Plant Circular RNA Database

Detail information of Os01g0678500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0678500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_003219
					
						Alias
						Os_ciR6002
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 27909226-27909521  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0678500						
					
						Parent gene annotation
						
							Voltage-gated Ca2+ channel  protein, Elicitor-induced defense re
ponses, Hypersensitive cell death, Activation of MAPK cascade (O
s01t0678500-01);Voltage-gated Ca2+ channel  protein, Elicitor-in
duced defense reponses, Hypersensitive cell death, Activation of
 MAPK cascade (Os01t0678500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0678500_circ_g.1 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						Os01t0678500-02:2
Os01t0678500-01:2

General Information
CircRNA Name	Os01g0678500_circ_g.2
ID in PlantcircBase	osa_circ_003219
Alias	Os_ciR6002
Organism	Oryza sativa
Position	chr1: 27909226-27909521 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os01g0678500
Parent gene annotation	Voltage-gated Ca2+ channel protein, Elicitor-induced defense re ponses, Hypersensitive cell death, Activation of MAPK cascade (O s01t0678500-01);Voltage-gated Ca2+ channel protein, Elicitor-in duced defense reponses, Hypersensitive cell death, Activation of MAPK cascade (Os01t0678500-02)
Parent gene strand	-
Alternative splicing	Os01g0678500_circ_g.1
Support reads	2
Tissues	root
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	Os01t0678500-02:2 Os01t0678500-01:2

			
						 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  
						
							AAATCAAAACGGTGAAATAAGAACAAAAAGGGTACTCGTTACTGAAGAGATCGGTTTCTTCTAG
TGTTGGATTTCCTGCATACACAATGCCCCCAAATATctccatccaagcttgccaattgcccatc
actaacaaattgaacagagttaccataccacttggatagtcattgaagttaaaaagaagatagc
tgcacatg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CTCCATCCAAGCTTGCCAATTGCCCATCACTAACAAATTGAACAGAGTTACCATACCACTTGGA
TAGTCATTGAAGTTAAAAAGAAGATAGCTGCACATGCCAAGGTAAAAGAGTGAGAATTTTGTCA
AAAATAAATAGAAGGTGAGATTTTAGTATAGAAGTTACTGGAACAAAAACACTTCTAAAACTTT
TTAGAAATCAAAACGGTGAAATAAGAACAAAAAGGGTACTCGTTACTGAAGAGATCGGTTTCTT
CTAGTGTTGGATTTCCTGCATACACAATGCCCCCAAATAT

Sequences
Splice junction sequence	AAATCAAAACGGTGAAATAAGAACAAAAAGGGTACTCGTTACTGAAGAGATCGGTTTCTTCTAG TGTTGGATTTCCTGCATACACAATGCCCCCAAATATctccatccaagcttgccaattgcccatc actaacaaattgaacagagttaccataccacttggatagtcattgaagttaaaaagaagatagc tgcacatg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTCCATCCAAGCTTGCCAATTGCCCATCACTAACAAATTGAACAGAGTTACCATACCACTTGGA TAGTCATTGAAGTTAAAAAGAAGATAGCTGCACATGCCAAGGTAAAAGAGTGAGAATTTTGTCA AAAATAAATAGAAGGTGAGATTTTAGTATAGAAGTTACTGGAACAAAAACACTTCTAAAACTTT TTAGAAATCAAAACGGTGAAATAAGAACAAAAAGGGTACTCGTTACTGAAGAGATCGGTTTCTT CTAGTGTTGGATTTCCTGCATACACAATGCCCCCAAATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.256472297

Conservation Information
Conserved circRNAs	NA
PMCS	0.256472297

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27909509-27909289(+)
27909281-27909228(-)
						
						Potential amino acid sequence
						
							MPPNISIQACQLPITNKLNRVTIPLG*(+)
MVTLFNLLVMGNWQAWMEIFGGIVYAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGN
WQAWMEIFGGIVYAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGNWQAWMEIFGGIV
YAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGNWQAWME(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27909509-27909289(+) 27909281-27909228(-)
Potential amino acid sequence	MPPNISIQACQLPITNKLNRVTIPLG*(+) MVTLFNLLVMGNWQAWMEIFGGIVYAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGN WQAWMEIFGGIVYAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGNWQAWMEIFGGIV YAGNPTLEETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGNWQAWME(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0678500_circ_g.2

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