Plant Circular RNA Database

Detail information of Os06g0133900_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os06g0133900_circ_g.2
					
						ID in PlantcircBase
						osa_circ_029551
					
						Alias
						Os_ciR3426
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 1818051-1818903  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os06g0133900						
					
						Parent gene annotation
						
							5-enolpyruvylshikimate-3-phosphate synthase (Os06t0133900-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0133900_circ_g.1 Os06g0133900_circ_g.3 Os06g0133900_circ_g.4 Os06g0133900_circ_g.5 						
					
						Support reads
						3/1
					
						Tissues
						root/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
						Os06t0133900-01:3

General Information
CircRNA Name	Os06g0133900_circ_g.2
ID in PlantcircBase	osa_circ_029551
Alias	Os_ciR3426
Organism	Oryza sativa
Position	chr6: 1818051-1818903 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os06g0133900
Parent gene annotation	5-enolpyruvylshikimate-3-phosphate synthase (Os06t0133900-01)
Parent gene strand	+
Alternative splicing	Os06g0133900_circ_g.1 Os06g0133900_circ_g.3 Os06g0133900_circ_g.4 Os06g0133900_circ_g.5
Support reads	3/1
Tissues	root/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	Os06t0133900-01:3

			
						 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  
						
							CTGAAAGCTGTTGATGTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTG
CACTCTTCGCTGATGGTCCAACTGCTATCAGAGATGgttaagctctctggttccatcagcagtc
agtacttgagtgccttgctgatggctgctcctttggcccttggggatgtggagatcgaaatcat
tgacaaac

						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: 544
Transcript exons: 1818051-1818265,1818359-1818476,1818693-1818903
GTTAAGCTCTCTGGTTCCATCAGCAGTCAGTACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGG
CCCTTGGGGATGTGGAGATCGAAATCATTGACAAACTAATCTCCATTCCTTACGTTGAAATGAC
ATTGAGATTGATGGAGCGTTTTGGTGTGAAGGCAGAGCATTCTGATAGTTGGGACAGATTCTAT
ATTAAGGGAGGGCAGAAGTACAAATCTCCTGGAAATGCCTATGTTGAAGGTGATGCCTCAAGCG
CGAGCTATTTCTTGGCTGGTGCTGCAATCACTGGAGGCACTGTGACAGTTCAAGGTTGTGGTAC
GACCAGTTTGCAGGGTGATGTCAAATTTGCTGAGGTACTTGAGATGATGGGAGCAAAGGTTACA
TGGACTGACACCAGTGTAACCGTAACTGGTCCACCACGTGAGCCTTATGGGAAGAAACACCTGA
AAGCTGTTGATGTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTGCACT
CTTCGCTGATGGTCCAACTGCTATCAGAGATG
						
						Genomic sequence
						
							GTTAAGCTCTCTGGTTCCATCAGCAGTCAGTACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGG
CCCTTGGGGATGTGGAGATCGAAATCATTGACAAACTAATCTCCATTCCTTACGTTGAAATGAC
ATTGAGATTGATGGAGCGTTTTGGTGTGAAGGCAGAGCATTCTGATAGTTGGGACAGATTCTAT
ATTAAGGGAGGGCAGAAGTACAAGTAAGCTTCTACCTGCCTTACTGAGCTGAATTATTCGGGTG
TTTATGATTAACTCCCTAAACTAACCCTTTTTCTTTTCTTTGGCATTGACAGATCTCCTGGAAA
TGCCTATGTTGAAGGTGATGCCTCAAGCGCGAGCTATTTCTTGGCTGGTGCTGCAATCACTGGA
GGCACTGTGACAGTTCAAGGTTGTGGTACGACCAGTTTGCAGGTATAACTGTAGTGCCTGTTTT
GACATTCTACCGTTTAGTCAAGTTTAGTCAGTAGTCACATATTCAGAATATAGCACAATCTGTA
TTATGCCACTGTTAATCAAATACGCTTGACCTAGAGAGTGCTATATACCCTAGCTTAATCTTCA
AACTAAACAGTTCTCTTGTGGCTTGCTGTGCTGTTATGTTCCCTGACCTACATGTTAATATTAC
AGGGTGATGTCAAATTTGCTGAGGTACTTGAGATGATGGGAGCAAAGGTTACATGGACTGACAC
CAGTGTAACCGTAACTGGTCCACCACGTGAGCCTTATGGGAAGAAACACCTGAAAGCTGTTGAT
GTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTGCACTCTTCGCTGATG
GTCCAACTGCTATCAGAGATG

