Plant Circular RNA Database

Detail information of Os04g0474500_circ_ag.3

			
						 General Information
					
						CircRNA Name
						Os04g0474500_circ_ag.3
					
						ID in PlantcircBase
						osa_circ_024182
					
						Alias
						Os_ciR276
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 23729810-23736592  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						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_g.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_g.3 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
						145/5
					
						Tissues
						root/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
						NA

General Information
CircRNA Name	Os04g0474500_circ_ag.3
ID in PlantcircBase	osa_circ_024182
Alias	Os_ciR276
Organism	Oryza sativa
Position	chr4: 23729810-23736592 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
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_g.1 Os04g0474500_circ_ag.2 Os04g0474500_circ_g.3 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	145/5
Tissues	root/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	NA

			
						 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  
						
							GACCATTCCAGATTGCTCTTTGCTGAACTCTGGCAAGCGATTTCCAACCAATTCTCTCATGCTT
AGTGGGTAGTCTCCTCTAATGAGAGGATCCATAAACcatccaagcatgaagtctagaacacgtc
ttgcagcatcattgctggatttggattgggagaaaggaacaaaccactctgagttcaaaattat
tccaatcc

									
								

					

						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: 686
Transcript exons: 23729810-23729903,23731110-23731286,23731341-23731412,23
731417-23731517,23731650-23731698,23731892-23731924,2373
2170-23732274,23735717-23735771
CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG
GAACAAACCACTCTGAGTTCAAAATTATTCCCTGAATCTCCAACTCTGCATTTTCCCTTCTCCC
AGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATAGCCCATAGAGCAGAAGTTCCAAGG
CTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAACTCTTTGAAGCATATTTCAGCATAG
TCCTTATAGTCATTTAGTAGCTGAAAAGACTATCACAAGGGAGCACTATTGAGGCTGGTGTCAG
TGGAAACAGGGGTTAAATCCTGTAGCAAAACCCGTCCTGACTCCCTTTCCAAAAATAGCAGTAA
ACAATATTCGCGACAAAAATCGGAAAGAGAACTCCAAAAGCTGTTGGCATTGAAATTTCGATGA
TATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGTGCCTGAGCTTCTCTGTTGACTCCACC
GCTGAGACTTCCATTTGGAAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCC
ATCTCCTTCATAATGCGCACATCTTCCTGCAATTTTTTTTGGTGATCAGGCCCTCCCTCATAGC
ACTTAGCAGGGCGAGAAGGTGCTTGTGATAGTATTCGATCCTGGTA
Transcript length: 720
Transcript exons: 23729810-23729901,23731072-23731286,23731650-23731690,23
731893-23731924,23732170-23732283,23735462-23735634,2373
5717-23735769
CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG
GAACAAACCACTCTGAGTTCAAAATTATCAAGTAGTTGGTGATGGCATGCAGTGTAAGGCTCCC
TTCCTGAATCTCCAACTCTGCATTTTCCCTTCTCCCAGGATGAACACCGGCCTGGTGCCATGGT
GCCAGATGCATAGCCCATAGAGCAGAAGTTCCAAGGCTCATTGAAGGTGATCCAATGTTTCACC
CGGTCACCAAACTCTTTGAAGCATATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGC
TAAGAAATCCTTTATATTTATCTTCCAGTTCTCTGTTGACTCCACCGCTGAGACTTCCATTTGG
AAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATAATGCGC
ACATCTTCCTGCAATTTTTTTTGGTGATCAGGCCCTCAGGCCTCAGTTTGATTTCTGGAGGAAC
TTCTTGAACCAACGGGCCGAGTTCTTGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGT
TTATCCCAAACCGAACTGTGTAGCCCTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAA
GTACCCCTTCACGTTTGCTCCATCCCTCCTCATAGCACTTAGCAGGGCGAGAAGGTGCTTGTGA
TAGTATTCGATCCTGG
