Plant Circular RNA Database

Detail information of Os03g0219300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0219300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_018555
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 6277988-6278845  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0219300						
					
						Parent gene annotation
						
							Similar to Tubulin alpha-2 chain (Alpha-2 tubulin). (Os03t021930
0-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0219300_circ_g.4 Os03g0219300_circ_g.5 						
					
						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
						Os03t0219300-01:2

General Information
CircRNA Name	Os03g0219300_circ_g.3
ID in PlantcircBase	osa_circ_018555
Alias	NA
Organism	Oryza sativa
Position	chr3: 6277988-6278845 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0219300
Parent gene annotation	Similar to Tubulin alpha-2 chain (Alpha-2 tubulin). (Os03t021930 0-01)
Parent gene strand	-
Alternative splicing	Os03g0219300_circ_g.4 Os03g0219300_circ_g.5
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	Os03t0219300-01:2

			
						 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  
						
							CTCCAGGTCGACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTG
TTGAATGCATCCCTTGCAATTCCAGGAGTTGTGTCGctgtggtgaaggatatattgtgaacccg
agcttcgacttcctaccgtaatctactgataggcgctccaaaagtaatgaaccaagtccagagc
cggttcct

						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: 415
Transcript exons: 6277988-6278187,6278631-6278845
CTGTGGTGAAGGATATATTGTGAACCCGAGCTTCGACTTCCTACCGTAATCTACTGATAGGCGC
TCCAAAAGTAATGAACCAAGTCCAGAGCCGGTTCCTCCACCAACAGCATTGAAAACCAGAAAAC
CTTGGAGACCAGTGCAGTTATCTGCCAGTTTTCTTAGTCGATCAAGGCAAAGATCTACCACCTC
TCTTCCAACTGTGTAGTGCCCACGAGCAAAGTTGTTAGCAGCGTCTTCCTTGTAGGAGATGAGC
TGCTCTGGGTGGAAGAGCTGGCGGTATGGCCCGGTCTTCACCTCATCAATCACCGTGGGCTCCA
GGTCGACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTGTTGAA
TGCATCCCTTGCAATTCCAGGAGTTGTGTCG
						
						Genomic sequence
						
							CTGTGGTGAAGGATATATTGTGAACCCGAGCTTCGACTTCCTACCGTAATCTACTGATAGGCGC
TCCAAAAGTAATGAACCAAGTCCAGAGCCGGTTCCTCCACCAACAGCATTGAAAACCAGAAAAC
CTTGGAGACCAGTGCAGTTATCTGCCAGTTTTCTTAGTCGATCAAGGCAAAGATCTACCACCTC
TCTTCCAACTGCAGCAGAAAAAAAAAAGGATTTGAATCATTACTAAAAAAATATTTTCATTATA
AAGGAATATGACAGTTTCTCTAGTATGACAATTTATTTATGGAGGAAGCTAAATTTATGGCGTC
ATATTTTTCACTAAAAAATAGTCGGCATGTCGTAAGTTCCTAAATTATTATTACAAGTCACCCC
AAGGATATAAGTTATAAACAATTAATGTTATTCCTTATGTGAGCAATAATCCTTATGGATCCCA
AGGATATGTAAGCAATATCATGGATTCAGACTCCTCTAAATCCACCCAAACCATATCTTTGTGG
ATCAATCATACCTGTAGAATGTTTCTTGTGAATACTATTCTAGTTGGAGTATATCAATATGTTG
GTTTAGACATTTTCATAGACACATTTTATTTCTGCAAAATGGCTCAGTTTCAGGGTAAGCATCA
CACCTGTGTAGTGCCCACGAGCAAAGTTGTTAGCAGCGTCTTCCTTGTAGGAGATGAGCTGCTC
TGGGTGGAAGAGCTGGCGGTATGGCCCGGTCTTCACCTCATCAATCACCGTGGGCTCCAGGTCG
ACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTGTTGAATGCAT
CCCTTGCAATTCCAGGAGTTGTGTCG

