Plant Circular RNA Database

Detail information of Os04g0280200_circ_g.22

			
						 General Information
					
						CircRNA Name
						Os04g0280200_circ_g.22
					
						ID in PlantcircBase
						osa_circ_023303
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11878215-11879118  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0280251						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0280251-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0280200_circ_g.2 Os04g0280200_circ_g.3 Os04g0280200_circ_g.4 Os04g0280200_circ_g.5 Os04g0280200_circ_g.6 Os04g0280200_circ_g.7 Os04g0280200_circ_g.8 Os04g0280200_circ_g.9 Os04g0280200_circ_g.10 Os04g0280200_circ_g.11 Os04g0280200_circ_g.12 Os04g0280200_circ_g.13 Os04g0280200_circ_g.14 Os04g0280200_circ_g.15 Os04g0280200_circ_g.16 Os04g0280200_circ_g.17 Os04g0280200_circ_g.18 Os04g0280200_circ_g.19 Os04g0280200_circ_g.20 Os04g0280200_circ_g.21 Os04g0280200_circ_g.23 Os04g0280200_circ_g.24 Os04g0280200_circ_g.25 Os04g0280200_circ_g.26 Os04g0280200_circ_g.27 Os04g0280200_circ_g.28 Os04g0280200_circ_g.29 						
					
						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
						Os04t0280200-01:2
Os04t0280251-00:2
Os04t0280200-01:2

General Information
CircRNA Name	Os04g0280200_circ_g.22
ID in PlantcircBase	osa_circ_023303
Alias	NA
Organism	Oryza sativa
Position	chr4: 11878215-11879118 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ui-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0280251
Parent gene annotation	Hypothetical protein. (Os04t0280251-00)
Parent gene strand	-
Alternative splicing	Os04g0280200_circ_g.2 Os04g0280200_circ_g.3 Os04g0280200_circ_g.4 Os04g0280200_circ_g.5 Os04g0280200_circ_g.6 Os04g0280200_circ_g.7 Os04g0280200_circ_g.8 Os04g0280200_circ_g.9 Os04g0280200_circ_g.10 Os04g0280200_circ_g.11 Os04g0280200_circ_g.12 Os04g0280200_circ_g.13 Os04g0280200_circ_g.14 Os04g0280200_circ_g.15 Os04g0280200_circ_g.16 Os04g0280200_circ_g.17 Os04g0280200_circ_g.18 Os04g0280200_circ_g.19 Os04g0280200_circ_g.20 Os04g0280200_circ_g.21 Os04g0280200_circ_g.23 Os04g0280200_circ_g.24 Os04g0280200_circ_g.25 Os04g0280200_circ_g.26 Os04g0280200_circ_g.27 Os04g0280200_circ_g.28 Os04g0280200_circ_g.29
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	Os04t0280200-01:2 Os04t0280251-00:2 Os04t0280200-01:2

			
						 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  
						
							GATCAGAAAGAATCACAAAGCAGAAGTTCCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAA
TTCGAGGAGCTTCAAGTCTCTGAGGAATGTGGAGTGgtggccctagtggatcaggcaagacaag
tttagctcagaagatggccaatataattggttgtgaagttataagcttggagagttattataag
cctgaaca

						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: 269
Transcript exons: 11878215-11878372,11879008-11879118
GTGGCCCTAGTGGATCAGGCAAGACAAGTTTAGCTCAGAAGATGGCCAATATAATTGGTTGTGA
AGTTATAAGCTTGGAGAGTTATTATAAGCCTGAACAAGTTAGGGATTATAAATATGATGAGTAT
AGCTCATTGGATATAGGTTTGCTTACTAAGAACATTATGGAGATCAGAAAGAATCACAAAGCAG
AAGTTCCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAATTCGAGGAGCTTCAAGTCTCTGA
GGAATGTGGAGTG
						
						Genomic sequence
						
							GTGGCCCTAGTGGATCAGGCAAGACAAGTTTAGCTCAGAAGATGGCCAATATAATTGGTTGTGA
AGTTATAAGCTTGGAGAGTTATTATAAGCCTGAACAAGTTAGGGATTATAAATATGATGAGTAT
AGCTCATTGGATATAGGTTTGCTTACTAAGGTGATTCCTTTTTATATTGATTCCTTTTCTGTAT
TATCATGTGAATTACAAATTCCTGTGCATAACTACTAGAATCTTAAATATTTCAAGCATGCTTC
CAAATTTCTATCTTGTTCTAAAAGTCGATGCAAGGCGCCGCCTAGGCACTTGGTAGCTGCCACG
ATTAGGCATTAGATAGTGCATTAGGAGGCTAACCTACTTTGGGCGCTATTGTGTTGCTATTTTT
CTCTATGTAATATGCTTGATAATTTCTTGGATTCTATGATTGGTATGTCCTAGGTGCCCGCTAG
GCACTAGGCACCAGCTCTGCTGACCCTCTAGCACCTAGCGCCTTCTTGAACCATGTTTCTATCT
ATACGAGATCACTTGAATTTAGGGTTCAAAATCTGGTGGTGAACAACCACATTACCAGATAATT
CTTGTATTTACAAAACTGATTTTAATTCAACAGAGACAGAAAATTATTATGTGACATTAATTTG
CCAGAAATATGTATTGGTTATATTAAGCATTCAATAGTGGTGATAAAATTATTCTTACTCCACA
GCATTTTGCATGCTGCCTTTTCTTTTCTGGAATCATATGGTTGGGTTCTATAGTGCCTGTTAAA
TGACGATTCTCTTATCGCCCCGCAGAACATTATGGAGATCAGAAAGAATCACAAAGCAGAAGTT
CCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAATTCGAGGAGCTTCAAGTCTCTGAGGAAT
GTGGAGTG