Transcript length: 782
Transcript exons: 23729810-23730024,23731079-23731286,23731650-23731698,23
731873-23731924,23732170-23732267,23735475-23735634
CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG
GAACAAACCACTCTGAGTTCAAAATTATTCCAATCCTCCCCTTTTGTAAAGCCTGCATTTGATA
TGCATCTTGTTATTCATTGTGTGGTGTGAGTGCTGAAGCTGAAACCAAGTCCATTGATTTGTAA
ACAAAATAAGCACTCAATATGCATTGGTGATGGCATGCAGTGTAAGGCTCCCTTCCTGAATCTC
CAACTCTGCATTTTCCCTTCTCCCAGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATA
GCCCATAGAGCAGAAGTTCCAAGGCTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAAC
TCTTTGAAGCATATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCTT
TATATTTATCTTCCAGTGCCTGAGTTGTTGTAGTAGTTGATGCCTTCTCTGTTGACTCCACCGC
TGAGACTTCCATTTGGAAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCAT
CTCCTTCATAATGCGCACATCTTCCTGCAATTTTTTTTGGTGATCAGGAACTTCTTGAACCAAC
GGGCCGAGTTCTTGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGTTTATCCCAAACCG
AACTGTGTAGCCCTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAAGTACCCCTTCACG
TTTGCTCCATCCCT
Transcript length: 812
Transcript exons: 23729810-23729925,23731125-23731286,23731650-23731696,23
731875-23731924,23732170-23732283,23735482-23735634,2373
5717-23735785,23736473-23736573
CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG
GAACAAACCACTCTGAGTTCAAAATTATTCCAATCCTCCCCTTTTGTAAAGCCTGCATTTTCCC
TTCTCCCAGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATAGCCCATAGAGCAGAAGT
TCCAAGGCTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAACTCTTTGAAGCATATTTC
AGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGT
GCCTGGTTGTAGTAGTTGATGCCTTCTCTGTTGACTCCACCGCTGAGACTTCCATTTGGAAGAA
TTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATAATGCGCACATC
TTCCTGCAATTTTTTTTGGTGATCAGGCCCTCAGGCCTCAGCTTGAACCAACGGGCCGAGTTCT
TGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGTTTATCCCAAACCGAACTGTGTAGCC
CTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAAGTACCCCTTCACGTTTGCTCCATCC
CTCCTCATAGCACTTAGCAGGGCGAGAAGGTGCTTGTGATAGTATTCGATCCTGGTATCATCCT
TCAGGGCATGAAATCGAATGCACCCTTGACCATTCCAGATTGCTCTTTGCTGAACTCTGGCAAG
CGATTTCCAACCAATTCTCTCATGCTTAGTGGGTAGTCTCCTCT
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	GACCATTCCAGATTGCTCTTTGCTGAACTCTGGCAAGCGATTTCCAACCAATTCTCTCATGCTT AGTGGGTAGTCTCCTCTAATGAGAGGATCCATAAACcatccaagcatgaagtctagaacacgtc ttgcagcatcattgctggatttggattgggagaaaggaacaaaccactctgagttcaaaattat tccaatcc
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: 686 Transcript exons: 23729810-23729903,23731110-23731286,23731341-23731412,23 731417-23731517,23731650-23731698,23731892-23731924,2373 2170-23732274,23735717-23735771 CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG GAACAAACCACTCTGAGTTCAAAATTATTCCCTGAATCTCCAACTCTGCATTTTCCCTTCTCCC AGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATAGCCCATAGAGCAGAAGTTCCAAGG CTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAACTCTTTGAAGCATATTTCAGCATAG TCCTTATAGTCATTTAGTAGCTGAAAAGACTATCACAAGGGAGCACTATTGAGGCTGGTGTCAG TGGAAACAGGGGTTAAATCCTGTAGCAAAACCCGTCCTGACTCCCTTTCCAAAAATAGCAGTAA ACAATATTCGCGACAAAAATCGGAAAGAGAACTCCAAAAGCTGTTGGCATTGAAATTTCGATGA TATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGTGCCTGAGCTTCTCTGTTGACTCCACC GCTGAGACTTCCATTTGGAAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCC ATCTCCTTCATAATGCGCACATCTTCCTGCAATTTTTTTTGGTGATCAGGCCCTCCCTCATAGC ACTTAGCAGGGCGAGAAGGTGCTTGTGATAGTATTCGATCCTGGTA Transcript length: 720 Transcript