Plant Circular RNA Database

Detail information of Os12g0489100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os12g0489100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_011496
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 18337798-18339151  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0489100						
					
						Parent gene annotation
						
							Similar to Ubiquitin-specific protease 12. (Os12t0489100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0489100_circ_g.2 						
					
						Support reads
						1
					
						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
						Os12t0489100-01:5

General Information
CircRNA Name	Os12g0489100_circ_g.1
ID in PlantcircBase	osa_circ_011496
Alias	NA
Organism	Oryza sativa
Position	chr12: 18337798-18339151 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0489100
Parent gene annotation	Similar to Ubiquitin-specific protease 12. (Os12t0489100-01)
Parent gene strand	+
Alternative splicing	Os12g0489100_circ_g.2
Support reads	1
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	Os12t0489100-01:5

			
						 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  
						
							GGATGCAAAGAAGGGAGTACTCTTCCTTGATTTCCCTCCTGTTTTGCAACTTCAACTGAAGCGT
TTTGAATATGATTACATGCGAGATACAATGGTCAAGatactcaacatcaatttaatgcacgtga
gagtgactggggtttcacatcttttatgcctttgagtgatctgtatgacccaagtaggggctac
cttgttaa

									
								

					

						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: 809
Transcript exons: 18337798-18338063,18338143-18338361,18338427-18338535,18
338606-18338721,18339053-18339151
ATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAG
TGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAATGACACCGTTGTTGTGGAAGCTGAGGTT
GCTGTTCGCAGAATGGTTGATTACTGGACTTATGACTCGAAAAAGGAAACAGGATATGTTGGTC
TAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATA
TTTCAGGAAGGCTGTATATCATATGCCAACTACTGAGAATGACATGCCATCTGGGAGTATTCCT
TTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATAGCGTAGCTACAAAGGAGT
TGACCAAATCTTTTGGATGGGACACTTATGATTCTTTCATGCAGCATGATGTTCAAGAGCTTAA
CAGAGTTCTTTGTGAGAAACTTGAAGACAAAATGAAGGAAACTGTTGTGGAAGGAACAATTGAA
CAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACA
GAAAAGAATCCTTTTATGATCTACAGCTTGATGTCAAAGGTTGTAGTGATGTTTATGCATCATT
TGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGAGCAGTATGGC
TTACAGGATGCAAAGAAGGGAGTACTCTTCCTTGATTTCCCTCCTGTTTTGCAACTTCAACTGA
AGCGTTTTGAATATGATTACATGCGAGATACAATGGTCAAG
						
					

						Genomic sequence
						
							ATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAG
TGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAATGACACCGTTGTTGTGGAAGCTGAGGTT
GCTGTTCGCAGAATGGTTGATTACTGGACTTATGACTCGAAAAAGGAAACAGGATATGTTGGTC
TAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATA
TTTCAGGAAGGTCTGAGATCATTACTTTTTCCTAGTCTACATGATTTGTTAAGTACCTGAACTT
AAGACTAATTGAAATTTCATCTTAGGCTGTATATCATATGCCAACTACTGAGAATGACATGCCA
TCTGGGAGTATTCCTTTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATAGCG
TAGCTACAAAGGAGTTGACCAAATCTTTTGGATGGGACACTTATGATTCTTTCATGCAGCATGA
TGTTCAAGAGCTTAACAGAGTTCTTTGTGAGAAACTTGAAGACAAAATGAAGGTGAATATTATA
ACAAACATTTTATTATATGTCTACGATTTGTTATTAACTTTGCGTTGACCCAGGAAACTGTTGT
GGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTT
GATTATAAATCTAACAGAAAAGAATCCTTTTATGGTAAGCTTTTTCACATTGAACATTCAGTAT
CATTTTTAATTTAGTGCTTACTCATGTTATAACATTGCAGATCTACAGCTTGATGTCAAAGGTT
GTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAA
ATATCATGCAGAGCAGTATGGCTTACAGGTACTGACAAATCCTGCACTCCGAAGTTGAATATTT
TGATGTAGTGAACTTCTTAGCAGGTTTTTTTGGGAGTACATGATACATGTGGAGTAAATTTAGG
TTATTACCTCTTTTTTTTTTTGTTTAGTAAAATAATAACTCTGTAATGTTGGTGTGTACTTGCA
TACAGTTTATTCATTGAGGAGCGATTTCCTTTAATGTAGACATAAAATTAAAAGATGTTAATCA
TCTGATTTTCCAAGTTAATGAATGGCAATATAGCATACATGCCATGATTATATTTTCTTACCTT
GATACTGCATTGGCACTTGATATTCTGTAATCTTTTCAGGATGCAAAGAAGGGAGTACTCTTCC
TTGATTTCCCTCCTGTTTTGCAACTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATAC
AATGGTCAAG
						
					

			
		

