Plant Circular RNA Database

Detail information of Os04g0566400_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os04g0566400_circ_g.5
					
						ID in PlantcircBase
						osa_circ_024909
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 28409515-28411606  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os04g0566400						
					
						Parent gene annotation
						
							Similar to INDETERMINATE-related protein 9. (Os04t0566400-01);Si
milar to INDETERMINATE-related protein 9. (Os04t0566400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0566400_circ_g.4 Os04g0566400_circ_g.6 						
					
						Support reads
						8
					
						Tissues
						shoot, 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  
						
							GT-AG							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
						Os04t0566400-02:2
Os04t0566400-01:1

General Information
CircRNA Name	Os04g0566400_circ_g.5
ID in PlantcircBase	osa_circ_024909
Alias	NA
Organism	Oryza sativa
Position	chr4: 28409515-28411606 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os04g0566400
Parent gene annotation	Similar to INDETERMINATE-related protein 9. (Os04t0566400-01);Si milar to INDETERMINATE-related protein 9. (Os04t0566400-02)
Parent gene strand	+
Alternative splicing	Os04g0566400_circ_g.4 Os04g0566400_circ_g.6
Support reads	8
Tissues	shoot, 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	GT-AG 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	Os04t0566400-02:2 Os04t0566400-01:1

			
						 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  
						
							AGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGGCACCCG
CGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAGccaggggggaagaaggaaggaagaagaa
gaacactgctgccaatccgaggaacaatccaacgggggcaacagaaaaggaaattttctgctcc
tgcggttg

									
								

					

						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: 335
Transcript exons: 28409515-28409595,28409622-28409722,28411450-28411602
CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG
GGCAACAGAAAAGGAAAAAAATTTGGGAGGTGATGGCATCGAATTCATCGGCTGCAGCTGCGGC
GGCGTTCTTCGGGATTAGCAGGGATGGGGACCAGCATGACCAGATTAAGCCGCTCCGGCATCAA
GAAGCACTTCTGCCGCAAGCACGGCGAGAAGAAGTGGAAGTGCGACAAGTGCTCCAAGCGCTAC
GCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGGCACCCGCGAGTACCGCTGCGACT
GCGGCACCCTCTTCT
Transcript length: 426
Transcript exons: 28409515-28409697,28411204-28411312,28411473-28411606
CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG
GGCAACAGAAAAGGAAATTTTCTGCTCCTGCGGTTGAGTTGGTAAAATTTGGGAGGTGATGGCA
TCGAATTCATCGGCTGCAGCTGCGGCGGCGTTCTTCGGGATTAGCAGGGATGGGGCAGACCCGG
ACGCGGAGGTGATAGCGCTGTCGCCCAAGACGCTGCTGGCGACGAACCGGTTCGTGTGCGAGGT
GTGCAACAAGGGATTCCAGCGGGAGCAGAACCTACACGCAAGCACGGCGAGAAGAAGTGGAAGT
GCGACAAGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGG
CACCCGCGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAG
						
					