exons: 23729810-23729901,23731072-23731286,23731650-23731690,23 731893-23731924,23732170-23732283,23735462-23735634,2373 5717-23735769 CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG GAACAAACCACTCTGAGTTCAAAATTATCAAGTAGTTGGTGATGGCATGCAGTGTAAGGCTCCC TTCCTGAATCTCCAACTCTGCATTTTCCCTTCTCCCAGGATGAACACCGGCCTGGTGCCATGGT GCCAGATGCATAGCCCATAGAGCAGAAGTTCCAAGGCTCATTGAAGGTGATCCAATGTTTCACC CGGTCACCAAACTCTTTGAAGCATATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGC TAAGAAATCCTTTATATTTATCTTCCAGTTCTCTGTTGACTCCACCGCTGAGACTTCCATTTGG AAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATAATGCGC ACATCTTCCTGCAATTTTTTTTGGTGATCAGGCCCTCAGGCCTCAGTTTGATTTCTGGAGGAAC TTCTTGAACCAACGGGCCGAGTTCTTGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGT TTATCCCAAACCGAACTGTGTAGCCCTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAA GTACCCCTTCACGTTTGCTCCATCCCTCCTCATAGCACTTAGCAGGGCGAGAAGGTGCTTGTGA TAGTATTCGATCCTGG Transcript length: 782 Transcript exons: 23729810-23730024,23731079-23731286,23731650-23731698,23 731873-23731924,23732170-23732267,23735475-23735634 CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG GAACAAACCACTCTGAGTTCAAAATTATTCCAATCCTCCCCTTTTGTAAAGCCTGCATTTGATA TGCATCTTGTTATTCATTGTGTGGTGTGAGTGCTGAAGCTGAAACCAAGTCCATTGATTTGTAA ACAAAATAAGCACTCAATATGCATTGGTGATGGCATGCAGTGTAAGGCTCCCTTCCTGAATCTC CAACTCTGCATTTTCCCTTCTCCCAGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATA GCCCATAGAGCAGAAGTTCCAAGGCTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAAC TCTTTGAAGCATATTTCAGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCTT TATATTTATCTTCCAGTGCCTGAGTTGTTGTAGTAGTTGATGCCTTCTCTGTTGACTCCACCGC TGAGACTTCCATTTGGAAGAATTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCAT CTCCTTCATAATGCGCACATCTTCCTGCAATTTTTTTTGGTGATCAGGAACTTCTTGAACCAAC GGGCCGAGTTCTTGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGTTTATCCCAAACCG AACTGTGTAGCCCTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAAGTACCCCTTCACG TTTGCTCCATCCCT Transcript length: 812 Transcript exons: 23729810-23729925,23731125-23731286,23731650-23731696,23 731875-23731924,23732170-23732283,23735482-23735634,2373 5717-23735785,23736473-23736573 CATCCAAGCATGAAGTCTAGAACACGTCTTGCAGCATCATTGCTGGATTTGGATTGGGAGAAAG GAACAAACCACTCTGAGTTCAAAATTATTCCAATCCTCCCCTTTTGTAAAGCCTGCATTTTCCC TTCTCCCAGGATGAACACCGGCCTGGTGCCATGGTGCCAGATGCATAGCCCATAGAGCAGAAGT TCCAAGGCTCATTGAAGGTGATCCAATGTTTCACCCGGTCACCAAACTCTTTGAAGCATATTTC AGCATAGTCCTTATAGTCATTTATGATATTAGGGCTAAGAAATCCTTTATATTTATCTTCCAGT GCCTGGTTGTAGTAGTTGATGCCTTCTCTGTTGACTCCACCGCTGAGACTTCCATTTGGAAGAA TTCTTGACCACGAGATGGAAAACCTGTATGCATCCATTCCCATCTCCTTCATAATGCGCACATC TTCCTGCAATTTTTTTTGGTGATCAGGCCCTCAGGCCTCAGCTTGAACCAACGGGCCGAGTTCT TGGGGTATCTCTTCATTCCGTCATCGTAATCCACAAAGTTTATCCCAAACCGAACTGTGTAGCC CTCTGCCCACTCAAAGTTGTCAAGCAGAGACCATGCAAAGTACCCCTTCACGTTTGCTCCATCC CTCCTCATAGCACTTAGCAGGGCGAGAAGGTGCTTGTGATAGTATTCGATCCTGGTATCATCCT TCAGGGCATGAAATCGAATGCACCCTTGACCATTCCAGATTGCTCTTTGCTGAACTCTGGCAAG CGATTTCCAACCAATTCTCTCATGCTTAGTGGGTAGTCTCCTCT
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.983069222

Conservation Information
Conserved circRNAs	NA
PMCS	0.983069222

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							osa-miR2868 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	osa-miR2868
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os04g0474500_circ_ag.3

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