Sequences
Splice junction sequence	CTCCAGGTCGACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTG TTGAATGCATCCCTTGCAATTCCAGGAGTTGTGTCGctgtggtgaaggatatattgtgaacccg agcttcgacttcctaccgtaatctactgataggcgctccaaaagtaatgaaccaagtccagagc cggttcct
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: 415 Transcript exons: 6277988-6278187,6278631-6278845 CTGTGGTGAAGGATATATTGTGAACCCGAGCTTCGACTTCCTACCGTAATCTACTGATAGGCGC TCCAAAAGTAATGAACCAAGTCCAGAGCCGGTTCCTCCACCAACAGCATTGAAAACCAGAAAAC CTTGGAGACCAGTGCAGTTATCTGCCAGTTTTCTTAGTCGATCAAGGCAAAGATCTACCACCTC TCTTCCAACTGTGTAGTGCCCACGAGCAAAGTTGTTAGCAGCGTCTTCCTTGTAGGAGATGAGC TGCTCTGGGTGGAAGAGCTGGCGGTATGGCCCGGTCTTCACCTCATCAATCACCGTGGGCTCCA GGTCGACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTGTTGAA TGCATCCCTTGCAATTCCAGGAGTTGTGTCG
Genomic sequence	CTGTGGTGAAGGATATATTGTGAACCCGAGCTTCGACTTCCTACCGTAATCTACTGATAGGCGC TCCAAAAGTAATGAACCAAGTCCAGAGCCGGTTCCTCCACCAACAGCATTGAAAACCAGAAAAC CTTGGAGACCAGTGCAGTTATCTGCCAGTTTTCTTAGTCGATCAAGGCAAAGATCTACCACCTC TCTTCCAACTGCAGCAGAAAAAAAAAAGGATTTGAATCATTACTAAAAAAATATTTTCATTATA AAGGAATATGACAGTTTCTCTAGTATGACAATTTATTTATGGAGGAAGCTAAATTTATGGCGTC ATATTTTTCACTAAAAAATAGTCGGCATGTCGTAAGTTCCTAAATTATTATTACAAGTCACCCC AAGGATATAAGTTATAAACAATTAATGTTATTCCTTATGTGAGCAATAATCCTTATGGATCCCA AGGATATGTAAGCAATATCATGGATTCAGACTCCTCTAAATCCACCCAAACCATATCTTTGTGG ATCAATCATACCTGTAGAATGTTTCTTGTGAATACTATTCTAGTTGGAGTATATCAATATGTTG GTTTAGACATTTTCATAGACACATTTTATTTCTGCAAAATGGCTCAGTTTCAGGGTAAGCATCA CACCTGTGTAGTGCCCACGAGCAAAGTTGTTAGCAGCGTCTTCCTTGTAGGAGATGAGCTGCTC TGGGTGGAAGAGCTGGCGGTATGGCCCGGTCTTCACCTCATCAATCACCGTGGGCTCCAGGTCG ACGAACAACGCCCTTGGGACGTGCTTGCCTGAACTCGTCTCGCTGAAGAACGTGTTGAATGCAT CCCTTGCAATTCCAGGAGTTGTGTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.318466715

Conservation Information
Conserved circRNAs	NA
PMCS	0.318466715

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6278682-6277993(+)
6278815-6278033(+)
						
						Potential amino acid sequence
						
							MSCSGWKSWRYGPVFTSSITVGSRSTNNALGTCLPELVSLKNVLNASLAIPGVVSLW*(+)
MHPLQFQELCRCGEGYIVNPSFDFLP*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6278682-6277993(+) 6278815-6278033(+)
Potential amino acid sequence	MSCSGWKSWRYGPVFTSSITVGSRSTNNALGTCLPELVSLKNVLNASLAIPGVVSLW(+) MHPLQFQELCRCGEGYIVNPSFDFLP(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0219300_circ_g.3

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