Plant Circular RNA Database

Detail information of Os01g0896300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0896300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_005208
					
						Alias
						Os01circ30192/Os_ciR534
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 38954786-38955732  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os01g0896300						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os01t0896300-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/53/5
					
						Tissues
						panicle/root/shoot, 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  
						
							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
						Os01t0896300-00:2

General Information
CircRNA Name	Os01g0896300_circ_g.2
ID in PlantcircBase	osa_circ_005208
Alias	Os01circ30192/Os_ciR534
Organism	Oryza sativa
Position	chr1: 38954786-38955732 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os01g0896300
Parent gene annotation	Hypothetical conserved gene. (Os01t0896300-00)
Parent gene strand	+
Alternative splicing	NA
Support reads	3/53/5
Tissues	panicle/root/shoot, 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	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	Os01t0896300-00:2

			
						 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  
						
							AGCTAAAGAGCCAATGCAAGAGATGGTGAAAAGCAATAACGATACTGGGATTATTGAGAATGTG
GATGACTCTCAGCTGCAAAAAAACACCTCAACTAATcaacgttatcagttctagaagctccggg
agctgaagctcaagtaaatgatatgaggaaagcatcactgaagttaagcaaagcactgaacctg
gaaggtat

									
								

					

						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: 125
Transcript exons: 38954786-38954842,38955665-38955732
CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAGCAATAA
CGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAACTAAT
Transcript length: 196
Transcript exons: 38954786-38954871,38955623-38955732
CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC
ACTGAAGTTAAGCAAAGCACTGCTGGATCAACAGCTAAAGAGCCAATGCAAGAGATGGTGAAAA
GCAATAACGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAAC
TAAT
Transcript length: 269
Transcript exons: 38954786-38954930,38955609-38955732
CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC
ACTGAAGTTAAGCAAAGCACTGAACCTGGAAGGTATTAAATCATTGGTGGAAAGAGCGACACAA
AAGAGCAACATTGAACGGGGTGCCAAAAATACTGGATCAACAGCTAAAGAGCCAATGCAAGAGA
TGGTGAAAAGCAATAACGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAA
CACCTCAACTAAT
						
					

						Genomic sequence
						
							CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC
ACTGAAGTTAAGCAAAGCACTGAACCTGGAAGGTATTAAATCATTGGTGGAAAGAGCGACACAA
AAGAGCAACATTGAACGGTTTGTACCTTCTTGTTAGAGTAAAGTGTACGGGCGGTCCTTAAACT
TGTAGGGGTGTGTCATCTAGGTCCCTAAACTCTCAAAATGTATATCCAAGTCTCAGAACTTGTC
ATAGTGTGTCATCTAGGTCTCAAATCGCCACAACCACTTCAGGATCATACATGGCGTTGATGTG
GCATGCCACACGGACATGACGTGGCATTATTTTGACTGACAAATAGGACCCATTTAAATTTTTT
CCTTTTTCTTTTTTCTTCTCTTTTTCCCCTTTATTCTCCTTTCTTTGTGACCTGAGCAGAAGAA
AGGAAAAAAAGAAGAATAAGAAGAAAACGGAAAAGAAAAAGAAAAAGAAAGAAGAAAAAAAAGA
AAAGGACACGTCATGTCCATGTGGCATGCCATATCAGCGCCACGTAGGATCCTAGAGGGGATGT
GTTGATTTGGGACCTAGATGATACACTTTGACAAGTTCTGGGACCTGGATATGCATTTTGAGAG
TTTAGGGACCTATATGACACAACCCTACAAGATTAAGGACCGCTAATACACTTTACTCTTCTCG
TTATTACTTTCTGTCCAAGGATTTTCTTGCACATTTTTTATGAGACAGGTGCACACATGATTTT
AATCTTGAATCTTTTAGCACTCTGATTTATATATTATATTTTCTTGACAAAACAGGGGTGCCAA
AAATACTGGATCAACAGCTAAAGAGCCAATGCAAGAGATGGTGAAAAGCAATAACGATACTGGG
ATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAACTAAT
						
					

			
		

