Plant Circular RNA Database

Detail information of Os04g0658300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0658300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_025763
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 33575777-33579041  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						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.3 Os04g0658300_circ_g.4 Os04g0658300_circ_g.5 Os04g0658300_circ_g.6 						
					
						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
						Os04t0658300-01:10

General Information
CircRNA Name	Os04g0658300_circ_g.2
ID in PlantcircBase	osa_circ_025763
Alias	NA
Organism	Oryza sativa
Position	chr4: 33575777-33579041 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
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.3 Os04g0658300_circ_g.4 Os04g0658300_circ_g.5 Os04g0658300_circ_g.6
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	Os04t0658300-01:10

			
						 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
TGGTCGCTTTCTGCCGGTAATCGAACACAATATCCGctttggaggaataaatgttggaagctcc
tctcctttctttcgcttgagaagcttttcatttagttgttcatgaccaccaatctcttctaccc
actgcacc

									
								

					

						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
						
							CTTTGGAGGAATAAATGTTGGAAGCTCCTCTCCTTTCTTTCGCTTGAGAAGCTTTTCATTTAGT
TGTTCATGACCACCAATCTCTTCTACCCACTGCACCCAGGAGATTTCCAGTTTACAGAAAAGTA
TGTCTGAAGTACAATACAGTAACTACTACCCTAATGGTACATTTATCGGAAATACAACTGTTAA
AACTTTTTGGAAAAAAATTGTCTGCTTGTCAAGTTGTTTGGTGCACGCTGTCTCCATACACGCT
GTTTGGTGCACACCAGTACATCTTCAACAGTATTTGCAAAAAAGTACATCTTCAACAACTAAAC
AGAGTAACAGACATGACATTGTTTCACATACAAAAAATCAGGTGAATTTTTTTTCTAAAACGAA
CTGGAAAATAGAATTGCGAACTCTGTCCTAAATCAACACAGGTACCTGCAAGATTGCCCGATCG
TATGTCCTGGATCTCAAAGCTCCATAAAAGTCCAGAGCTGCAGTGGGTTGAGTTCGCTCTTGAA
TATACTTTTCAAATGTAGTTGAAAAATGGATACTTTCTATGCTAAATAATAATAATAACTAGTT
TCCACCAGCAACTGAACAAGGAAAATAATGAAGTTTGAGAAAAGGAAAAAAAGAATAGGTATTT
TGCTTGAGGGAATGATGGCTATGTTACTGTTCTAGTTCCTCTTCTATTTTTCTTTTCCCTACAT
ATCATCTAAGTATGTTTGTATAAAAAGAAACATAGACCTTGTTTCATATGCTGCAAAATGAAAT
TACAGTTCTGGAGAAATGGTTACCTTGGTTTGGAAAAGTGTCTACAACTTTTGATACATCCTCG
AAAGACAAACCATCCTTTATATACATGCGGTGAACAATGTTAATTATATCTTCACGGCCAGGCT
GCCTATTAATCACATATCACATTCAAGTATCATTCTTTGAAGTTTTTTTGCCAAATTAAATCCG
ACTAGTTGTTGCAAATAAAATTCAGTCTGTACTTTGTTGCAACAAAATTTATTCAGATGCAAGA
