Plant Circular RNA Database

Detail information of Os03g0639200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0639200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_020736
					
						Alias
						Os_ciR4731
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 24520088-24522348  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os03g0639200						
					
						Parent gene annotation
						
							Similar to DIRP family protein, expressed. (Os03t0639200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0639200_circ_g.2 						
					
						Support reads
						4
					
						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  
						
							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
						Os03t0639200-01:4

General Information
CircRNA Name	Os03g0639200_circ_g.1
ID in PlantcircBase	osa_circ_020736
Alias	Os_ciR4731
Organism	Oryza sativa
Position	chr3: 24520088-24522348 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Os03g0639200
Parent gene annotation	Similar to DIRP family protein, expressed. (Os03t0639200-01)
Parent gene strand	+
Alternative splicing	Os03g0639200_circ_g.2
Support reads	4
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	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	Os03t0639200-01:4

			
						 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  
						
							CTAAGTTCTGTGGCATGCGCAGGCATATTTATCTCTTCCTGAGGGAACAGCTACTGCTGCAGGG
TTAATTGCAATGATGACTGATCACTATAATATTCTGgcaggctctgtgtgactgactttcaatg
tcttctacaaggaaagtgagaaatgtgaataaacgatatgccaaaataaatgaagattggcagg
acaaagat

									
								

					

						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: 370
Transcript exons: 24520088-24520217,24521180-24521278,24521445-24521507,24
522271-24522348
GCAGGCTCTGTGTGACTGACTTTCAATGTCTTCTACAAGGAAAGTGAGAAATGTGAATAAACGA
TATGCCAAAATAAATGAAGATTGGCAGGACAAAGATGCAACAAATGTGCATAAAAGTAAAGTGC
GAAAGAAAAAACTGTCTGACATGCTAGGTTCTCAATGGAGCAAAGATGAGCTAGAGCGTTTTTA
TGGATCCTATAGAAAATATGGAAAAGATTGGAGAAAGGTGGCCAGTTCTATCCGTGATAGAACA
TCTGAAATGGTGGAGGCTCTTTACAACATGAATAAGGCATATTTATCTCTTCCTGAGGGAACAG
CTACTGCTGCAGGGTTAATTGCAATGATGACTGATCACTATAATATTCTG
						
					

						Genomic sequence
						
							GCAGGCTCTGTGTGACTGACTTTCAATGTCTTCTACAAGGAAAGTGAGAAATGTGAATAAACGA
TATGCCAAAATAAATGAAGATTGGCAGGACAAAGATGCAACAAATGTGCATAAAAGTAAAGTGC
GAGTAAGTATCTATATTCTGCAGTCCTGAATATGGCAAAGCTATTTAAAAATGTACGTGTGTGA
CAAATGAGTGTACTGTTGGCAATGGCAGCCCTAAATTACATGTGAGTAAGCCAGTAATATGATA
TGCACTTAAAATTAGCCTTTTGGTTTATGGAAGTGTAACTCTGGCATGGGACACAGGAATCGAA
ATCCATGGATTTGGTCTTTGGCTTGGCAACTTCAATATGATTCAAGGATACGTCTAACATAATT
AATTTTATTATAAAAAGTTTCATTACCACAGTTATTAATGTTCAACAAATTTTTATATTGCCTT
AGCCATAGAAGATTGGTCTAGTTTTTTTTTTGTCCCTATGAGCACATGTGTCCCTCAAGTTAAG
AGGAAATTAGCATCCGCCACAATAAAAATATGGTAGCAAAGGCTTCACTTCACACTCTTTAATT
CCAATCCTTCTCCGGTTCTCCCTCCCCAGATTCCCCACCCCGCAACCAGCTGTACACCCACCTA
ACTAAGGAACACATTCTTTTCTGACAGCTGATCAGACTGAGCTGGGAAGTGTAAGATGCATGAC
TTGACTTGACTTGATATGCCAGCATTATTCATGCACGCATATCTGCCATATAGTGATATAAATA
TAATCAGTTATACTAACAATATACGTAAAACATACTCTGTGAATCAGCAAATCGATATTATTTT
TTCACATGCAACCTCTCTTTTTTTTTCTTCTTATCCTATAAATAAGACCTGCTTCTTTACTTGA
TATGTGATATTACGGAGTGTAAACTTTAAATAAAAGTTGGACCATTGAGATGCATTAGAGTTAT
ACAAGGGGAAAAGTTCAGTTTTGTGCTTGGCTTTGTCGACTGCTAATGCATTTATCTGTTTTAA
GTTGTTGATTCTGTTATACTCAATCATACCAACTGCGCTGCTTATTGATCAATGAGTATTATTT
GCAGAAGAAAAAACTGTCTGACATGCTAGGTTCTCAATGGAGCAAAGATGAGCTAGAGCGTTTT
TATGGATCCTATAGAAAATATGGAAAAGATTGGAGAAAGGTTTGCTTTATGCTGTATTTATTAT
GAAATGTTATTTATTTTATGAAGCAGATGTTGCTTCAGGAATCAAAACTTGGAATTTAGGCTAT
AATTAAAACTTTAGTTGTACTTGTTCTGCACTCAGACATGCCCCTTTGGAGTACTGAATGCCCA
TTTCGTTTTGCAGGTGGCCAGTTCTATCCGTGATAGAACATCTGAAATGGTGGAGGCTCTTTAC
AACATGAATAAGGTAAATCCTAGTCTTGTGTATGAATGGCCCTTCAGATTGCATAATTTTAAGG
ATCCACTATCTACCCCCTTGTTACAATTTCAAACTCTGACTCTAAATTATGACATCAGTTTTTT
CGGGTATGATTCTGTTTCTTGTATGTTACTAGGATAGTTTCTAGTAGCTCATCTTTTTAAAAGG
AATAATTTCCAGCAACAACACTATAGTTTTCCACTTCTACTGCAACATGAGAAGTTCACATGTC
GTTTTCTGTTAGCTGTACCATTTGCTGTTTTGTAAGGCTTCAGATCCCACTTATTTGATCTGTC
CTTTCTCCTCCTATATATCTATTTAGGCCCTCTTTATTTAGGCTTATAAACCGGCTTATGAGCC
GAAAAGTCTAAGCTTTTTCGTTTGTTTTTTTTAAAGCCATAAGCCACTCTTACACTATTAAGCC
AAAAGCAAGGTTGAAGTAGTTCTTTTGTCTTATGTGAAGTGGAGGTATGACTCCTCCATTAAAC
TTAAGGCTTCAAAGCCACCGACTTATAAAACATACAGACAAAAAAGTTGGCTTAAATGCAACAT
ACAGGCAAAAAAGTTGGCTTAAATGCCTAAGTCAATAAGCCTAAGCCTAAACAAAGAGCCTGCA
GATCTGTTCAGTAGACCTCTTAAGTAGTAACACTCAATATTTCTGGTTCATGTTTTTGGTCAAT
GGTTCTCTCACAATTTTTCTTACACTTTGTCTATGCTGATATAAATTAACTAAGTTCTGTGGCA
TGCGCAGGCATATTTATCTCTTCCTGAGGGAACAGCTACTGCTGCAGGGTTAATTGCAATGATG
ACTGATCACTATAATATTCTG
						
