t0567400-01);Similar to Isoform 2 of Chl orophyllide a oxygenase, chloroplastic. (Os10t0567400-02);Simila r to Isoform 2 of Chlorophyllide a oxygenase, chloroplastic. (Os 10t0567400-03)
Parent gene strand	-
Alternative splicing	Os10g0567200_circ_ag.1 EPlOSAG00000036674_circ_ig.1 Os10g0567300_circ_g.1 Os10g0567300_circ_g.2 Os10g0567300_circ_g.3 Os10g0567400_circ_g.1 Os10g0567400_circ_g.2 Os10g0567400_circ_g.4 Os10g0567400_circ_g.5 Os10g0567400_circ_g.6 Os10g0567400_circ_g.7 Os10g0567400_circ_g.8 Os10g0567400_circ_g.9 Os10g0567400_circ_g.10 Os10g0567400_circ_g.11
Support reads	2
Tissues	shoot, seed
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os10t0567400-02:3 Os10t0567400-03:3 Os10t0567400-01:3

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							ATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCA
TTTTCTCACATTTTCCATCAGTTGAATACTCCCAACcttctcagcaaaatgtgaccatagtata
tgcatgaaagggacatgcttgatccatggagcgaagtcgagagacatccggtagagcagcctgg
ttttattc

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 366
Transcript exons: 22483668-22483833,22484100-22484197,22484308-22484337,22
484421-22484492
CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG
TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT
GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCCTTGGCAAAGGTGGATGTATGAGTAA
AAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCAT
CACTATCTCTCTGCGTGAATTGTAAATCCTGAAGGAGGACCGGATGCGCACGTTGAGCATCTTT
GTGGATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC
Transcript length: 593
Transcript exons: 22483668-22483962,22484083-22484195,22484308-22484492
CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG
TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT
GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCTCTAGTTTTCCAGGCTTTGAGATGCC
AATGGTTGACAACACCATGCATGGTGGTCGAAATTCCATGTCGATCGGGTATGGATCCCAGTAT
CCTTGAAGCCCAGATGAAGGTGTCAAGAACTTCACCAAGCTTGGAACACTCCAACCCTTGGCAA
AGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATG
CTCCACTGGTAGCTCCATCACTATCTCTGCGTGAATTGTAAATCCTGAAGGAGGCAGCAGAGAA
GGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATCCAAACCATTCCTTCTTGCTCAAAGC
ATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCATTTTCTCACATTTTCCATC
AGTTGAATACTCCCAAC
						
					

						Genomic sequence
						
							CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG
TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT
GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCTCTAGTTTTCCAGGCTTTGAGATGCC
AATGGTTGACAACACCATGCATGGTGGTCGAAATTCCATGTCGATCGGGTATGGATCCCAGTAT
CCTTGAAGCCCAGATGAAGGTGTCAAGAACTTCACCAAGCTGGGAAATGAACATAGCATCAGCA
TGATGATTTCTGAAGACATTTCCACATGGCTATCCATTTTCTAAAAAAAAAAAAAAGAATTCCA
CATGGCTGTGAAAATATATGTATGTAAATACCTTGGAACACTCCAACCCTTGGCAAAGGTGGAT
GTATGAGTAAAAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATGCTCCACTG
GTAGCTCCATCACTATCTGTTGATGATCAAGAACAATTCCATTACTTTTCAGTCCAGTAAAAAT
CTTGAAATGCACAGGACAGTTCCACATAGTATGGTTGCTGCAGCATGACATGATCTCCTTTTAC
CTCTGCGTGAATTGTAAATCCTGAAGGAGGCAGCAGAGAAGGGATAGTCGACTTCGGTGGGTCA
TTGCCAGGCCATATCCAAACCATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGT
TGAGCATCTTTGTGGATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC
						
					

			
		

