Plant Circular RNA Database

Detail information of Os01g0639100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0639100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_002844
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 25637316-25637578  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							i-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0639100						
					
						Parent gene annotation
						
							DEAD box RNA helicase homologous to eukaryotic initiation factor
 4AIII (eIF4AIII), Core components of the exon junction complex 
(EJC), Regulation of plant height, pollen, and seed development 
(Os01t0639100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						root
					
						Exon boundary  
						
							No-No							"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  
						
							AT-GA							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
						0

General Information
CircRNA Name	Os01g0639100_circ_g.1
ID in PlantcircBase	osa_circ_002844
Alias	NA
Organism	Oryza sativa
Position	chr1: 25637316-25637578 JBrowse»
Reference genome	IRGSP-1.0.38
Type	i-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0639100
Parent gene annotation	DEAD box RNA helicase homologous to eukaryotic initiation factor 4AIII (eIF4AIII), Core components of the exon junction complex (EJC), Regulation of plant height, pollen, and seed development (Os01t0639100-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	root
Exon boundary	No-No "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	AT-GA 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	0

			
						 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  
						
							CCAAATTTATTAGAGCTGTACTGCTGTACACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTA
TTGTTCACTGTTGTTGTCTATGTTCCCGTAATCCTAgtacgcctcttacccaccaatctgacat
tttacttcagtatttccactttttccccctactgtgcgatctattttgctctagattaacttgc
attgcagc

						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: 263
Transcript exons: 25637316-25637578
GTACGCCTCTTACCCACCAATCTGACATTTTACTTCAGTATTTCCACTTTTTCCCCCTACTGTG
CGATCTATTTTGCTCTAGATTAACTTGCATTGCAGCATCGTGCTAGTACTGTGCGATCTATTTT
ACTAGGGTTTAGCATAATGTTATAGGTGATGGCTTCCAAATTTATTAGAGCTGTACTGCTGTAC
ACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTATTGTTCACTGTTGTTGTCTATGTTCCCGT
AATCCTA
						
						Genomic sequence
						
							GTACGCCTCTTACCCACCAATCTGACATTTTACTTCAGTATTTCCACTTTTTCCCCCTACTGTG
CGATCTATTTTGCTCTAGATTAACTTGCATTGCAGCATCGTGCTAGTACTGTGCGATCTATTTT
ACTAGGGTTTAGCATAATGTTATAGGTGATGGCTTCCAAATTTATTAGAGCTGTACTGCTGTAC
ACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTATTGTTCACTGTTGTTGTCTATGTTCCCGT
AATCCTA

Sequences
Splice junction sequence	CCAAATTTATTAGAGCTGTACTGCTGTACACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTA TTGTTCACTGTTGTTGTCTATGTTCCCGTAATCCTAgtacgcctcttacccaccaatctgacat tttacttcagtatttccactttttccccctactgtgcgatctattttgctctagattaacttgc attgcagc
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: 263 Transcript exons: 25637316-25637578 GTACGCCTCTTACCCACCAATCTGACATTTTACTTCAGTATTTCCACTTTTTCCCCCTACTGTG CGATCTATTTTGCTCTAGATTAACTTGCATTGCAGCATCGTGCTAGTACTGTGCGATCTATTTT ACTAGGGTTTAGCATAATGTTATAGGTGATGGCTTCCAAATTTATTAGAGCTGTACTGCTGTAC ACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTATTGTTCACTGTTGTTGTCTATGTTCCCGT AATCCTA
Genomic sequence	GTACGCCTCTTACCCACCAATCTGACATTTTACTTCAGTATTTCCACTTTTTCCCCCTACTGTG CGATCTATTTTGCTCTAGATTAACTTGCATTGCAGCATCGTGCTAGTACTGTGCGATCTATTTT ACTAGGGTTTAGCATAATGTTATAGGTGATGGCTTCCAAATTTATTAGAGCTGTACTGCTGTAC ACAAATTCTTTCCATGCCTGTTTTGGTGCTGATTATTGTTCACTGTTGTTGTCTATGTTCCCGT AATCCTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.323496691

Conservation Information
Conserved circRNAs	NA
PMCS	0.323496691

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0639100_circ_g.1

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