Plant Circular RNA Database

Detail information of Os04g0474500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0474500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024185
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 23731650-23731924  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0474500						
					
						Parent gene annotation
						
							Similar to Cyanogenic beta-glucosidase precursor (EC 3.2.1.21) (
Linamarase) (Fragment). (Os04t0474500-01);Similar to OSIGBa0135C
13.5 protein. (Os04t0474500-02);Similar to Cyanogenic beta-gluco
sidase precursor (EC 3.2.1.21) (Linamarase) (Fragment). (Os04t04
74500-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0474300_circ_ag.1 Os04g0474300_circ_ag.2 Os04g0474300_circ_ag.3 Os04g0474300_circ_ag.4 Os04g0474300_circ_ag.5 Os04g0474300_circ_ag.6 Os04g0474300_circ_ag.7 Os04g0474300_circ_ag.8 Os04g0474300_circ_ag.9 EPlOSAG00000016679_circ_ig.1 Os04g0474500_circ_ag.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_ag.3 Os04g0474500_circ_g.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_ag.4 Os04g0474500_circ_ag.5 Os04g0474500_circ_ag.6 Os04g0474550_circ_ag.1 Os04g0474700_circ_g.1 Os04g0474800_circ_ag.1 Os04g0474800_circ_g.1 Os04g0474800_circ_ag.2 Os04g0474800_circ_g.3 Os04g0474800_circ_ag.4 Os04g0474800_circ_g.5 Os04g0474800_circ_g.6 Os04g0474800_circ_ag.7 Os04g0474800_circ_g.8 Os04g0474800_circ_g.9 Os04g0474800_circ_ag.10 Os04g0474800_circ_ag.11 Os04g0474800_circ_ag.12 Os04g0474800_circ_g.13 Os04g0474800_circ_g.14 						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0474500-03:2
Os04t0474500-02:2
Os04t0474500-01:2

General Information
CircRNA Name	Os04g0474500_circ_g.3
ID in PlantcircBase	osa_circ_024185
Alias	NA
Organism	Oryza sativa
Position	chr4: 23731650-23731924 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0474500
Parent gene annotation	Similar to Cyanogenic beta-glucosidase precursor (EC 3.2.1.21) ( Linamarase) (Fragment). (Os04t0474500-01);Similar to OSIGBa0135C 13.5 protein. (Os04t0474500-02);Similar to Cyanogenic beta-gluco sidase precursor (EC 3.2.1.21) (Linamarase) (Fragment). (Os04t04 74500-03)
Parent gene strand	-
Alternative splicing	Os04g0474300_circ_ag.1 Os04g0474300_circ_ag.2 Os04g0474300_circ_ag.3 Os04g0474300_circ_ag.4 Os04g0474300_circ_ag.5 Os04g0474300_circ_ag.6 Os04g0474300_circ_ag.7 Os04g0474300_circ_ag.8 Os04g0474300_circ_ag.9 EPlOSAG00000016679_circ_ig.1 Os04g0474500_circ_ag.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_ag.3 Os04g0474500_circ_g.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_ag.4 Os04g0474500_circ_ag.5 Os04g0474500_circ_ag.6 Os04g0474550_circ_ag.1 Os04g0474700_circ_g.1 Os04g0474800_circ_ag.1 Os04g0474800_circ_g.1 Os04g0474800_circ_ag.2 Os04g0474800_circ_g.3 Os04g0474800_circ_ag.4 Os04g0474800_circ_g.5 Os04g0474800_circ_g.6 Os04g0474800_circ_ag.7 Os04g0474800_circ_g.8 Os04g0474800_circ_g.9 Os04g0474800_circ_ag.10 Os04g0474800_circ_ag.11 Os04g0474800_circ_ag.12 Os04g0474800_circ_g.13 Os04g0474800_circ_g.14
Support reads	1
Tissues	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	Os04t0474500-03:2 Os04t0474500-02:2 Os04t0474500-01:2

			
						 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  
						
							AGTGAAGACTAGACATGCATACCTTTTGATAATAGTTCATTGATCAAATTGTTGTAGTAGTTGA
TGCCTTCTCTGTTGACTCCACCGCTGAGACTTCCATatgatattagggctaagaaatcctttat
atttatcttccagtgcctgaggtgtatcaaaatggaatagggtagcaaatggttggacctctgc
aaatgtat

						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
						
							ATGATATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGTGCCTGAGGTGTATCAAAATGGA
ATAGGGTAGCAAATGGTTGGACCTCTGCAAATGTATAAGATTATTTTGCATCTTGAATAAAGAA
ATCTGGTTGTCACAAGTTGCATCTAGTGACTGAACTTGAAACTAAATAGTGAAGACTAGACATG
CATACCTTTTGATAATAGTTCATTGATCAAATTGTTGTAGTAGTTGATGCCTTCTCTGTTGACT
CCACCGCTGAGACTTCCAT

Sequences
Splice junction sequence	AGTGAAGACTAGACATGCATACCTTTTGATAATAGTTCATTGATCAAATTGTTGTAGTAGTTGA TGCCTTCTCTGTTGACTCCACCGCTGAGACTTCCATatgatattagggctaagaaatcctttat atttatcttccagtgcctgaggtgtatcaaaatggaatagggtagcaaatggttggacctctgc aaatgtat
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	ATGATATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGTGCCTGAGGTGTATCAAAATGGA ATAGGGTAGCAAATGGTTGGACCTCTGCAAATGTATAAGATTATTTTGCATCTTGAATAAAGAA ATCTGGTTGTCACAAGTTGCATCTAGTGACTGAACTTGAAACTAAATAGTGAAGACTAGACATG CATACCTTTTGATAATAGTTCATTGATCAAATTGTTGTAGTAGTTGATGCCTTCTCTGTTGACT CCACCGCTGAGACTTCCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.430735688

Conservation Information
Conserved circRNAs	NA
PMCS	0.430735688

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23731889-23731714(+)
23731866-23731863(-)
						
						Potential amino acid sequence
						
							MPSLLTPPLRLPYDIRAKKSFIFIFQCLRCIKME*(+)
MNYYQKRSNHLLPYSILIHLRHWKINIKDFLALISYGSLSGGVNREGINYYNNLINELLSKEVQ
PFATLFHFDTPQALEDKYKGFLSPNIIWKSQRWSQQRRHQLLQQFDQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23731889-23731714(+) 23731866-23731863(-)
Potential amino acid sequence	MPSLLTPPLRLPYDIRAKKSFIFIFQCLRCIKME(+) MNYYQKRSNHLLPYSILIHLRHWKINIKDFLALISYGSLSGGVNREGINYYNNLINELLSKEVQ PFATLFHFDTPQALEDKYKGFLSPNIIWKSQRWSQQRRHQLLQQFDQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0474500_circ_g.3

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