						Genomic sequence
						
							CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG
GGCAACAGAAAAGGAAATTTTCTGCTCCTGCGGTTGAGTTGGTAAAATTTGGGAGGTGATGGCA
TCGAATTCATCGGCTGCAGCTGCGGCGGCGTTCTTCGGGATTAGCAGGGATGGGGACCAGCATG
ACCAGATTAAGCCGCTGATATCACACCAACAGCACCAGCACCAGCAGCAGCAGCTGGCAGCGTC
ACTGACCGGCGTGGCAACAGCGGCGCCTACTGCGGCGTCCAGCCAAGGCGCACCGCCGGCGGCG
CCACCGGCCAAGAAGAAGAGAAATCTACCAGGCAATCCATCCAACCAACCCAAGTACCCTTTTA
CGATTTCAGCCATGCATGCATACATATCTGTTCTCCGAGATCTTGTCTCGATTGATTGGAGTCT
TATCATTTGTTTTCTGACAGTGAAAGCATCTTATCGATCTCACAGGCGCGCTTGATGATTTTCT
TTTTCTCTCTCTATCTAGTCTCTATACTTAATTGTTGCATCTGTTCTTTGGTTTCTTGCTTCCG
AAATATCATTCCTCATCAGTGCTGAATTGCCTGTTTCTTTTTTATGTAGACTGAATTTTGTGAA
CTGGTTCTTTGTCTTTTTGTTTTTTTACCCAGTTCGTACTTCGTCATCTATCTTTTCCTTATTC
CATTTCTTCAGTCTGGAATCTGGATCCCTTCCCTACCATGCATCTAGGCGTCTACCAGTTCAAT
AAAAGCGAATAGACATGAACAACTTGGCTTTCATCAGTTTGCTCCTAGTACTTCATTTAAAGCT
CTGTACTGTCACCTGAAAGAAAGAGAATTAATTCAGGTGAAGAATACAGAAAGTACTCCGTCTT
TCATGGTTAAACTATTCTTTTTTTTCCCTTGTCAAGGAGTATCGATCTCTTGCGTTTTAGTTAG
ATCAATCAGTAGTCCCAGAATTCCCAGTTCTTCCATGAGAAGTTTTAAGAGCATGGGCATAGTT
CCATATATTTCGCAAGATAAAACAAAATCAGTTCATTTTTCAAGATTCCATGCATGTACATGAG
CTGTTATCCTCTTCAGTAGTATAGATCAATATTCTTTTTTCTTCCCCCAATTATGAGAAGCAAA
TAGGAGCCATGGCACACAATCCATGTCTATTCCCTTGTTCTCTATATCTCTTCAAGCAAAGTTC
TTTTTTCCTAAAATCTCATGCAAATATTCCCTTCTCCATGGTCTAGTTTGTCTCTACCTCTCAG
CCCCACCAACAGAAAGAAAAAAAAACATCTTCCCCAAATTAATCCATCATCAGTACTAGCTCCC
ACCACCATTAGTTAATCATGCATGCCTAACTTATAAGCAAACAAATCCAATATAGATAATTGTC
GTGAGATAATTAAGACCCATACTTGTGATAATATATCCCTTCATCGCGACTACTGTTCGATATG
CCTCTTTCCTAATCCACACAAAATGTTGACGACTGCCACTACCTCCATTAACTCCATGCTTGTG
TGTAAAATGGATGCATTGTTTAATTTCTTTGCAAAGTGTCACGCACATATACATATATCTGAAG
CGAAATGTAATATACACATTGATCATCAAGGAATTAATGAGCTGATTAACTGAACTTTGTGTGT
CTTAGTACTGGTTTTTGATTTTCAGCAGACCCGGACGCGGAGGTGATAGCGCTGTCGCCCAAGA
CGCTGCTGGCGACGAACCGGTTCGTGTGCGAGGTGTGCAACAAGGGATTCCAGCGGGAGCAGAA
CCTACAGCTGCACCGGCGAGGCCACAACCTGCCGTGGAAGCTGAAGCAGAAGAACCCGGCGCAG
GCGCAGCGCCGCCGCGTGTACCTGTGCCCGGAGCCGACGTGCGTCCACCACGACCCGGCCCGCG
CCCTCGGCGACCTCACCGGCATCAAGAAGCACTTCTGCCGCAAGCACGGCGAGAAGAAGTGGAA
GTGCGACAAGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGC
GGCACCCGCGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAG
						
					

			
		