Sequences
Splice junction sequence	GGATGCAAAGAAGGGAGTACTCTTCCTTGATTTCCCTCCTGTTTTGCAACTTCAACTGAAGCGT TTTGAATATGATTACATGCGAGATACAATGGTCAAGatactcaacatcaatttaatgcacgtga gagtgactggggtttcacatcttttatgcctttgagtgatctgtatgacccaagtaggggctac cttgttaa
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: 809 Transcript exons: 18337798-18338063,18338143-18338361,18338427-18338535,18 338606-18338721,18339053-18339151 ATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAG TGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAATGACACCGTTGTTGTGGAAGCTGAGGTT GCTGTTCGCAGAATGGTTGATTACTGGACTTATGACTCGAAAAAGGAAACAGGATATGTTGGTC TAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATA TTTCAGGAAGGCTGTATATCATATGCCAACTACTGAGAATGACATGCCATCTGGGAGTATTCCT TTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATAGCGTAGCTACAAAGGAGT TGACCAAATCTTTTGGATGGGACACTTATGATTCTTTCATGCAGCATGATGTTCAAGAGCTTAA CAGAGTTCTTTGTGAGAAACTTGAAGACAAAATGAAGGAAACTGTTGTGGAAGGAACAATTGAA CAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACA GAAAAGAATCCTTTTATGATCTACAGCTTGATGTCAAAGGTTGTAGTGATGTTTATGCATCATT TGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGAGCAGTATGGC TTACAGGATGCAAAGAAGGGAGTACTCTTCCTTGATTTCCCTCCTGTTTTGCAACTTCAACTGA AGCGTTTTGAATATGATTACATGCGAGATACAATGGTCAAG
Genomic sequence	ATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAG TGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAATGACACCGTTGTTGTGGAAGCTGAGGTT GCTGTTCGCAGAATGGTTGATTACTGGACTTATGACTCGAAAAAGGAAACAGGATATGTTGGTC TAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATA TTTCAGGAAGGTCTGAGATCATTACTTTTTCCTAGTCTACATGATTTGTTAAGTACCTGAACTT AAGACTAATTGAAATTTCATCTTAGGCTGTATATCATATGCCAACTACTGAGAATGACATGCCA TCTGGGAGTATTCCTTTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATAGCG TAGCTACAAAGGAGTTGACCAAATCTTTTGGATGGGACACTTATGATTCTTTCATGCAGCATGA TGTTCAAGAGCTTAACAGAGTTCTTTGTGAGAAACTTGAAGACAAAATGAAGGTGAATATTATA ACAAACATTTTATTATATGTCTACGATTTGTTATTAACTTTGCGTTGACCCAGGAAACTGTTGT GGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTT GATTATAAATCTAACAGAAAAGAATCCTTTTATGGTAAGCTTTTTCACATTGAACATTCAGTAT CATTTTTAATTTAGTGCTTACTCATGTTATAACATTGCAGATCTACAGCTTGATGTCAAAGGTT GTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAA ATATCATGCAGAGCAGTATGGCTTACAGGTACTGACAAATCCTGCACTCCGAAGTTGAATATTT TGATGTAGTGAACTTCTTAGCAGGTTTTTTTGGGAGTACATGATACATGTGGAGTAAATTTAGG TTATTACCTCTTTTTTTTTTTGTTTAGTAAAATAATAACTCTGTAATGTTGGTGTGTACTTGCA TACAGTTTATTCATTGAGGAGCGATTTCCTTTAATGTAGACATAAAATTAAAAGATGTTAATCA TCTGATTTTCCAAGTTAATGAATGGCAATATAGCATACATGCCATGATTATATTTTCTTACCTT GATACTGCATTGGCACTTGATATTCTGTAATCTTTTCAGGATGCAAAGAAGGGAGTACTCTTCC TTGATTTCCCTCCTGTTTTGCAACTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATAC AATGGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003438* osi_circ_009733 osi_circ_009135 						
					
						PMCS
						0.46117833

Conservation Information
Conserved circRNAs	osi_circ_003438* osi_circ_009733 osi_circ_009135
PMCS	0.46117833

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18337852-18337857(+)
						
						Potential amino acid sequence
						
							MPLSDLYDPSRGYLVNDTVVVEAEVAVRRMVDYWTYDSKKETGYVGLKNQGATCYMNSLLQTLY
HIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYKLQYSDNSVATKELTKSFGWDTYDSFMQHDV
QELNRVLCEKLEDKMKETVVEGTIEQLFEGHHINYIECINVDYKSNRKESFYDLQLDVKGCSDV
YASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFLDFPPVLQLQLKRFEYDYMRDTMVKILNI
NLMHVRVTGVSHLLCL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18337852-18337857(+)
Potential amino acid sequence	MPLSDLYDPSRGYLVNDTVVVEAEVAVRRMVDYWTYDSKKETGYVGLKNQGATCYMNSLLQTLY HIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYKLQYSDNSVATKELTKSFGWDTYDSFMQHDV QELNRVLCEKLEDKMKETVVEGTIEQLFEGHHINYIECINVDYKSNRKESFYDLQLDVKGCSDV YASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFLDFPPVLQLQLKRFEYDYMRDTMVKILNI NLMHVRVTGVSHLLCL*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0489100_circ_g.1

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