Plant Circular RNA Database

Detail information of Os04g0596400_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0596400_circ_g.2
					
						ID in PlantcircBase
						osa_circ_025041
					
						Alias
						Os04circ12552
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 30082588-30083167  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os04g0596400						
					
						Parent gene annotation
						
							Similar to UPF0195 protein CG30152. (Os04t0596400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0596400_circ_g.1 Os04g0596400_circ_g.3 						
					
						Support reads
						2/1
					
						Tissues
						leaf/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  
						
							CT-AC							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
						Os04t0596400-01:3

General Information
CircRNA Name	Os04g0596400_circ_g.2
ID in PlantcircBase	osa_circ_025041
Alias	Os04circ12552
Organism	Oryza sativa
Position	chr4: 30082588-30083167 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os04g0596400
Parent gene annotation	Similar to UPF0195 protein CG30152. (Os04t0596400-01)
Parent gene strand	-
Alternative splicing	Os04g0596400_circ_g.1 Os04g0596400_circ_g.3
Support reads	2/1
Tissues	leaf/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	CT-AC 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	Os04t0596400-01:3

			
						 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  
						
							CGCCTCTCTTTTTTCTCATAAACTACAGGGTTAGCATTTATTAACCCCACAACCATTTTTCTGA
TGCAATGCACTAATTTATATCAGAATGGCGAAATTCcttgtatcgagggggaagactccgcata
agtttcacacgcaggcaaagtccaatgacggtcgccatactgcaacgctccactgttggggtaa
aagtaacc

						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: 374
Transcript exons: 30082588-30082687,30082773-30082876,30082998-30083167
CTTGTATCGAGGGGGAAGACTCCGCATAAGTTTCACACGCAGGCAAAGTCCAATGACGGTCGCC
ATACTGCAACGCTCCACTGTTGGGGTAAAAGTAACCCTGACATGACTAAGTTCATCATTGATTT
CAACTGAATCCTCAGTTACAACATTAAGCTCTTCGAGTGAGTATGGGTGCTCTGGATCCTTTAT
GTCTCTAATATGATCAAATATTTCTAGCTGGTCAATAGCCTCTGCCGCATTTTCATCTGTGGTT
TCTGGTGCCTGCCGAGAACGCCTCTCTTTTTTCTCATAAACTACAGGGTTAGCATTTATTAACC
CCACAACCATTTTTCTGATGCAATGCACTAATTTATATCAGAATGGCGAAATTC
						
						Genomic sequence
						
							CTTGTATCGAGGGGGAAGACTCCGCATAAGTTTCACACGCAGGCAAAGTCCAATGACGGTCGCC
ATACTGCAACGCTCCACTGTTGGGGTAAAAGTAACCCTGAAGAGAATAACAGTGAATTGTTGTG
ACTGAATTTCATTAACAACCCATTGTAGCATACAATGATAGAGAGACGTAAACTTACCTGACAT
GACTAAGTTCATCATTGATTTCAACTGAATCCTCAGTTACAACATTAAGCTCTTCGAGTGAGTA
TGGGTGCTCTGGATCCTTTATGTCTCTAATATGATGTAAGAAGGTTAAGGAGTGCAAACAAAAG
AAAAATTGAGGGCAGCAGAACTCCAGATAGAGGTAAGTATAACAGGAAAGAGAGGTACACAGCA
TGTAGATAAGGAAACAAAGAAAGGATATCAAATATTTCTAGCTGGTCAATAGCCTCTGCCGCAT
TTTCATCTGTGGTTTCTGGTGCCTGCCGAGAACGCCTCTCTTTTTTCTCATAAACTACAGGGTT
AGCATTTATTAACCCCACAACCATTTTTCTGATGCAATGCACTAATTTATATCAGAATGGCGAA
ATTC

