Plant Circular RNA Database

Detail information of Os11g0549635_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0549635_circ_g.3
					
						ID in PlantcircBase
						osa_circ_009577
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 20360991-20368483  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os11g0549635						
					
						Parent gene annotation
						
							Similar to ABC1 family protein. (Os11t0549635-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0549635_circ_g.1 Os11g0549635_circ_g.2 Os11g0549635_circ_ag.1 Os11g0549635_circ_ag.2 Os11g0549635_circ_ag.3 Os11g0549635_circ_ag.4 Os11g0549650_circ_g.1 Os11g0549650_circ_g.2 Os11g0549650_circ_ag.1 Os11g0549650_circ_ag.2 Os11g0549650_circ_ag.3 Os11g0549650_circ_ag.4 Os11g0549650_circ_ag.5 Os11g0549650_circ_ag.6 Os11g0549655_circ_ag.1 Os11g0549655_circ_ag.2 Os11g0549655_circ_ag.3 Os11g0549655_circ_ag.4 Os11g0549655_circ_ag.5 Os11g0549665_circ_g.1 Os11g0549665_circ_g.2 Os11g0549665_circ_g.3 Os11g0549670_circ_g.1 Os11g0549680_circ_g.1 Os11g0549680_circ_g.2 Os11g0549690_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os11t0549635-00:12

General Information
CircRNA Name	Os11g0549635_circ_g.3
ID in PlantcircBase	osa_circ_009577
Alias	NA
Organism	Oryza sativa
Position	chr11: 20360991-20368483 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os11g0549635
Parent gene annotation	Similar to ABC1 family protein. (Os11t0549635-00)
Parent gene strand	+
Alternative splicing	Os11g0549635_circ_g.1 Os11g0549635_circ_g.2 Os11g0549635_circ_ag.1 Os11g0549635_circ_ag.2 Os11g0549635_circ_ag.3 Os11g0549635_circ_ag.4 Os11g0549650_circ_g.1 Os11g0549650_circ_g.2 Os11g0549650_circ_ag.1 Os11g0549650_circ_ag.2 Os11g0549650_circ_ag.3 Os11g0549650_circ_ag.4 Os11g0549650_circ_ag.5 Os11g0549650_circ_ag.6 Os11g0549655_circ_ag.1 Os11g0549655_circ_ag.2 Os11g0549655_circ_ag.3 Os11g0549655_circ_ag.4 Os11g0549655_circ_ag.5 Os11g0549665_circ_g.1 Os11g0549665_circ_g.2 Os11g0549665_circ_g.3 Os11g0549670_circ_g.1 Os11g0549680_circ_g.1 Os11g0549680_circ_g.2 Os11g0549690_circ_g.1
Support reads	1
Tissues	shoot
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	Os11t0549635-00:12

			
						 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  
						
							TCAATTTTAGGTAATCTAGGTGCACCACGCCATGTGCGACTTCTTACCTATGCAAAATGCGCTT
TGTACGGCCTTGAAGAACAGCCCAAATCACAGTCAGgttcatttgcgttcagcaaaaaagatac
tcaaactatgtgaagcgaacagagggttttatgtaaaggctggtcaatttgtttcgtcaataag
acaagtac

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	TCAATTTTAGGTAATCTAGGTGCACCACGCCATGTGCGACTTCTTACCTATGCAAAATGCGCTT TGTACGGCCTTGAAGAACAGCCCAAATCACAGTCAGgttcatttgcgttcagcaaaaaagatac tcaaactatgtgaagcgaacagagggttttatgtaaaggctggtcaatttgtttcgtcaataag acaagtac
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.095108564

Conservation Information
Conserved circRNAs	NA
PMCS	0.095108564

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20363643-20361028(+)
20368416-20361028(+)
20360998-20368429(-)
						
						Potential amino acid sequence
						
							MKIDIMTMSFLSKSLSWIFPDYRFEKLLTEFERTMSMELDFIQEAKNSERTASCFRKNNVVKVP
CVFWELTSKEVLTMEFCSGYKVDNLNSLRKADISPTKVAKALIELFGEMIFVHGFVHGDPHPGN
ILVSPQGQGKFSLVLLDHGIYKELDQKFRLDYCQLWKALILLDSQKILELGEHFGVGKYAKYFP
VIFTGRTIESKSILGTQMSIEEKTRLKQDLNSLGMDDISSFMESLPPDFLTILRTDGLLRSILG
NLGAPRHVRLLTYAKCALYGLEEQPKSQSGSFAFSKKDTQTM*(+)
MCDFLPMQNALCTALKNSPNHSQVHLRSAKKILKLCEANRGFYVKAGQFVSSIRQVPKEYSSTL
SCLQDQATPCNFQDIKIVIEQKLGKDLHSIFLEFDEHPIAAASIAQVHRGRLNNNQEVAVKVQY
PGLERRMKIDIMTMSFLSKSLSWIFPDYRFEKLLTEFERTMSMELDFIQEAKNSERTASCFRKN
NVVKVPCVFWELTSKEVLTMEFCSGYKVDNLNSLRKADISPTKVAKALIELFGEMIFVHGFVHG
DPHPGNILVSPQGQGKFSLVLLDHGIYKELDQKFRLDYCQLWKALILLDSQKILELGEHFGVGK
YAKYFPVIFTGRTIESKSILGTQMSIEEKTRLKQDLNSLGMDDISSFMESLPPDFLTILRTDGL
LRSILGNLGAPRHVRLLTYAKCALYGLEEQPKSQSGSFAFSKKDTQTM*(+)
MNLTVIWAVLQGRTKRILHR*(-)
						
						Sponge-miRNAs
						
							osa-miR5144-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20363643-20361028(+) 20368416-20361028(+) 20360998-20368429(-)
Potential amino acid sequence	MKIDIMTMSFLSKSLSWIFPDYRFEKLLTEFERTMSMELDFIQEAKNSERTASCFRKNNVVKVP CVFWELTSKEVLTMEFCSGYKVDNLNSLRKADISPTKVAKALIELFGEMIFVHGFVHGDPHPGN ILVSPQGQGKFSLVLLDHGIYKELDQKFRLDYCQLWKALILLDSQKILELGEHFGVGKYAKYFP VIFTGRTIESKSILGTQMSIEEKTRLKQDLNSLGMDDISSFMESLPPDFLTILRTDGLLRSILG NLGAPRHVRLLTYAKCALYGLEEQPKSQSGSFAFSKKDTQTM(+) MCDFLPMQNALCTALKNSPNHSQVHLRSAKKILKLCEANRGFYVKAGQFVSSIRQVPKEYSSTL SCLQDQATPCNFQDIKIVIEQKLGKDLHSIFLEFDEHPIAAASIAQVHRGRLNNNQEVAVKVQY PGLERRMKIDIMTMSFLSKSLSWIFPDYRFEKLLTEFERTMSMELDFIQEAKNSERTASCFRKN NVVKVPCVFWELTSKEVLTMEFCSGYKVDNLNSLRKADISPTKVAKALIELFGEMIFVHGFVHG DPHPGNILVSPQGQGKFSLVLLDHGIYKELDQKFRLDYCQLWKALILLDSQKILELGEHFGVGK YAKYFPVIFTGRTIESKSILGTQMSIEEKTRLKQDLNSLGMDDISSFMESLPPDFLTILRTDGL LRSILGNLGAPRHVRLLTYAKCALYGLEEQPKSQSGSFAFSKKDTQTM(+) MNLTVIWAVLQGRTKRILHR*(-)
Sponge-miRNAs	osa-miR5144-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os11g0549635_circ_g.3

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