Plant Circular RNA Database

Detail information of Os03g0834000_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0834000_circ_g.2
					
						ID in PlantcircBase
						osa_circ_022599
					
						Alias
						Os03circ31914/Os_ciR8993
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 35048011-35048354  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os03g0834000						
					
						Parent gene annotation
						
							Flap endonuclease-1b (EC 3.-.-.-) (OsFEN-1b). (Os03t0834000-01);
Similar to Flap endonuclease 1b. (Os03t0834000-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0834000_circ_g.1 Os03g0834000_circ_g.3 						
					
						Support reads
						2/2
					
						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  
						
							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
						Os03t0834000-01:3
Os03t0834000-02:3

General Information
CircRNA Name	Os03g0834000_circ_g.2
ID in PlantcircBase	osa_circ_022599
Alias	Os03circ31914/Os_ciR8993
Organism	Oryza sativa
Position	chr3: 35048011-35048354 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os03g0834000
Parent gene annotation	Flap endonuclease-1b (EC 3.-.-.-) (OsFEN-1b). (Os03t0834000-01); Similar to Flap endonuclease 1b. (Os03t0834000-02)
Parent gene strand	+
Alternative splicing	Os03g0834000_circ_g.1 Os03g0834000_circ_g.3
Support reads	2/2
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	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	Os03t0834000-01:3 Os03t0834000-02:3

			
						 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  
						
							GGTGATTTATCTGTTATTGCATTGCACCTCTGAGGCAGCATTTATGTTACAGGTTGGAGATGAG
GATTTAATTGAAAAATTTAGCAAAAGGACTGTAAAGttttgtgtttgatggtgagccacctgac
atgaagaaaaaggaactggcaaaaaggtatactctgaatagtgcctttgctttgattgtttctt
gtgagtgt

						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: 151
Transcript exons: 35048011-35048064,35048146-35048194,35048307-35048354
TTTTGTGTTTGATGGTGAGCCACCTGACATGAAGAAAAAGGAACTGGCAAAAAGGTCTTTGAAG
AGAGATGGTTCTTCCGAAGATCTAAATAGAGCTATTGAGGTTGGAGATGAGGATTTAATTGAAA
AATTTAGCAAAAGGACTGTAAAG
						
						Genomic sequence
						
							TTTTGTGTTTGATGGTGAGCCACCTGACATGAAGAAAAAGGAACTGGCAAAAAGGTATACTCTG
AATAGTGCCTTTGCTTTGATTGTTTCTTGTGAGTGTCAGTATTTTTATTTCCTATGTTTACCAC
TCTTTAGGTCTTTGAAGAGAGATGGTTCTTCCGAAGATCTAAATAGAGCTATTGAGGTCATCTG
ATCCTAACCGTAGTACTATTGCCTCCTTCTTATTGTACCTTTTTACTTTTGGGGTGATTTATCT
GTTATTGCATTGCACCTCTGAGGCAGCATTTATGTTACAGGTTGGAGATGAGGATTTAATTGAA
AAATTTAGCAAAAGGACTGTAAAG

Sequences
Splice junction sequence	GGTGATTTATCTGTTATTGCATTGCACCTCTGAGGCAGCATTTATGTTACAGGTTGGAGATGAG GATTTAATTGAAAAATTTAGCAAAAGGACTGTAAAGttttgtgtttgatggtgagccacctgac atgaagaaaaaggaactggcaaaaaggtatactctgaatagtgcctttgctttgattgtttctt gtgagtgt
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: 151 Transcript exons: 35048011-35048064,35048146-35048194,35048307-35048354 TTTTGTGTTTGATGGTGAGCCACCTGACATGAAGAAAAAGGAACTGGCAAAAAGGTCTTTGAAG AGAGATGGTTCTTCCGAAGATCTAAATAGAGCTATTGAGGTTGGAGATGAGGATTTAATTGAAA AATTTAGCAAAAGGACTGTAAAG
Genomic sequence	TTTTGTGTTTGATGGTGAGCCACCTGACATGAAGAAAAAGGAACTGGCAAAAAGGTATACTCTG AATAGTGCCTTTGCTTTGATTGTTTCTTGTGAGTGTCAGTATTTTTATTTCCTATGTTTACCAC TCTTTAGGTCTTTGAAGAGAGATGGTTCTTCCGAAGATCTAAATAGAGCTATTGAGGTCATCTG ATCCTAACCGTAGTACTATTGCCTCCTTCTTATTGTACCTTTTTACTTTTGGGGTGATTTATCT GTTATTGCATTGCACCTCTGAGGCAGCATTTATGTTACAGGTTGGAGATGAGGATTTAATTGAA AAATTTAGCAAAAGGACTGTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013853 						
					
						PMCS
						0.247412766

Conservation Information
Conserved circRNAs	osi_circ_013853
PMCS	0.247412766

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35048040-35048019(+)
35048042-35048324(-)
						
						Potential amino acid sequence
						
							MKKKELAKRSLKRDGSSEDLNRAIEVGDEDLIEKFSKRTVKFCV*(+)
MSGGSPSNTKLYSPFAKFFN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35048040-35048019(+) 35048042-35048324(-)
Potential amino acid sequence	MKKKELAKRSLKRDGSSEDLNRAIEVGDEDLIEKFSKRTVKFCV(+) MSGGSPSNTKLYSPFAKFFN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0834000_circ_g.2

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