					

			
		

Sequences
Splice junction sequence	CTAAGTTCTGTGGCATGCGCAGGCATATTTATCTCTTCCTGAGGGAACAGCTACTGCTGCAGGG TTAATTGCAATGATGACTGATCACTATAATATTCTGgcaggctctgtgtgactgactttcaatg tcttctacaaggaaagtgagaaatgtgaataaacgatatgccaaaataaatgaagattggcagg acaaagat
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: 370 Transcript exons: 24520088-24520217,24521180-24521278,24521445-24521507,24 522271-24522348 GCAGGCTCTGTGTGACTGACTTTCAATGTCTTCTACAAGGAAAGTGAGAAATGTGAATAAACGA TATGCCAAAATAAATGAAGATTGGCAGGACAAAGATGCAACAAATGTGCATAAAAGTAAAGTGC GAAAGAAAAAACTGTCTGACATGCTAGGTTCTCAATGGAGCAAAGATGAGCTAGAGCGTTTTTA TGGATCCTATAGAAAATATGGAAAAGATTGGAGAAAGGTGGCCAGTTCTATCCGTGATAGAACA TCTGAAATGGTGGAGGCTCTTTACAACATGAATAAGGCATATTTATCTCTTCCTGAGGGAACAG CTACTGCTGCAGGGTTAATTGCAATGATGACTGATCACTATAATATTCTG
Genomic sequence	GCAGGCTCTGTGTGACTGACTTTCAATGTCTTCTACAAGGAAAGTGAGAAATGTGAATAAACGA TATGCCAAAATAAATGAAGATTGGCAGGACAAAGATGCAACAAATGTGCATAAAAGTAAAGTGC GAGTAAGTATCTATATTCTGCAGTCCTGAATATGGCAAAGCTATTTAAAAATGTACGTGTGTGA CAAATGAGTGTACTGTTGGCAATGGCAGCCCTAAATTACATGTGAGTAAGCCAGTAATATGATA TGCACTTAAAATTAGCCTTTTGGTTTATGGAAGTGTAACTCTGGCATGGGACACAGGAATCGAA ATCCATGGATTTGGTCTTTGGCTTGGCAACTTCAATATGATTCAAGGATACGTCTAACATAATT AATTTTATTATAAAAAGTTTCATTACCACAGTTATTAATGTTCAACAAATTTTTATATTGCCTT AGCCATAGAAGATTGGTCTAGTTTTTTTTTTGTCCCTATGAGCACATGTGTCCCTCAAGTTAAG AGGAAATTAGCATCCGCCACAATAAAAATATGGTAGCAAAGGCTTCACTTCACACTCTTTAATT CCAATCCTTCTCCGGTTCTCCCTCCCCAGATTCCCCACCCCGCAACCAGCTGTACACCCACCTA ACTAAGGAACACATTCTTTTCTGACAGCTGATCAGACTGAGCTGGGAAGTGTAAGATGCATGAC TTGACTTGACTTGATATGCCAGCATTATTCATGCACGCATATCTGCCATATAGTGATATAAATA TAATCAGTTATACTAACAATATACGTAAAACATACTCTGTGAATCAGCAAATCGATATTATTTT TTCACATGCAACCTCTCTTTTTTTTTCTTCTTATCCTATAAATAAGACCTGCTTCTTTACTTGA TATGTGATATTACGGAGTGTAAACTTTAAATAAAAGTTGGACCATTGAGATGCATTAGAGTTAT ACAAGGGGAAAAGTTCAGTTTTGTGCTTGGCTTTGTCGACTGCTAATGCATTTATCTGTTTTAA GTTGTTGATTCTGTTATACTCAATCATACCAACTGCGCTGCTTATTGATCAATGAGTATTATTT GCAGAAGAAAAAACTGTCTGACATGCTAGGTTCTCAATGGAGCAAAGATGAGCTAGAGCGTTTT TATGGATCCTATAGAAAATATGGAAAAGATTGGAGAAAGGTTTGCTTTATGCTGTATTTATTAT