Sequences
Splice junction sequence	ATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCA TTTTCTCACATTTTCCATCAGTTGAATACTCCCAACcttctcagcaaaatgtgaccatagtata tgcatgaaagggacatgcttgatccatggagcgaagtcgagagacatccggtagagcagcctgg ttttattc
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 366 Transcript exons: 22483668-22483833,22484100-22484197,22484308-22484337,22 484421-22484492 CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCCTTGGCAAAGGTGGATGTATGAGTAA AAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCAT CACTATCTCTCTGCGTGAATTGTAAATCCTGAAGGAGGACCGGATGCGCACGTTGAGCATCTTT GTGGATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC Transcript length: 593 Transcript exons: 22483668-22483962,22484083-22484195,22484308-22484492 CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCTCTAGTTTTCCAGGCTTTGAGATGCC AATGGTTGACAACACCATGCATGGTGGTCGAAATTCCATGTCGATCGGGTATGGATCCCAGTAT CCTTGAAGCCCAGATGAAGGTGTCAAGAACTTCACCAAGCTTGGAACACTCCAACCCTTGGCAA AGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATG CTCCACTGGTAGCTCCATCACTATCTCTGCGTGAATTGTAAATCCTGAAGGAGGCAGCAGAGAA GGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATCCAAACCATTCCTTCTTGCTCAAAGC ATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCATTTTCTCACATTTTCCATC AGTTGAATACTCCCAAC
Genomic sequence	CTTCTCAGCAAAATGTGACCATAGTATATGCATGAAAGGGACATGCTTGATCCATGGAGCGAAG TCGAGAGACATCCGGTAGAGCAGCCTGGTTTTATTCCTAGAGGAGGGCAAACAGATATGGAGCT GGTGGAGATGCGTCGAACATTGCTTGGTGCTCTTCCCCTCTAGTTTTCCAGGCTTTGAGATGCC AATGGTTGACAACACCATGCATGGTGGTCGAAATTCCATGTCGATCGGGTATGGATCCCAGTAT CCTTGAAGCCCAGATGAAGGTGTCAAGAACTTCACCAAGCTGGGAAATGAACATAGCATCAGCA TGATGATTTCTGAAGACATTTCCACATGGCTATCCATTTTCTAAAAAAAAAAAAAAGAATTCCA CATGGCTGTGAAAATATATGTATGTAAATACCTTGGAACACTCCAACCCTTGGCAAAGGTGGAT GTATGAGTAAAAGGAGCATGAGCAAGATCTAATAGATTGTCCAGAAGAAGTCCATGCTCCACTG GTAGCTCCATCACTATCTGTTGATGATCAAGAACAATTCCATTACTTTTCAGTCCAGTAAAAAT CTTGAAATGCACAGGACAGTTCCACATAGTATGGTTGCTGCAGCATGACATGATCTCCTTTTAC CTCTGCGTGAATTGTAAATCCTGAAGGAGGCAGCAGAGAAGGGATAGTCGACTTCGGTGGGTCA TTGCCAGGCCATATCCAAACCATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGT TGAGCATCTTTGTGGATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002964* osi_circ_008723 						
					
						PMCS
						0.58569697

Conservation Information
Conserved circRNAs	osi_circ_002964* osi_circ_008723
PMCS	0.58569697

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22484427-22483699(+)
22483713-22484476(-)
22484459-22484194(-)
						
						Potential amino acid sequence
						
							MRTLSIFVDGIFSHFPSVEYSQPSQQNVTIVYA*(+)
MSLSCIYYGHILLRRLGVFN*(-)
MPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKSTIPSLLPPSGFTIHAEIVMELPVEHGLLLD
NLLDLAHAPFTHTSTFAKGWSVPSLVKFLTPSSGLQGYWDPYPIDMEFRPPCMVLSTIGISKPG
KLEGKSTKQCSTHLHQLHICLPSSRNKTRLLYRMSLDFAPWIKHVPFMHILWSHFAEKVGSIQL
MENVRKCHPQRCSTCASGHYHALSKKEWFGYGLAMTHRSRLSLLCCLLQDLQFTQR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22484427-22483699(+) 22483713-22484476(-) 22484459-22484194(-)
Potential amino acid sequence	MRTLSIFVDGIFSHFPSVEYSQPSQQNVTIVYA(+) MSLSCIYYGHILLRRLGVFN(-) MPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKSTIPSLLPPSGFTIHAEIVMELPVEHGLLLD NLLDLAHAPFTHTSTFAKGWSVPSLVKFLTPSSGLQGYWDPYPIDMEFRPPCMVLSTIGISKPG KLEGKSTKQCSTHLHQLHICLPSSRNKTRLLYRMSLDFAPWIKHVPFMHILWSHFAEKVGSIQL MENVRKCHPQRCSTCASGHYHALSKKEWFGYGLAMTHRSRLSLLCCLLQDLQFTQR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os10g0567400_circ_g.3

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