Sequences
Splice junction sequence	GATCAGAAAGAATCACAAAGCAGAAGTTCCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAA TTCGAGGAGCTTCAAGTCTCTGAGGAATGTGGAGTGgtggccctagtggatcaggcaagacaag tttagctcagaagatggccaatataattggttgtgaagttataagcttggagagttattataag cctgaaca
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: 269 Transcript exons: 11878215-11878372,11879008-11879118 GTGGCCCTAGTGGATCAGGCAAGACAAGTTTAGCTCAGAAGATGGCCAATATAATTGGTTGTGA AGTTATAAGCTTGGAGAGTTATTATAAGCCTGAACAAGTTAGGGATTATAAATATGATGAGTAT AGCTCATTGGATATAGGTTTGCTTACTAAGAACATTATGGAGATCAGAAAGAATCACAAAGCAG AAGTTCCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAATTCGAGGAGCTTCAAGTCTCTGA GGAATGTGGAGTG
Genomic sequence	GTGGCCCTAGTGGATCAGGCAAGACAAGTTTAGCTCAGAAGATGGCCAATATAATTGGTTGTGA AGTTATAAGCTTGGAGAGTTATTATAAGCCTGAACAAGTTAGGGATTATAAATATGATGAGTAT AGCTCATTGGATATAGGTTTGCTTACTAAGGTGATTCCTTTTTATATTGATTCCTTTTCTGTAT TATCATGTGAATTACAAATTCCTGTGCATAACTACTAGAATCTTAAATATTTCAAGCATGCTTC CAAATTTCTATCTTGTTCTAAAAGTCGATGCAAGGCGCCGCCTAGGCACTTGGTAGCTGCCACG ATTAGGCATTAGATAGTGCATTAGGAGGCTAACCTACTTTGGGCGCTATTGTGTTGCTATTTTT CTCTATGTAATATGCTTGATAATTTCTTGGATTCTATGATTGGTATGTCCTAGGTGCCCGCTAG GCACTAGGCACCAGCTCTGCTGACCCTCTAGCACCTAGCGCCTTCTTGAACCATGTTTCTATCT ATACGAGATCACTTGAATTTAGGGTTCAAAATCTGGTGGTGAACAACCACATTACCAGATAATT CTTGTATTTACAAAACTGATTTTAATTCAACAGAGACAGAAAATTATTATGTGACATTAATTTG CCAGAAATATGTATTGGTTATATTAAGCATTCAATAGTGGTGATAAAATTATTCTTACTCCACA GCATTTTGCATGCTGCCTTTTCTTTTCTGGAATCATATGGTTGGGTTCTATAGTGCCTGTTAAA TGACGATTCTCTTATCGCCCCGCAGAACATTATGGAGATCAGAAAGAATCACAAAGCAGAAGTT CCTTGCTTTGACTTTGAGAAGTGCAAAAGAAAGAAATTCGAGGAGCTTCAAGTCTCTGAGGAAT GTGGAGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015183 						
					
						PMCS
						0.138467542

Conservation Information
Conserved circRNAs	osi_circ_015183
PMCS	0.138467542

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11879110-11878244(+)
11878257-11878244(+)
						
						Potential amino acid sequence
						
							MWSGGPSGSGKTSLAQKMANIIGCEVISLESYYKPEQVRDYKYDEYSSLDIGLLTKNIMEIRKN
HKAEVPCFDFEKCKRKKFEELQVSEECGVVALVDQARQV*(+)
MANIIGCEVISLESYYKPEQVRDYKYDEYSSLDIGLLTKNIMEIRKNHKAEVPCFDFEKCKRKK
FEELQVSEECGVVALVDQARQV*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11879110-11878244(+) 11878257-11878244(+)
Potential amino acid sequence	MWSGGPSGSGKTSLAQKMANIIGCEVISLESYYKPEQVRDYKYDEYSSLDIGLLTKNIMEIRKN HKAEVPCFDFEKCKRKKFEELQVSEECGVVALVDQARQV(+) MANIIGCEVISLESYYKPEQVRDYKYDEYSSLDIGLLTKNIMEIRKNHKAEVPCFDFEKCKRKK FEELQVSEECGVVALVDQARQV(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0280200_circ_g.22

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