Plant Circular RNA Database

Detail information of Os03g0401300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0401300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_020221
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 16301984-16302228  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os03g0401300						
					
						Parent gene annotation
						
							Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferas
e 2). (Os03t0401300-01);Similar to Sucrose synthase 1. (Os03t040
1300-02);Similar to Sucrose synthase metabolism (Fragment). (Os0
3t0401300-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0401300_circ_g.4 Os03g0401300_circ_g.5 Os03g0401300_circ_g.6 Os03g0401300_circ_g.7 Os03g0401300_circ_g.8 Os03g0401300_circ_g.9 Os03g0401300_circ_g.10 Os03g0401300_circ_g.11 						
					
						Support reads
						4
					
						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  
						
							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
						Os03t0401333-00:1
Os03t0401300-03:1
Os03t0401300-01:1
Os03t0401333-00:1
Os03t0401300-02:1

General Information
CircRNA Name	Os03g0401300_circ_g.3
ID in PlantcircBase	osa_circ_020221
Alias	NA
Organism	Oryza sativa
Position	chr3: 16301984-16302228 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os03g0401300
Parent gene annotation	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferas e 2). (Os03t0401300-01);Similar to Sucrose synthase 1. (Os03t040 1300-02);Similar to Sucrose synthase metabolism (Fragment). (Os0 3t0401300-03)
Parent gene strand	-
Alternative splicing	Os03g0401300_circ_g.4 Os03g0401300_circ_g.5 Os03g0401300_circ_g.6 Os03g0401300_circ_g.7 Os03g0401300_circ_g.8 Os03g0401300_circ_g.9 Os03g0401300_circ_g.10 Os03g0401300_circ_g.11
Support reads	4
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	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	Os03t0401333-00:1 Os03t0401300-03:1 Os03t0401300-01:1 Os03t0401333-00:1 Os03t0401300-02:1

			
						 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  
						
							CGATGATCTCAGCTGGACCACCATAGGCGGTTGCGAATGTCGGGAGACCACAGGTCATGGACTC
AACAACAGTGAGACCGAATGCCTCGTAGAAAGCGGGttctcctcgatacgctgaagaccgccct
gcgagatcttggtccagtggctggggtcttcctggcacttctcaaagaactcaacgagcagcgc
cgaggcct

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TTCTCCTCGATACGCTGAAGACCGCCCTGCGAGATCTTGGTCCAGTGGCTGGGGTCTTCCTGGC
ACTTCTCAAAGAACTCAACGAGCAGCGCCGAGGCCTTGTCACCCTGGTATGGGTCAATGTGGAA
GCCAGACACTCCGTTCACGATGATCTCAGCTGGACCACCATAGGCGGTTGCGAATGTCGGGAGA
CCACAGGTCATGGACTCAACAACAGTGAGACCGAATGCCTCGTAGAAAGCGGG

Sequences
Splice junction sequence	CGATGATCTCAGCTGGACCACCATAGGCGGTTGCGAATGTCGGGAGACCACAGGTCATGGACTC AACAACAGTGAGACCGAATGCCTCGTAGAAAGCGGGttctcctcgatacgctgaagaccgccct gcgagatcttggtccagtggctggggtcttcctggcacttctcaaagaactcaacgagcagcgc cgaggcct
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTCTCCTCGATACGCTGAAGACCGCCCTGCGAGATCTTGGTCCAGTGGCTGGGGTCTTCCTGGC ACTTCTCAAAGAACTCAACGAGCAGCGCCGAGGCCTTGTCACCCTGGTATGGGTCAATGTGGAA GCCAGACACTCCGTTCACGATGATCTCAGCTGGACCACCATAGGCGGTTGCGAATGTCGGGAGA CCACAGGTCATGGACTCAACAACAGTGAGACCGAATGCCTCGTAGAAAGCGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.463264354

Conservation Information
Conserved circRNAs	NA
PMCS	0.463264354

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16302211-16301998(+)
16302188-16302185(-)
						
						Potential amino acid sequence
						
							MPRRKRVLLDTLKTALRDLGPVAGVFLALLKELNEQRRGLVTLVWVNVEARHSVHDDLSWTTIG
GCECRETTGHGLNNSETECLVESGFSSIR*(+)
MTCGLPTFATAYGGPAEIIVNGVSGFHIDPYQGDKASALLVEFFEKCQEDPSHWTKISQGGLQR
IEENPLSTRHSVSLLLSP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16302211-16301998(+) 16302188-16302185(-)
Potential amino acid sequence	MPRRKRVLLDTLKTALRDLGPVAGVFLALLKELNEQRRGLVTLVWVNVEARHSVHDDLSWTTIG GCECRETTGHGLNNSETECLVESGFSSIR(+) MTCGLPTFATAYGGPAEIIVNGVSGFHIDPYQGDKASALLVEFFEKCQEDPSHWTKISQGGLQR IEENPLSTRHSVSLLLSP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0401300_circ_g.3

Address

Any questions?

Supported by