Plant Circular RNA Database

Detail information of Os10g0567400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os10g0567400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_008062
					
						Alias
						NA, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 22484083-22484492  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, CIRI-long
					
						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.3 Os10g0567400_circ_g.4 Os10g0567400_circ_g.5 Os10g0567400_circ_g.7 Os10g0567400_circ_g.8 Os10g0567400_circ_g.9 Os10g0567400_circ_g.10 Os10g0567400_circ_g.11 						
					
						Support reads
						3
					
						Tissues
						shoot, root, seed, leaf
					
						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
						Os10t0567400-01:2
Os10t0567400-03:2
Os10t0567400-02:2

General Information
CircRNA Name	Os10g0567400_circ_g.6
ID in PlantcircBase	osa_circ_008062
Alias	NA,
Organism	Oryza sativa
Position	chr10: 22484083-22484492 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, CIRI-long
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.3 Os10g0567400_circ_g.4 Os10g0567400_circ_g.5 Os10g0567400_circ_g.7 Os10g0567400_circ_g.8 Os10g0567400_circ_g.9 Os10g0567400_circ_g.10 Os10g0567400_circ_g.11
Support reads	3
Tissues	shoot, root, seed, leaf
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	Os10t0567400-01:2 Os10t0567400-03:2 Os10t0567400-02:2

			
						 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
TTTTCTCACATTTTCCATCAGTTGAATACTCCCAACcttggaacactccaacccttggcaaagg
tggatgtatgagtaaaaggagcatgagcaagatctaatagattgtccagaagaagtccatgctc
cactggta

						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: 298
Transcript exons: 22484083-22484195,22484308-22484492
CTTGGAACACTCCAACCCTTGGCAAAGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTA
ATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCATCACTATCTCTGCGTGAATTGT
AAATCCTGAAGGAGGCAGCAGAGAAGGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATC
CAAACCATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGG
ATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC
						
						Genomic sequence
						
							CTTGGAACACTCCAACCCTTGGCAAAGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTA
ATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCATCACTATCTGTTGATGATCAAG
AACAATTCCATTACTTTTCAGTCCAGTAAAAATCTTGAAATGCACAGGACAGTTCCACATAGTA
TGGTTGCTGCAGCATGACATGATCTCCTTTTACCTCTGCGTGAATTGTAAATCCTGAAGGAGGC
AGCAGAGAAGGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATCCAAACCATTCCTTCTT
GCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCATTTTCTCACA
TTTTCCATCAGTTGAATACTCCCAAC

Sequences
Splice junction sequence	ATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCA TTTTCTCACATTTTCCATCAGTTGAATACTCCCAACcttggaacactccaacccttggcaaagg tggatgtatgagtaaaaggagcatgagcaagatctaatagattgtccagaagaagtccatgctc cactggta
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: 298 Transcript exons: 22484083-22484195,22484308-22484492 CTTGGAACACTCCAACCCTTGGCAAAGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTA ATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCATCACTATCTCTGCGTGAATTGT AAATCCTGAAGGAGGCAGCAGAGAAGGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATC CAAACCATTCCTTCTTGCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGG ATGGCATTTTCTCACATTTTCCATCAGTTGAATACTCCCAAC
Genomic sequence	CTTGGAACACTCCAACCCTTGGCAAAGGTGGATGTATGAGTAAAAGGAGCATGAGCAAGATCTA ATAGATTGTCCAGAAGAAGTCCATGCTCCACTGGTAGCTCCATCACTATCTGTTGATGATCAAG AACAATTCCATTACTTTTCAGTCCAGTAAAAATCTTGAAATGCACAGGACAGTTCCACATAGTA TGGTTGCTGCAGCATGACATGATCTCCTTTTACCTCTGCGTGAATTGTAAATCCTGAAGGAGGC AGCAGAGAAGGGATAGTCGACTTCGGTGGGTCATTGCCAGGCCATATCCAAACCATTCCTTCTT GCTCAAAGCATGGTAATGACCGGATGCGCACGTTGAGCATCTTTGTGGATGGCATTTTCTCACA TTTTCCATCAGTTGAATACTCCCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.508337988

Conservation Information
Conserved circRNAs	NA
PMCS	0.508337988

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22484427-22484144(+)
22484452-22484118(+)
22484136-22484476(-)
22484459-22484476(-)
						
						Potential amino acid sequence
						
							MRTLSIFVDGIFSHFPSVEYSQPWNTPTLGKGGCMSKRSMSKI*(+)
MAFSHIFHQLNTPNLGTLQPLAKVDV*(+)
MLLLLIHPPLPRVGVFQGWEYSTDGKCEKMPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKST
IPSLLPPSGFTIHAEIVMELPVEHGLLLDNLLDLAHAPFTHTSTFAKGWSVPRLGVFN*(-)
MPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKSTIPSLLPPSGFTIHAEIVMELPVEHGLLLD
NLLDLAHAPFTHTSTFAKGWSVPRLGVFN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22484427-22484144(+) 22484452-22484118(+) 22484136-22484476(-) 22484459-22484476(-)
Potential amino acid sequence	MRTLSIFVDGIFSHFPSVEYSQPWNTPTLGKGGCMSKRSMSKI(+) MAFSHIFHQLNTPNLGTLQPLAKVDV(+) MLLLLIHPPLPRVGVFQGWEYSTDGKCEKMPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKST IPSLLPPSGFTIHAEIVMELPVEHGLLLDNLLDLAHAPFTHTSTFAKGWSVPRLGVFN(-) MPSTKMLNVRIRSLPCFEQEGMVWIWPGNDPPKSTIPSLLPPSGFTIHAEIVMELPVEHGLLLD NLLDLAHAPFTHTSTFAKGWSVPRLGVFN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017; this study

circRNA

Detail information of Os10g0567400_circ_g.6

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