Sequences
Splice junction sequence	CTGAAAGCTGTTGATGTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTG CACTCTTCGCTGATGGTCCAACTGCTATCAGAGATGgttaagctctctggttccatcagcagtc agtacttgagtgccttgctgatggctgctcctttggcccttggggatgtggagatcgaaatcat tgacaaac
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: 544 Transcript exons: 1818051-1818265,1818359-1818476,1818693-1818903 GTTAAGCTCTCTGGTTCCATCAGCAGTCAGTACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGG CCCTTGGGGATGTGGAGATCGAAATCATTGACAAACTAATCTCCATTCCTTACGTTGAAATGAC ATTGAGATTGATGGAGCGTTTTGGTGTGAAGGCAGAGCATTCTGATAGTTGGGACAGATTCTAT ATTAAGGGAGGGCAGAAGTACAAATCTCCTGGAAATGCCTATGTTGAAGGTGATGCCTCAAGCG CGAGCTATTTCTTGGCTGGTGCTGCAATCACTGGAGGCACTGTGACAGTTCAAGGTTGTGGTAC GACCAGTTTGCAGGGTGATGTCAAATTTGCTGAGGTACTTGAGATGATGGGAGCAAAGGTTACA TGGACTGACACCAGTGTAACCGTAACTGGTCCACCACGTGAGCCTTATGGGAAGAAACACCTGA AAGCTGTTGATGTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTGCACT CTTCGCTGATGGTCCAACTGCTATCAGAGATG
Genomic sequence	GTTAAGCTCTCTGGTTCCATCAGCAGTCAGTACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGG CCCTTGGGGATGTGGAGATCGAAATCATTGACAAACTAATCTCCATTCCTTACGTTGAAATGAC ATTGAGATTGATGGAGCGTTTTGGTGTGAAGGCAGAGCATTCTGATAGTTGGGACAGATTCTAT ATTAAGGGAGGGCAGAAGTACAAGTAAGCTTCTACCTGCCTTACTGAGCTGAATTATTCGGGTG TTTATGATTAACTCCCTAAACTAACCCTTTTTCTTTTCTTTGGCATTGACAGATCTCCTGGAAA TGCCTATGTTGAAGGTGATGCCTCAAGCGCGAGCTATTTCTTGGCTGGTGCTGCAATCACTGGA GGCACTGTGACAGTTCAAGGTTGTGGTACGACCAGTTTGCAGGTATAACTGTAGTGCCTGTTTT GACATTCTACCGTTTAGTCAAGTTTAGTCAGTAGTCACATATTCAGAATATAGCACAATCTGTA TTATGCCACTGTTAATCAAATACGCTTGACCTAGAGAGTGCTATATACCCTAGCTTAATCTTCA AACTAAACAGTTCTCTTGTGGCTTGCTGTGCTGTTATGTTCCCTGACCTACATGTTAATATTAC AGGGTGATGTCAAATTTGCTGAGGTACTTGAGATGATGGGAGCAAAGGTTACATGGACTGACAC CAGTGTAACCGTAACTGGTCCACCACGTGAGCCTTATGGGAAGAAACACCTGAAAGCTGTTGAT GTCAACATGAACAAAATGCCTGATGTTGCCATGACCCTTGCCGTTGTTGCACTCTTCGCTGATG GTCCAACTGCTATCAGAGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_006502* osi_circ_016261 						
					
						PMCS
						0.443609127

Conservation Information
Conserved circRNAs	osi_circ_006502* osi_circ_016261
PMCS	0.443609127

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1818100-1818052(+)
1818881-1818052(+)
1818072-1818395(-)
						
						Potential amino acid sequence
						
							MAAPLALGDVEIEIIDKLISIPYVEMTLRLMERFGVKAEHSDSWDRFYIKGGQKYKSPGNAYVE
GDASSASYFLAGAAITGGTVTVQGCGTTSLQGDVKFAEVLEMMGAKVTWTDTSVTVTGPPREPY
GKKHLKAVDVNMNKMPDVAMTLAVVALFADGPTAIRDG*(+)
MVQLLSEMVKLSGSISSQYLSALLMAAPLALGDVEIEIIDKLISIPYVEMTLRLMERFGVKAEH
SDSWDRFYIKGGQKYKSPGNAYVEGDASSASYFLAGAAITGGTVTVQGCGTTSLQGDVKFAEVL
EMMGAKVTWTDTSVTVTGPPREPYGKKHLKAVDVNMNKMPDVAMTLAVVALFADGPTAIRDG*(
+)
MEPESLTISDSSWTISEECNNGKGHGNIRHFVHVDINSFQVFLPIRLTWWTSYGYTGVSPCNLC
SHHLKYLSKFDITLQTGRTTTLNCHSASSDCSTSQEIARA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1818100-1818052(+) 1818881-1818052(+) 1818072-1818395(-)
Potential amino acid sequence	MAAPLALGDVEIEIIDKLISIPYVEMTLRLMERFGVKAEHSDSWDRFYIKGGQKYKSPGNAYVE GDASSASYFLAGAAITGGTVTVQGCGTTSLQGDVKFAEVLEMMGAKVTWTDTSVTVTGPPREPY GKKHLKAVDVNMNKMPDVAMTLAVVALFADGPTAIRDG(+) MVQLLSEMVKLSGSISSQYLSALLMAAPLALGDVEIEIIDKLISIPYVEMTLRLMERFGVKAEH SDSWDRFYIKGGQKYKSPGNAYVEGDASSASYFLAGAAITGGTVTVQGCGTTSLQGDVKFAEVL EMMGAKVTWTDTSVTVTGPPREPYGKKHLKAVDVNMNKMPDVAMTLAVVALFADGPTAIRDG( +) MEPESLTISDSSWTISEECNNGKGHGNIRHFVHVDINSFQVFLPIRLTWWTSYGYTGVSPCNLC SHHLKYLSKFDITLQTGRTTTLNCHSASSDCSTSQEIARA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os06g0133900_circ_g.2

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