Sequences
Splice junction sequence	CGCCTCTCTTTTTTCTCATAAACTACAGGGTTAGCATTTATTAACCCCACAACCATTTTTCTGA TGCAATGCACTAATTTATATCAGAATGGCGAAATTCcttgtatcgagggggaagactccgcata agtttcacacgcaggcaaagtccaatgacggtcgccatactgcaacgctccactgttggggtaa aagtaacc
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: 374 Transcript exons: 30082588-30082687,30082773-30082876,30082998-30083167 CTTGTATCGAGGGGGAAGACTCCGCATAAGTTTCACACGCAGGCAAAGTCCAATGACGGTCGCC ATACTGCAACGCTCCACTGTTGGGGTAAAAGTAACCCTGACATGACTAAGTTCATCATTGATTT CAACTGAATCCTCAGTTACAACATTAAGCTCTTCGAGTGAGTATGGGTGCTCTGGATCCTTTAT GTCTCTAATATGATCAAATATTTCTAGCTGGTCAATAGCCTCTGCCGCATTTTCATCTGTGGTT TCTGGTGCCTGCCGAGAACGCCTCTCTTTTTTCTCATAAACTACAGGGTTAGCATTTATTAACC CCACAACCATTTTTCTGATGCAATGCACTAATTTATATCAGAATGGCGAAATTC
Genomic sequence	CTTGTATCGAGGGGGAAGACTCCGCATAAGTTTCACACGCAGGCAAAGTCCAATGACGGTCGCC ATACTGCAACGCTCCACTGTTGGGGTAAAAGTAACCCTGAAGAGAATAACAGTGAATTGTTGTG ACTGAATTTCATTAACAACCCATTGTAGCATACAATGATAGAGAGACGTAAACTTACCTGACAT GACTAAGTTCATCATTGATTTCAACTGAATCCTCAGTTACAACATTAAGCTCTTCGAGTGAGTA TGGGTGCTCTGGATCCTTTATGTCTCTAATATGATGTAAGAAGGTTAAGGAGTGCAAACAAAAG AAAAATTGAGGGCAGCAGAACTCCAGATAGAGGTAAGTATAACAGGAAAGAGAGGTACACAGCA TGTAGATAAGGAAACAAAGAAAGGATATCAAATATTTCTAGCTGGTCAATAGCCTCTGCCGCAT TTTCATCTGTGGTTTCTGGTGCCTGCCGAGAACGCCTCTCTTTTTTCTCATAAACTACAGGGTT AGCATTTATTAACCCCACAACCATTTTTCTGATGCAATGCACTAATTTATATCAGAATGGCGAA ATTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014726 						
					
						PMCS
						0.398308649

Conservation Information
Conserved circRNAs	osi_circ_014726
PMCS	0.398308649

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30083132-30082613(+)
30083157-30082804(+)
30083125-30083143(-)
						
						Potential amino acid sequence
						
							MQCTNLYQNGEIPCIEGEDSA*(+)
MAKFLVSRGKTPHKFHTQAKSNDGRHTATLHCWGKSNPDMTKFIIDFN*(+)
MVVGLINANPVVYEKKERRSRQAPETTDENAAEAIDQLEIFDHIRDIKDPEHPYSLEELNVVTE
DSVEINDELSHVRVTFTPTVERCSMATVIGLCLRVKLMRSLPPRYKEFRHSDIN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30083132-30082613(+) 30083157-30082804(+) 30083125-30083143(-)
Potential amino acid sequence	MQCTNLYQNGEIPCIEGEDSA(+) MAKFLVSRGKTPHKFHTQAKSNDGRHTATLHCWGKSNPDMTKFIIDFN(+) MVVGLINANPVVYEKKERRSRQAPETTDENAAEAIDQLEIFDHIRDIKDPEHPYSLEELNVVTE DSVEINDELSHVRVTFTPTVERCSMATVIGLCLRVKLMRSLPPRYKEFRHSDIN*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0596400_circ_g.2

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