GAAATGTTATTTATTTTATGAAGCAGATGTTGCTTCAGGAATCAAAACTTGGAATTTAGGCTAT AATTAAAACTTTAGTTGTACTTGTTCTGCACTCAGACATGCCCCTTTGGAGTACTGAATGCCCA TTTCGTTTTGCAGGTGGCCAGTTCTATCCGTGATAGAACATCTGAAATGGTGGAGGCTCTTTAC AACATGAATAAGGTAAATCCTAGTCTTGTGTATGAATGGCCCTTCAGATTGCATAATTTTAAGG ATCCACTATCTACCCCCTTGTTACAATTTCAAACTCTGACTCTAAATTATGACATCAGTTTTTT CGGGTATGATTCTGTTTCTTGTATGTTACTAGGATAGTTTCTAGTAGCTCATCTTTTTAAAAGG AATAATTTCCAGCAACAACACTATAGTTTTCCACTTCTACTGCAACATGAGAAGTTCACATGTC GTTTTCTGTTAGCTGTACCATTTGCTGTTTTGTAAGGCTTCAGATCCCACTTATTTGATCTGTC CTTTCTCCTCCTATATATCTATTTAGGCCCTCTTTATTTAGGCTTATAAACCGGCTTATGAGCC GAAAAGTCTAAGCTTTTTCGTTTGTTTTTTTTAAAGCCATAAGCCACTCTTACACTATTAAGCC AAAAGCAAGGTTGAAGTAGTTCTTTTGTCTTATGTGAAGTGGAGGTATGACTCCTCCATTAAAC TTAAGGCTTCAAAGCCACCGACTTATAAAACATACAGACAAAAAAGTTGGCTTAAATGCAACAT ACAGGCAAAAAAGTTGGCTTAAATGCCTAAGTCAATAAGCCTAAGCCTAAACAAAGAGCCTGCA GATCTGTTCAGTAGACCTCTTAAGTAGTAACACTCAATATTTCTGGTTCATGTTTTTGGTCAAT GGTTCTCTCACAATTTTTCTTACACTTTGTCTATGCTGATATAAATTAACTAAGTTCTGTGGCA TGCGCAGGCATATTTATCTCTTCCTGAGGGAACAGCTACTGCTGCAGGGTTAATTGCAATGATG ACTGATCACTATAATATTCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013346 						
					
						PMCS
						0.211331306

Conservation Information
Conserved circRNAs	osi_circ_013346
PMCS	0.211331306

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24520114-24520099(+)
24521201-24522315(-)
						
						Potential amino acid sequence
						
							MSSTRKVRNVNKRYAKINEDWQDKDATNVHKSKVRKKKLSDMLGSQWSKDELERFYGSYRKYGK
DWRKVASSIRDRTSEMVEALYNMNKAYLSLPEGTATAAGLIAMMTDHYNILAGSV*(+)
MSDSFFFRTLLLCTFVASLSCQSSFILAYRLFTFLTFLVEDIESQSHRACQNIIVISHHCN*(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24520114-24520099(+) 24521201-24522315(-)
Potential amino acid sequence	MSSTRKVRNVNKRYAKINEDWQDKDATNVHKSKVRKKKLSDMLGSQWSKDELERFYGSYRKYGK DWRKVASSIRDRTSEMVEALYNMNKAYLSLPEGTATAAGLIAMMTDHYNILAGSV(+) MSDSFFFRTLLLCTFVASLSCQSSFILAYRLFTFLTFLVEDIESQSHRACQNIIVISHHCN(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os03g0639200_circ_g.1

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