Plant Circular RNA Database

Detail information of Os02g0553200_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os02g0553200_circ_g.4
					
						ID in PlantcircBase
						osa_circ_014992
					
						Alias
						Os02circ15106
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 20868848-20869679  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os02g0553200						
					
						Parent gene annotation
						
							Thylakoid membrane-bound ascorbate peroxidase, Tolerance to bact
erial blight, Response to NaCl (Os02t0553200-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os02g0553200_circ_g.1 Os02g0553200_circ_g.2 Os02g0553200_circ_g.3 Os02g0553200_circ_g.5 Os02g0553200_circ_g.6 Os02g0553200_circ_g.7 Os02g0553200_circ_g.8 Os02g0553200_circ_g.9 						
					
						Support reads
						2/3
					
						Tissues
						leaf/shoot
					
						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
						Os02t0553200-01:2

General Information
CircRNA Name	Os02g0553200_circ_g.4
ID in PlantcircBase	osa_circ_014992
Alias	Os02circ15106
Organism	Oryza sativa
Position	chr2: 20868848-20869679 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os02g0553200
Parent gene annotation	Thylakoid membrane-bound ascorbate peroxidase, Tolerance to bact erial blight, Response to NaCl (Os02t0553200-01)
Parent gene strand	-
Alternative splicing	Os02g0553200_circ_g.1 Os02g0553200_circ_g.2 Os02g0553200_circ_g.3 Os02g0553200_circ_g.5 Os02g0553200_circ_g.6 Os02g0553200_circ_g.7 Os02g0553200_circ_g.8 Os02g0553200_circ_g.9
Support reads	2/3
Tissues	leaf/shoot
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	Os02t0553200-01:2

			
						 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  
						
							GTGGATCGAACTTTGCACCAAGGTCGCTCAGTTTAGCATGAGCTTCAGCGTAGTCTTTAAAGAA
TGCCTCCTGATCCTCTGCATATTTTTCGGCATATACctttccgtaggagtatttcgcagcgacg
aagggctctggttgcggtgctgcaccgttgttgtcatccgctggcgatgatgccactgctgctc
ctaccgtt

						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: 333
Transcript exons: 20868848-20869075,20869575-20869679
CTTTCCGTAGGAGTATTTCGCAGCGACGAAGGGCTCTGGTTGCGGTGCTGCACCGTTGTTGTCA
TCCGCTGGCGATGATGCCACTGCTGCTCCTACCGTTACTGGTACTGGAGTTGGTTCAGCTTCCT
TCTTCTCCTCGACTGGTGGAGGTGGTGGTGCTGCTGCTGGCGCTGGTGCTGGTTCAGGATCCTT
CTCTTCGACGGCTGGTTCATCGTCCAGTGAAAATCCCTCAGGTGGATCGAACTTTGCACCAAGG
TCGCTCAGTTTAGCATGAGCTTCAGCGTAGTCTTTAAAGAATGCCTCCTGATCCTCTGCATATT
TTTCGGCATATAC
						
						Genomic sequence
						
							CTTTCCGTAGGAGTATTTCGCAGCGACGAAGGGCTCTGGTTGCGGTGCTGCACCGTTGTTGTCA
TCCGCTGGCGATGATGCCACTGCTGCTCCTACCGTTACTGGTACTGGAGTTGGTTCAGCTTCCT
TCTTCTCCTCGACTGGTGGAGGTGGTGGTGCTGCTGCTGGCGCTGGTGCTGGTTCAGGATCCTT
CTCTTCGACGGCTGGTTCATCGTCCAGTGAAAATCCCTGCAGGAAAATCACATCCATCACTTCC
TGATCGAAGGCTGGTAAAGTTGGACTCTGTAAATATCCAACCTACAATTGCACTGGTTTTTACA
TGAAGAACAGCTAAGAAAAGCTGCCATAGTAAACCCCATTTCGTTGCATTGCAGAAGAAAGATT
GATATGATGGACTACCTCAAACTCCCAGTGTTTGGATTACATTCGGTAAAAAGAAAAACTATCT
GAACTATATTTCTGTCCTGAAGGTCCAGTACTCCATCTTACTGTCACATAAGTACATTACTGAA
TTCTCTAGAAAAAAAATACATTACAAAAGATATCTACTCGATGTGGACGAGGAATCAGGGAGTC
ATGTTTTGAACTTGCAAACAAGAGGAAGAAAATCTGGCATGTTCTAATAAAAGAACTTAAGAGC
TTAAGTGTCTTTCGTATTGTTTATGATTGTTTAGGCACAATTGGTTGCCAGGAGATCAAAATGA
AAAAAAAAGATGGTAGTCCTCACCTCAGGTGGATCGAACTTTGCACCAAGGTCGCTCAGTTTAG
CATGAGCTTCAGCGTAGTCTTTAAAGAATGCCTCCTGATCCTCTGCATATTTTTCGGCATATAC

