Plant Circular RNA Database

Detail information of Os03g0566800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0566800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_020487
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 20493445-20493777  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							Os03g0566800						
					
						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 
(Os03t0566800-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						36
					
						Tissues
						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  
						
							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
						Os03t0566800-01:2

General Information
CircRNA Name	Os03g0566800_circ_g.1
ID in PlantcircBase	osa_circ_020487
Alias	NA
Organism	Oryza sativa
Position	chr3: 20493445-20493777 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	Os03g0566800
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 (Os03t0566800-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	36
Tissues	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	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	Os03t0566800-01:2

			
						 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  
						
							ATTCACCCATAATGGCATCCCTTTCCTTTTGAGGCATGTCACCATGCATAGCTGATACCGTGAA
GTTATTGCTGCGCATTCTTTCTGTAAGCCAATCAACcttgcgaccaaaacgtccagagcgacca
atgcgatggatgtaaagttcacgattatttggaagatcatagtttatgacaagagagacctgaa
aatgaaaa

						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
						
							CTTGCGACCAAAACGTCCAGAGCGACCAATGCGATGGATGTAAAGTTCACGATTATTTGGAAGA
TCATAGTTTATGACAAGAGAGACCTGAAAATGAAAATAATAATCAATACTCCACGCGCAGTAAA
ATCAATAGTCTTCAAACAAAAATCACAACAATCTTGCCTGCTGAACATCCAGGCCTCGAGCCCA
CACATCTGTCGTAATTAGAACACGGGTTGCACCAGACCTGAATTCACCCATAATGGCATCCCTT
TCCTTTTGAGGCATGTCACCATGCATAGCTGATACCGTGAAGTTATTGCTGCGCATTCTTTCTG
TAAGCCAATCAAC

Sequences
Splice junction sequence	ATTCACCCATAATGGCATCCCTTTCCTTTTGAGGCATGTCACCATGCATAGCTGATACCGTGAA GTTATTGCTGCGCATTCTTTCTGTAAGCCAATCAACcttgcgaccaaaacgtccagagcgacca atgcgatggatgtaaagttcacgattatttggaagatcatagtttatgacaagagagacctgaa aatgaaaa
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	CTTGCGACCAAAACGTCCAGAGCGACCAATGCGATGGATGTAAAGTTCACGATTATTTGGAAGA TCATAGTTTATGACAAGAGAGACCTGAAAATGAAAATAATAATCAATACTCCACGCGCAGTAAA ATCAATAGTCTTCAAACAAAAATCACAACAATCTTGCCTGCTGAACATCCAGGCCTCGAGCCCA CACATCTGTCGTAATTAGAACACGGGTTGCACCAGACCTGAATTCACCCATAATGGCATCCCTT TCCTTTTGAGGCATGTCACCATGCATAGCTGATACCGTGAAGTTATTGCTGCGCATTCTTTCTG TAAGCCAATCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.322877903

Conservation Information
Conserved circRNAs	NA
PMCS	0.322877903

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20493714-20493484(+)
20493758-20493447(-)
20493514-20493653(-)
						
						Potential amino acid sequence
						
							MSPCIADTVKLLLRILSVSQSTLRPKRPERPMRWM*(+)
MRSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNREL
YIHRIGRSGRFGRKVDWLTERMRSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWAR
GLDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKVDWLTERMRSNNFTVSAMHGDMPQKERDA
IMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKVDWLTERM
RSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNRELY
IHRIGRSGRFGRK(-)
MIFQIIVNFTSIALVALDVLVARLIGLQKECAAITSRYQLCMVTCLKRKGMPLWVNSGLVQPVF
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20493714-20493484(+) 20493758-20493447(-) 20493514-20493653(-)
Potential amino acid sequence	MSPCIADTVKLLLRILSVSQSTLRPKRPERPMRWM(+) MRSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNREL YIHRIGRSGRFGRKVDWLTERMRSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWAR GLDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKVDWLTERMRSNNFTVSAMHGDMPQKERDA IMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKVDWLTERM RSNNFTVSAMHGDMPQKERDAIMGEFRSGATRVLITTDVWARGLDVQQVSLVINYDLPNNRELY IHRIGRSGRFGRK(-) MIFQIIVNFTSIALVALDVLVARLIGLQKECAAITSRYQLCMVTCLKRKGMPLWVNSGLVQPVF (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0566800_circ_g.1

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