Plant Circular RNA Database

Detail information of Os04g0658300_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os04g0658300_circ_g.6
					
						ID in PlantcircBase
						osa_circ_025767
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 33577274-33579041  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os04g0658300						
					
						Parent gene annotation
						
							Similar to Ribulose bisphosphate carboxylase/oxygenase activase,
 chloroplast precursor (RuBisCO activase) (RA). (Os04t0658300-01
)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0658300_circ_g.1 Os04g0658300_circ_g.2 Os04g0658300_circ_g.3 Os04g0658300_circ_g.4 Os04g0658300_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						seed
					
						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
						Os04t0658300-01:6

General Information
CircRNA Name	Os04g0658300_circ_g.6
ID in PlantcircBase	osa_circ_025767
Alias	NA
Organism	Oryza sativa
Position	chr4: 33577274-33579041 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os04g0658300
Parent gene annotation	Similar to Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA). (Os04t0658300-01 )
Parent gene strand	-
Alternative splicing	Os04g0658300_circ_g.1 Os04g0658300_circ_g.2 Os04g0658300_circ_g.3 Os04g0658300_circ_g.4 Os04g0658300_circ_g.5
Support reads	1
Tissues	seed
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	Os04t0658300-01:6

			
						 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  
						
							AAAATTACACTCACAAGGAAGAGGGGTGCGATGTAATAATCTCCTTGCAGGTACTCAAACGTCC
TGGTCGCTTTCTGCCGGTAATCGAACACAATATCCGcaaatcttccaacaccagcatctaggtc
attgatcatcaaaacactcattttcccctataccatgaaaaaaattgtgaaaacaggaatcatt
gaagtaaa

									
								

					

						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
						
							CAAATCTTCCAACACCAGCATCTAGGTCATTGATCATCAAAACACTCATTTTCCCCTATACCAT
GAAAAAAATTGTGAAAACAGGAATCATTGAAGTAAACTGAAAATTAACAAAACCCACAGGCATC
ATTAATCTGTTAACTTTATCATGATAATACAGTAATAACACAGAAGAGTAAAGCACTACAGAGT
TGAGAGCACTTGTATTTCTCATAACGGACAAGCATCAAGTCATTCAGGAACATTTGCGCTATCT
TGATGTATAAAAAAGAAAAAGGAAACACCAAATATTGAATCAGCTGTTTGAAAAGATGGTAATA
GAAAACTAAAATATGTAAGGAGCATTTTTGCCATATTCAGAACTGAGTGACAGTAGTAATAGAA
TTTTCGACAATCTTTTTTTATGATTTCAAGTGTCAATTACGAAGCTAGTCAGATACTGGAGCTT
TCCACACATACCAAAAAAAAAAAACTCAAACAGGTGAAATAACACTCAAGTTTTAAAAATTGAG
ACATTATTTTGTTTTGTGCTCAAAACTGAGAACTGAATTTGAAGGTACATATCTGAAACTGAGT
AGCCGAAAACACCTGCTTACTTGGTTTTGAATTACTTGAGAAGCCGTCCTGTATCGGTCACGTA
TAAGCCTCCCAGGTTCTCCTGCAACAATAGCAGAAACACACATGAGAAACTAATGAACGTGAGA
CCCTTTGATGATCTACGGAGCACCACATTGATAGCAACCTTGCAAAATATAGCAGAGTACATAA
AGCATGTAAACAGTAAGCACAAATTCAAGTGTCTTTGACCTGCTTTCTCAGATTCTAGTTCTCC
AGCAGACATAATAACAGGTTCAACACCCATTGCTCTAAATATAAGTTCAGTCTGGAATGTTTTC
CCTTGGCCTTTTCCACCCCAGATTCCTGCATTGTGCAATGTTCCTCAAAAATATTGAAAACGAA
CTAAAGAATAATATTGAACTACAACCATGTATTATTTCATATCCCAATTACACAGAGAGAAACA
AAGAGAAGTGCACTACCAAGTATAAGGGGAATCTTGATAGTAAGAATATGTGCAAGGTAGTTCT
TCACAATATGACATGCTGCAAACATCAAGCAGTCCTTTTAGTATGTGTGCCTGGAGAAAAAGAA
TAAAATAAATTTGTCATGCACACTATAGCCACAAGAATATATACCATATAAAAGTTCAAGATAT
TATTAAGGAAGAGTTTAGCATAATCACAATTAATGTAAATGTAAGATTTGCATATATTTCACAT
GCTGCCAACATTGCATGCCATTATTTGATAGTTTGACCCAAAAATATATATATTCAGTCTAGGC
CTCTAGGGACTGTTGGTATATGGTGGTAAGCTTATTCGGCAACTGTTACACCTTTGTATAACTT
GTTCAGTTTCTTATACAGAAGGACACTGATACTTCAGTAGCCACTGTTTATGCAGGTGAAACGA
AAGATGTAGTCTCTTCAAACTGTAAGAGTGAGATACCTGATTATAACAATGTGCTTCCTCCTAC
ATTAAATTGCTTACCAACTTTATCCTGCACCACAACGAATCTGCAGTGTCAAATCTTTGTCAAT
CAGGTACCTAGAACAGCATAAAAGTACGAGGATGCAGTAAAAAAAAAAAGATCAGCTGAAGATG
AACTAAAATTACACTCACAAGGAAGAGGGGTGCGATGTAATAATCTCCTTGCAGGTACTCAAAC
GTCCTGGTCGCTTTCTGCCGGTAATCGAACACAATATCCG
						
					

			
		