Sequences
Splice junction sequence	AGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGGCACCCG CGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAGccaggggggaagaaggaaggaagaagaa gaacactgctgccaatccgaggaacaatccaacgggggcaacagaaaaggaaattttctgctcc tgcggttg
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: 335 Transcript exons: 28409515-28409595,28409622-28409722,28411450-28411602 CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG GGCAACAGAAAAGGAAAAAAATTTGGGAGGTGATGGCATCGAATTCATCGGCTGCAGCTGCGGC GGCGTTCTTCGGGATTAGCAGGGATGGGGACCAGCATGACCAGATTAAGCCGCTCCGGCATCAA GAAGCACTTCTGCCGCAAGCACGGCGAGAAGAAGTGGAAGTGCGACAAGTGCTCCAAGCGCTAC GCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGGCACCCGCGAGTACCGCTGCGACT GCGGCACCCTCTTCT Transcript length: 426 Transcript exons: 28409515-28409697,28411204-28411312,28411473-28411606 CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG GGCAACAGAAAAGGAAATTTTCTGCTCCTGCGGTTGAGTTGGTAAAATTTGGGAGGTGATGGCA TCGAATTCATCGGCTGCAGCTGCGGCGGCGTTCTTCGGGATTAGCAGGGATGGGGCAGACCCGG ACGCGGAGGTGATAGCGCTGTCGCCCAAGACGCTGCTGGCGACGAACCGGTTCGTGTGCGAGGT GTGCAACAAGGGATTCCAGCGGGAGCAGAACCTACACGCAAGCACGGCGAGAAGAAGTGGAAGT GCGACAAGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGCGG CACCCGCGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAG
Genomic sequence	CCAGGGGGGAAGAAGGAAGGAAGAAGAAGAACACTGCTGCCAATCCGAGGAACAATCCAACGGG GGCAACAGAAAAGGAAATTTTCTGCTCCTGCGGTTGAGTTGGTAAAATTTGGGAGGTGATGGCA TCGAATTCATCGGCTGCAGCTGCGGCGGCGTTCTTCGGGATTAGCAGGGATGGGGACCAGCATG ACCAGATTAAGCCGCTGATATCACACCAACAGCACCAGCACCAGCAGCAGCAGCTGGCAGCGTC ACTGACCGGCGTGGCAACAGCGGCGCCTACTGCGGCGTCCAGCCAAGGCGCACCGCCGGCGGCG CCACCGGCCAAGAAGAAGAGAAATCTACCAGGCAATCCATCCAACCAACCCAAGTACCCTTTTA CGATTTCAGCCATGCATGCATACATATCTGTTCTCCGAGATCTTGTCTCGATTGATTGGAGTCT TATCATTTGTTTTCTGACAGTGAAAGCATCTTATCGATCTCACAGGCGCGCTTGATGATTTTCT TTTTCTCTCTCTATCTAGTCTCTATACTTAATTGTTGCATCTGTTCTTTGGTTTCTTGCTTCCG AAATATCATTCCTCATCAGTGCTGAATTGCCTGTTTCTTTTTTATGTAGACTGAATTTTGTGAA CTGGTTCTTTGTCTTTTTGTTTTTTTACCCAGTTCGTACTTCGTCATCTATCTTTTCCTTATTC CATTTCTTCAGTCTGGAATCTGGATCCCTTCCCTACCATGCATCTAGGCGTCTACCAGTTCAAT AAAAGCGAATAGACATGAACAACTTGGCTTTCATCAGTTTGCTCCTAGTACTTCATTTAAAGCT CTGTACTGTCACCTGAAAGAAAGAGAATTAATTCAGGTGAAGAATACAGAAAGTACTCCGTCTT TCATGGTTAAACTATTCTTTTTTTTCCCTTGTCAAGGAGTATCGATCTCTTGCGTTTTAGTTAG ATCAATCAGTAGTCCCAGAATTCCCAGTTCTTCCATGAGAAGTTTTAAGAGCATGGGCATAGTT CCATATATTTCGCAAGATAAAACAAAATCAGTTCATTTTTCAAGATTCCATGCATGTACATGAG CTGTTATCCTCTTCAGTAGTATAGATCAATATTCTTTTTTCTTCCCCCAATTATGAGAAGCAAA TAGGAGCCATGGCACACAATCCATGTCTATTCCCTTGTTCTCTATATCTCTTCAAGCAAAGTTC TTTTTTCCTAAAATCTCATGCAAATATTCCCTTCTCCATGGTCTAGTTTGTCTCTACCTCTCAG CCCCACCAACAGAAAGAAAAAAAAACATCTTCCCCAAATTAATCCATCATCAGTACTAGCTCCC ACCACCATTAGTTAATCATGCATGCCTAACTTATAAGCAAACAAATCCAATATAGATAATTGTC GTGAGATAATTAAGACCCATACTTGTGATAATATATCCCTTCATCGCGACTACTGTTCGATATG CCTCTTTCCTAATCCACACAAAATGTTGACGACTGCCACTACCTCCATTAACTCCATGCTTGTG TGTAAAATGGATGCATTGTTTAATTTCTTTGCAAAGTGTCACGCACATATACATATATCTGAAG CGAAATGTAATATACACATTGATCATCAAGGAATTAATGAGCTGATTAACTGAACTTTGTGTGT CTTAGTACTGGTTTTTGATTTTCAGCAGACCCGGACGCGGAGGTGATAGCGCTGTCGCCCAAGA CGCTGCTGGCGACGAACCGGTTCGTGTGCGAGGTGTGCAACAAGGGATTCCAGCGGGAGCAGAA CCTACAGCTGCACCGGCGAGGCCACAACCTGCCGTGGAAGCTGAAGCAGAAGAACCCGGCGCAG GCGCAGCGCCGCCGCGTGTACCTGTGCCCGGAGCCGACGTGCGTCCACCACGACCCGGCCCGCG CCCTCGGCGACCTCACCGGCATCAAGAAGCACTTCTGCCGCAAGCACGGCGAGAAGAAGTGGAA GTGCGACAAGTGCTCCAAGCGCTACGCTGTCCAGTCCGACTGGAAGGCCCACTCCAAGATCTGC GGCACCCGCGAGTACCGCTGCGACTGCGGCACCCTCTTCTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005665* osi_circ_014665 osi_circ_014666 zma_circ_003237 
						
						PMCS
						0.561576428

Conservation Information
Conserved circRNAs	osi_circ_005665* osi_circ_014665 osi_circ_014666 zma_circ_003237
PMCS	0.561576428

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							osa-miR2093-3p 						
					
						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-miR2093-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0566400_circ_g.5

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