ACGAACATACCAATAGAACTTTTCCATCCTCCCATCACGAATCAAGGGAGCATACAGTGTCGAA
AAATCATTTCCGGTAACTATTATTGGCACTCTGTGTGTTACATCAGATTCTCTCCATTTCTGGC
CAATGCTAACCCTGGTTGGATTATCCGCCAAGTTCATTAAAGTTCCAATCACAATTTGATTATT
TACTGTCATTTGTGTGTTACCTGAAAACAACGGTGATATATAGCACTTAGTTTGCTGTCAAAAA
GAAATCACCATATGTTCGATGAAAAATAAAACTCTAAGATCCATCTCTTCCTACAAAAGGTGCT
CTTCTTCTGAAGAATATTTGGAAAATAATTAATACACCAGATGAATACACTATTGTAGTATTGT
TGACAGGCTCTCAAAAAGGAAGCATAAACAAAATATCCTAGGTCACTGTGATCAACAATTACCA
TACAAAATATGTTTACAAAACTTACCAAATCTTCCAACACCAGCATCTAGGTCATTGATCATCA
AAACACTCATTTTCCCCTATACCATGAAAAAAATTGTGAAAACAGGAATCATTGAAGTAAACTG
AAAATTAACAAAACCCACAGGCATCATTAATCTGTTAACTTTATCATGATAATACAGTAATAAC
ACAGAAGAGTAAAGCACTACAGAGTTGAGAGCACTTGTATTTCTCATAACGGACAAGCATCAAG
TCATTCAGGAACATTTGCGCTATCTTGATGTATAAAAAAGAAAAAGGAAACACCAAATATTGAA
TCAGCTGTTTGAAAAGATGGTAATAGAAAACTAAAATATGTAAGGAGCATTTTTGCCATATTCA
GAACTGAGTGACAGTAGTAATAGAATTTTCGACAATCTTTTTTTATGATTTCAAGTGTCAATTA
CGAAGCTAGTCAGATACTGGAGCTTTCCACACATACCAAAAAAAAAAAACTCAAACAGGTGAAA
TAACACTCAAGTTTTAAAAATTGAGACATTATTTTGTTTTGTGCTCAAAACTGAGAACTGAATT
TGAAGGTACATATCTGAAACTGAGTAGCCGAAAACACCTGCTTACTTGGTTTTGAATTACTTGA
GAAGCCGTCCTGTATCGGTCACGTATAAGCCTCCCAGGTTCTCCTGCAACAATAGCAGAAACAC
ACATGAGAAACTAATGAACGTGAGACCCTTTGATGATCTACGGAGCACCACATTGATAGCAACC
TTGCAAAATATAGCAGAGTACATAAAGCATGTAAACAGTAAGCACAAATTCAAGTGTCTTTGAC
CTGCTTTCTCAGATTCTAGTTCTCCAGCAGACATAATAACAGGTTCAACACCCATTGCTCTAAA
TATAAGTTCAGTCTGGAATGTTTTCCCTTGGCCTTTTCCACCCCAGATTCCTGCATTGTGCAAT
GTTCCTCAAAAATATTGAAAACGAACTAAAGAATAATATTGAACTACAACCATGTATTATTTCA
TATCCCAATTACACAGAGAGAAACAAAGAGAAGTGCACTACCAAGTATAAGGGGAATCTTGATA
GTAAGAATATGTGCAAGGTAGTTCTTCACAATATGACATGCTGCAAACATCAAGCAGTCCTTTT
AGTATGTGTGCCTGGAGAAAAAGAATAAAATAAATTTGTCATGCACACTATAGCCACAAGAATA
TATACCATATAAAAGTTCAAGATATTATTAAGGAAGAGTTTAGCATAATCACAATTAATGTAAA
TGTAAGATTTGCATATATTTCACATGCTGCCAACATTGCATGCCATTATTTGATAGTTTGACCC
AAAAATATATATATTCAGTCTAGGCCTCTAGGGACTGTTGGTATATGGTGGTAAGCTTATTCGG
CAACTGTTACACCTTTGTATAACTTGTTCAGTTTCTTATACAGAAGGACACTGATACTTCAGTA
GCCACTGTTTATGCAGGTGAAACGAAAGATGTAGTCTCTTCAAACTGTAAGAGTGAGATACCTG
ATTATAACAATGTGCTTCCTCCTACATTAAATTGCTTACCAACTTTATCCTGCACCACAACGAA
TCTGCAGTGTCAAATCTTTGTCAATCAGGTACCTAGAACAGCATAAAAGTACGAGGATGCAGTA
AAAAAAAAAAGATCAGCTGAAGATGAACTAAAATTACACTCACAAGGAAGAGGGGTGCGATGTA
ATAATCTCCTTGCAGGTACTCAAACGTCCTGGTCGCTTTCTGCCGGTAATCGAACACAATATCC
G
						
					

			
		