Sequences
Splice junction sequence	AGCTAAAGAGCCAATGCAAGAGATGGTGAAAAGCAATAACGATACTGGGATTATTGAGAATGTG GATGACTCTCAGCTGCAAAAAAACACCTCAACTAATcaacgttatcagttctagaagctccggg agctgaagctcaagtaaatgatatgaggaaagcatcactgaagttaagcaaagcactgaacctg gaaggtat
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: 125 Transcript exons: 38954786-38954842,38955665-38955732 CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAGCAATAA CGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAACTAAT Transcript length: 196 Transcript exons: 38954786-38954871,38955623-38955732 CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC ACTGAAGTTAAGCAAAGCACTGCTGGATCAACAGCTAAAGAGCCAATGCAAGAGATGGTGAAAA GCAATAACGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAAC TAAT Transcript length: 269 Transcript exons: 38954786-38954930,38955609-38955732 CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC ACTGAAGTTAAGCAAAGCACTGAACCTGGAAGGTATTAAATCATTGGTGGAAAGAGCGACACAA AAGAGCAACATTGAACGGGGTGCCAAAAATACTGGATCAACAGCTAAAGAGCCAATGCAAGAGA TGGTGAAAAGCAATAACGATACTGGGATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAA CACCTCAACTAAT
Genomic sequence	CAACGTTATCAGTTCTAGAAGCTCCGGGAGCTGAAGCTCAAGTAAATGATATGAGGAAAGCATC ACTGAAGTTAAGCAAAGCACTGAACCTGGAAGGTATTAAATCATTGGTGGAAAGAGCGACACAA AAGAGCAACATTGAACGGTTTGTACCTTCTTGTTAGAGTAAAGTGTACGGGCGGTCCTTAAACT TGTAGGGGTGTGTCATCTAGGTCCCTAAACTCTCAAAATGTATATCCAAGTCTCAGAACTTGTC ATAGTGTGTCATCTAGGTCTCAAATCGCCACAACCACTTCAGGATCATACATGGCGTTGATGTG GCATGCCACACGGACATGACGTGGCATTATTTTGACTGACAAATAGGACCCATTTAAATTTTTT CCTTTTTCTTTTTTCTTCTCTTTTTCCCCTTTATTCTCCTTTCTTTGTGACCTGAGCAGAAGAA AGGAAAAAAAGAAGAATAAGAAGAAAACGGAAAAGAAAAAGAAAAAGAAAGAAGAAAAAAAAGA AAAGGACACGTCATGTCCATGTGGCATGCCATATCAGCGCCACGTAGGATCCTAGAGGGGATGT GTTGATTTGGGACCTAGATGATACACTTTGACAAGTTCTGGGACCTGGATATGCATTTTGAGAG TTTAGGGACCTATATGACACAACCCTACAAGATTAAGGACCGCTAATACACTTTACTCTTCTCG TTATTACTTTCTGTCCAAGGATTTTCTTGCACATTTTTTATGAGACAGGTGCACACATGATTTT AATCTTGAATCTTTTAGCACTCTGATTTATATATTATATTTTCTTGACAAAACAGGGGTGCCAA AAATACTGGATCAACAGCTAAAGAGCCAATGCAAGAGATGGTGAAAAGCAATAACGATACTGGG ATTATTGAGAATGTGGATGACTCTCAGCTGCAAAAAAACACCTCAACTAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011054 						
					
						PMCS
						0.411670679

Conservation Information
Conserved circRNAs	osi_circ_011054
PMCS	0.411670679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							38955693-38954816(+)
38954837-38954800(+)
38954850-38955726(-)
						
						Potential amino acid sequence
						
							MWMTLSCKKTPQLINVISSRSSGS*(+)
MRKASLKLSKALNLEGIKSLVERATQKSNIERGAKNTGSTAKEPMQEMVKSNNDTGIIENVDDS
QLQKNTSTNQRYQF*(+)
MLSSYHLLELQLPELLELITLIS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	38955693-38954816(+) 38954837-38954800(+) 38954850-38955726(-)
Potential amino acid sequence	MWMTLSCKKTPQLINVISSRSSGS(+) MRKASLKLSKALNLEGIKSLVERATQKSNIERGAKNTGSTAKEPMQEMVKSNNDTGIIENVDDS QLQKNTSTNQRYQF(+) MLSSYHLLELQLPELLELITLIS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0896300_circ_g.2

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