Sequences
Splice junction sequence	AAAATTACACTCACAAGGAAGAGGGGTGCGATGTAATAATCTCCTTGCAGGTACTCAAACGTCC TGGTCGCTTTCTGCCGGTAATCGAACACAATATCCGcaaatcttccaacaccagcatctaggtc attgatcatcaaaacactcattttcccctataccatgaaaaaaattgtgaaaacaggaatcatt gaagtaaa
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	CAAATCTTCCAACACCAGCATCTAGGTCATTGATCATCAAAACACTCATTTTCCCCTATACCAT GAAAAAAATTGTGAAAACAGGAATCATTGAAGTAAACTGAAAATTAACAAAACCCACAGGCATC ATTAATCTGTTAACTTTATCATGATAATACAGTAATAACACAGAAGAGTAAAGCACTACAGAGT TGAGAGCACTTGTATTTCTCATAACGGACAAGCATCAAGTCATTCAGGAACATTTGCGCTATCT TGATGTATAAAAAAGAAAAAGGAAACACCAAATATTGAATCAGCTGTTTGAAAAGATGGTAATA GAAAACTAAAATATGTAAGGAGCATTTTTGCCATATTCAGAACTGAGTGACAGTAGTAATAGAA TTTTCGACAATCTTTTTTTATGATTTCAAGTGTCAATTACGAAGCTAGTCAGATACTGGAGCTT TCCACACATACCAAAAAAAAAAAACTCAAACAGGTGAAATAACACTCAAGTTTTAAAAATTGAG ACATTATTTTGTTTTGTGCTCAAAACTGAGAACTGAATTTGAAGGTACATATCTGAAACTGAGT AGCCGAAAACACCTGCTTACTTGGTTTTGAATTACTTGAGAAGCCGTCCTGTATCGGTCACGTA TAAGCCTCCCAGGTTCTCCTGCAACAATAGCAGAAACACACATGAGAAACTAATGAACGTGAGA CCCTTTGATGATCTACGGAGCACCACATTGATAGCAACCTTGCAAAATATAGCAGAGTACATAA AGCATGTAAACAGTAAGCACAAATTCAAGTGTCTTTGACCTGCTTTCTCAGATTCTAGTTCTCC AGCAGACATAATAACAGGTTCAACACCCATTGCTCTAAATATAAGTTCAGTCTGGAATGTTTTC CCTTGGCCTTTTCCACCCCAGATTCCTGCATTGTGCAATGTTCCTCAAAAATATTGAAAACGAA CTAAAGAATAATATTGAACTACAACCATGTATTATTTCATATCCCAATTACACAGAGAGAAACA AAGAGAAGTGCACTACCAAGTATAAGGGGAATCTTGATAGTAAGAATATGTGCAAGGTAGTTCT TCACAATATGACATGCTGCAAACATCAAGCAGTCCTTTTAGTATGTGTGCCTGGAGAAAAAGAA TAAAATAAATTTGTCATGCACACTATAGCCACAAGAATATATACCATATAAAAGTTCAAGATAT TATTAAGGAAGAGTTTAGCATAATCACAATTAATGTAAATGTAAGATTTGCATATATTTCACAT GCTGCCAACATTGCATGCCATTATTTGATAGTTTGACCCAAAAATATATATATTCAGTCTAGGC CTCTAGGGACTGTTGGTATATGGTGGTAAGCTTATTCGGCAACTGTTACACCTTTGTATAACTT GTTCAGTTTCTTATACAGAAGGACACTGATACTTCAGTAGCCACTGTTTATGCAGGTGAAACGA AAGATGTAGTCTCTTCAAACTGTAAGAGTGAGATACCTGATTATAACAATGTGCTTCCTCCTAC ATTAAATTGCTTACCAACTTTATCCTGCACCACAACGAATCTGCAGTGTCAAATCTTTGTCAAT CAGGTACCTAGAACAGCATAAAAGTACGAGGATGCAGTAAAAAAAAAAAGATCAGCTGAAGATG AACTAAAATTACACTCACAAGGAAGAGGGGTGCGATGTAATAATCTCCTTGCAGGTACTCAAAC GTCCTGGTCGCTTTCTGCCGGTAATCGAACACAATATCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.129153931

Conservation Information
Conserved circRNAs	NA
PMCS	0.129153931

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33578375-33577303(+)
33578346-33577295(+)
33577296-33578364(-)
33578137-33577276(-)
						
						Potential amino acid sequence
						
							MQLYQGRGVRCNNLLAGTQTSWSLSAGNRTQYPQIFQHQHLGH*(+)
MCKVVLHNMTCNFIKEEGCDVIISLQVLKRPGRFLPVIEHNIRKSSNTSI*(+)
MLVLEDLRILCSITGRKRPGRLSTCKEIITSHPSSLIKLHVIL*(-)
MGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADIVFDY
RQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQTELIF
RAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADIVF
DYRQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQTEL
IFRAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADI
VFDYRQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQT
ELIFRAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRF(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33578375-33577303(+) 33578346-33577295(+) 33577296-33578364(-) 33578137-33577276(-)
Potential amino acid sequence	MQLYQGRGVRCNNLLAGTQTSWSLSAGNRTQYPQIFQHQHLGH(+) MCKVVLHNMTCNFIKEEGCDVIISLQVLKRPGRFLPVIEHNIRKSSNTSI(+) MLVLEDLRILCSITGRKRPGRLSTCKEIITSHPSSLIKLHVIL*(-) MGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADIVFDY RQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQTELIF RAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADIVF DYRQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQTEL IFRAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFADI VFDYRQKATRTFEYLQGDYYIAPLFLDKVACHIVKNYLAHILTIKIPLILGIWGGKGQGKTFQT ELIFRAMGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRF( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0658300_circ_g.6

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