Sequences
Splice junction sequence	AAAATTACACTCACAAGGAAGAGGGGTGCGATGTAATAATCTCCTTGCAGGTACTCAAACGTCC TGGTCGCTTTCTGCCGGTAATCGAACACAATATCCGctttggaggaataaatgttggaagctcc tctcctttctttcgcttgagaagcttttcatttagttgttcatgaccaccaatctcttctaccc actgcacc
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	CTTTGGAGGAATAAATGTTGGAAGCTCCTCTCCTTTCTTTCGCTTGAGAAGCTTTTCATTTAGT TGTTCATGACCACCAATCTCTTCTACCCACTGCACCCAGGAGATTTCCAGTTTACAGAAAAGTA TGTCTGAAGTACAATACAGTAACTACTACCCTAATGGTACATTTATCGGAAATACAACTGTTAA AACTTTTTGGAAAAAAATTGTCTGCTTGTCAAGTTGTTTGGTGCACGCTGTCTCCATACACGCT GTTTGGTGCACACCAGTACATCTTCAACAGTATTTGCAAAAAAGTACATCTTCAACAACTAAAC AGAGTAACAGACATGACATTGTTTCACATACAAAAAATCAGGTGAATTTTTTTTCTAAAACGAA CTGGAAAATAGAATTGCGAACTCTGTCCTAAATCAACACAGGTACCTGCAAGATTGCCCGATCG TATGTCCTGGATCTCAAAGCTCCATAAAAGTCCAGAGCTGCAGTGGGTTGAGTTCGCTCTTGAA TATACTTTTCAAATGTAGTTGAAAAATGGATACTTTCTATGCTAAATAATAATAATAACTAGTT TCCACCAGCAACTGAACAAGGAAAATAATGAAGTTTGAGAAAAGGAAAAAAAGAATAGGTATTT TGCTTGAGGGAATGATGGCTATGTTACTGTTCTAGTTCCTCTTCTATTTTTCTTTTCCCTACAT ATCATCTAAGTATGTTTGTATAAAAAGAAACATAGACCTTGTTTCATATGCTGCAAAATGAAAT TACAGTTCTGGAGAAATGGTTACCTTGGTTTGGAAAAGTGTCTACAACTTTTGATACATCCTCG AAAGACAAACCATCCTTTATATACATGCGGTGAACAATGTTAATTATATCTTCACGGCCAGGCT GCCTATTAATCACATATCACATTCAAGTATCATTCTTTGAAGTTTTTTTGCCAAATTAAATCCG ACTAGTTGTTGCAAATAAAATTCAGTCTGTACTTTGTTGCAACAAAATTTATTCAGATGCAAGA ACGAACATACCAATAGAACTTTTCCATCCTCCCATCACGAATCAAGGGAGCATACAGTGTCGAA AAATCATTTCCGGTAACTATTATTGGCACTCTGTGTGTTACATCAGATTCTCTCCATTTCTGGC CAATGCTAACCCTGGTTGGATTATCCGCCAAGTTCATTAAAGTTCCAATCACAATTTGATTATT TACTGTCATTTGTGTGTTACCTGAAAACAACGGTGATATATAGCACTTAGTTTGCTGTCAAAAA GAAATCACCATATGTTCGATGAAAAATAAAACTCTAAGATCCATCTCTTCCTACAAAAGGTGCT CTTCTTCTGAAGAATATTTGGAAAATAATTAATACACCAGATGAATACACTATTGTAGTATTGT TGACAGGCTCTCAAAAAGGAAGCATAAACAAAATATCCTAGGTCACTGTGATCAACAATTACCA TACAAAATATGTTTACAAAACTTACCAAATCTTCCAACACCAGCATCTAGGTCATTGATCATCA AAACACTCATTTTCCCCTATACCATGAAAAAAATTGTGAAAACAGGAATCATTGAAGTAAACTG AAAATTAACAAAACCCACAGGCATCATTAATCTGTTAACTTTATCATGATAATACAGTAATAAC ACAGAAGAGTAAAGCACTACAGAGTTGAGAGCACTTGTATTTCTCATAACGGACAAGCATCAAG TCATTCAGGAACATTTGCGCTATCTTGATGTATAAAAAAGAAAAAGGAAACACCAAATATTGAA TCAGCTGTTTGAAAAGATGGTAATAGAAAACTAAAATATGTAAGGAGCATTTTTGCCATATTCA GAACTGAGTGACAGTAGTAATAGAATTTTCGACAATCTTTTTTTATGATTTCAAGTGTCAATTA CGAAGCTAGTCAGATACTGGAGCTTTCCACACATACCAAAAAAAAAAAACTCAAACAGGTGAAA TAACACTCAAGTTTTAAAAATTGAGACATTATTTTGTTTTGTGCTCAAAACTGAGAACTGAATT TGAAGGTACATATCTGAAACTGAGTAGCCGAAAACACCTGCTTACTTGGTTTTGAATTACTTGA GAAGCCGTCCTGTATCGGTCACGTATAAGCCTCCCAGGTTCTCCTGCAACAATAGCAGAAACAC ACATGAGAAACTAATGAACGTGAGACCCTTTGATGATCTACGGAGCACCACATTGATAGCAACC TTGCAAAATATAGCAGAGTACATAAAGCATGTAAACAGTAAGCACAAATTCAAGTGTCTTTGAC CTGCTTTCTCAGATTCTAGTTCTCCAGCAGACATAATAACAGGTTCAACACCCATTGCTCTAAA TATAAGTTCAGTCTGGAATGTTTTCCCTTGGCCTTTTCCACCCCAGATTCCTGCATTGTGCAAT GTTCCTCAAAAATATTGAAAACGAACTAAAGAATAATATTGAACTACAACCATGTATTATTTCA TATCCCAATTACACAGAGAGAAACAAAGAGAAGTGCACTACCAAGTATAAGGGGAATCTTGATA GTAAGAATATGTGCAAGGTAGTTCTTCACAATATGACATGCTGCAAACATCAAGCAGTCCTTTT AGTATGTGTGCCTGGAGAAAAAGAATAAAATAAATTTGTCATGCACACTATAGCCACAAGAATA TATACCATATAAAAGTTCAAGATATTATTAAGGAAGAGTTTAGCATAATCACAATTAATGTAAA TGTAAGATTTGCATATATTTCACATGCTGCCAACATTGCATGCCATTATTTGATAGTTTGACCC AAAAATATATATATTCAGTCTAGGCCTCTAGGGACTGTTGGTATATGGTGGTAAGCTTATTCGG CAACTGTTACACCTTTGTATAACTTGTTCAGTTTCTTATACAGAAGGACACTGATACTTCAGTA GCCACTGTTTATGCAGGTGAAACGAAAGATGTAGTCTCTTCAAACTGTAAGAGTGAGATACCTG ATTATAACAATGTGCTTCCTCCTACATTAAATTGCTTACCAACTTTATCCTGCACCACAACGAA TCTGCAGTGTCAAATCTTTGTCAATCAGGTACCTAGAACAGCATAAAAGTACGAGGATGCAGTA AAAAAAAAAAGATCAGCTGAAGATGAACTAAAATTACACTCACAAGGAAGAGGGGTGCGATGTA ATAATCTCCTTGCAGGTACTCAAACGTCCTGGTCGCTTTCTGCCGGTAATCGAACACAATATCC G