Sequences
Splice junction sequence	GTGGATCGAACTTTGCACCAAGGTCGCTCAGTTTAGCATGAGCTTCAGCGTAGTCTTTAAAGAA TGCCTCCTGATCCTCTGCATATTTTTCGGCATATACctttccgtaggagtatttcgcagcgacg aagggctctggttgcggtgctgcaccgttgttgtcatccgctggcgatgatgccactgctgctc ctaccgtt
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: 333 Transcript exons: 20868848-20869075,20869575-20869679 CTTTCCGTAGGAGTATTTCGCAGCGACGAAGGGCTCTGGTTGCGGTGCTGCACCGTTGTTGTCA TCCGCTGGCGATGATGCCACTGCTGCTCCTACCGTTACTGGTACTGGAGTTGGTTCAGCTTCCT TCTTCTCCTCGACTGGTGGAGGTGGTGGTGCTGCTGCTGGCGCTGGTGCTGGTTCAGGATCCTT CTCTTCGACGGCTGGTTCATCGTCCAGTGAAAATCCCTCAGGTGGATCGAACTTTGCACCAAGG TCGCTCAGTTTAGCATGAGCTTCAGCGTAGTCTTTAAAGAATGCCTCCTGATCCTCTGCATATT TTTCGGCATATAC
Genomic sequence	CTTTCCGTAGGAGTATTTCGCAGCGACGAAGGGCTCTGGTTGCGGTGCTGCACCGTTGTTGTCA TCCGCTGGCGATGATGCCACTGCTGCTCCTACCGTTACTGGTACTGGAGTTGGTTCAGCTTCCT TCTTCTCCTCGACTGGTGGAGGTGGTGGTGCTGCTGCTGGCGCTGGTGCTGGTTCAGGATCCTT CTCTTCGACGGCTGGTTCATCGTCCAGTGAAAATCCCTGCAGGAAAATCACATCCATCACTTCC TGATCGAAGGCTGGTAAAGTTGGACTCTGTAAATATCCAACCTACAATTGCACTGGTTTTTACA TGAAGAACAGCTAAGAAAAGCTGCCATAGTAAACCCCATTTCGTTGCATTGCAGAAGAAAGATT GATATGATGGACTACCTCAAACTCCCAGTGTTTGGATTACATTCGGTAAAAAGAAAAACTATCT GAACTATATTTCTGTCCTGAAGGTCCAGTACTCCATCTTACTGTCACATAAGTACATTACTGAA TTCTCTAGAAAAAAAATACATTACAAAAGATATCTACTCGATGTGGACGAGGAATCAGGGAGTC ATGTTTTGAACTTGCAAACAAGAGGAAGAAAATCTGGCATGTTCTAATAAAAGAACTTAAGAGC TTAAGTGTCTTTCGTATTGTTTATGATTGTTTAGGCACAATTGGTTGCCAGGAGATCAAAATGA AAAAAAAAGATGGTAGTCCTCACCTCAGGTGGATCGAACTTTGCACCAAGGTCGCTCAGTTTAG CATGAGCTTCAGCGTAGTCTTTAAAGAATGCCTCCTGATCCTCTGCATATTTTTCGGCATATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_004001* osi_circ_011862 						
					
						PMCS
						0.244661729

Conservation Information
Conserved circRNAs	osi_circ_004001* osi_circ_011862
PMCS	0.244661729

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20869618-20868922(+)
20869644-20869612(+)
20868914-20869609(-)
						
						Potential amino acid sequence
						
							MSFSVVFKECLLILCIFFGIYLSVGVFRSDEGLWLRCCTVVVIRWR*(+)
MPPDPLHIFRHIPFRRSISQRRRALVAVLHRCCHPLAMMPLLLLPLLVLELVQLPSSPRLVEVV
VLLLALVLVQDPSLRRLVHRPVKIPQVDRTLHQGRSV*(+)
MTTTVQHRNQSPSSLRNTPTERYMPKNMQRIRRHSLKTTLKLMLN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20869618-20868922(+) 20869644-20869612(+) 20868914-20869609(-)
Potential amino acid sequence	MSFSVVFKECLLILCIFFGIYLSVGVFRSDEGLWLRCCTVVVIRWR(+) MPPDPLHIFRHIPFRRSISQRRRALVAVLHRCCHPLAMMPLLLLPLLVLELVQLPSSPRLVEVV VLLLALVLVQDPSLRRLVHRPVKIPQVDRTLHQGRSV(+) MTTTVQHRNQSPSSLRNTPTERYMPKNMQRIRRHSLKTTLKLMLN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Chu et al., 2017

circRNA

Detail information of Os02g0553200_circ_g.4

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