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.113660487

Conservation Information
Conserved circRNAs	NA
PMCS	0.113660487

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33578346-33575846(+)
33578375-33575836(+)
33575837-33578998(-)
33578137-33578364(-)
						
						Potential amino acid sequence
						
							MCKVVLHNMTCNFIKEEGCDVIISLQVLKRPGRFLPVIEHNIRFGGINVGSSSPFFRLRSFSFS
CS*(+)
MQLYQGRGVRCNNLLAGTQTSWSLSAGNRTQYPLWRNKCWKLLSFLSLEKLFI*(+)
MKSFSSERKERSFQHLFLQSGYCVRLPAESDQDV*(-)
MGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFGNTQMTV
NNQIVIGTLMNLADNPTRVSIGQKWRESDVTHRVPIIVTGNDFSTLYAPLIRDGRMEKFYWQPG
REDIINIVHRMYIKDGLSFEDVSKVVDTFPNQALDFYGALRSRTYDRAILQWVEEIGGHEQLNE
KLLKRKKGEELPTFIPPKRILCSITGRKRPGRLSTCKEIITSHPSSLIKLHVIL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33578346-33575846(+) 33578375-33575836(+) 33575837-33578998(-) 33578137-33578364(-)
Potential amino acid sequence	MCKVVLHNMTCNFIKEEGCDVIISLQVLKRPGRFLPVIEHNIRFGGINVGSSSPFFRLRSFSFS CS(+) MQLYQGRGVRCNNLLAGTQTSWSLSAGNRTQYPLWRNKCWKLLSFLSLEKLFI(+) MKSFSSERKERSFQHLFLQSGYCVRLPAESDQDV(-) MGVEPVIMSAGELESEKAGEPGRLIRDRYRTASQVIQNQGKMSVLMINDLDAGVGRFGNTQMTV NNQIVIGTLMNLADNPTRVSIGQKWRESDVTHRVPIIVTGNDFSTLYAPLIRDGRMEKFYWQPG REDIINIVHRMYIKDGLSFEDVSKVVDTFPNQALDFYGALRSRTYDRAILQWVEEIGGHEQLNE KLLKRKKGEELPTFIPPKRILCSITGRKRPGRLSTCKEIITSHPSSLIKLHVIL(-)
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.2

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