Plant Circular RNA Database

Detail information of AT5G38470_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G38470_circ_g.3
					
						ID in PlantcircBase
						ath_circ_041503
					
						Alias
						Ath_circ_FC3608
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 15405695-15407273  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT5G38470						
					
						Parent gene annotation
						
							Ubiquitin receptor RAD23d
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G38470_circ_g.1 AT5G38470_circ_g.2 AT5G38470_circ_g.4 AT5G38470_circ_g.5 AT5G38470_circ_g.6 AT5G38470_circ_g.7 AT5G38470_circ_g.8 AT5G38470_circ_g.9 						
					
						Support reads
						2
					
						Tissues
						root, whole_plant
					
						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
						AT5G38470.1:9
AT5G38470.2:9

General Information
CircRNA Name	AT5G38470_circ_g.3
ID in PlantcircBase	ath_circ_041503
Alias	Ath_circ_FC3608
Organism	Arabidpsis thaliana
Position	chr5: 15405695-15407273 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT5G38470
Parent gene annotation	Ubiquitin receptor RAD23d
Parent gene strand	+
Alternative splicing	AT5G38470_circ_g.1 AT5G38470_circ_g.2 AT5G38470_circ_g.4 AT5G38470_circ_g.5 AT5G38470_circ_g.6 AT5G38470_circ_g.7 AT5G38470_circ_g.8 AT5G38470_circ_g.9
Support reads	2
Tissues	root, whole_plant
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	AT5G38470.1:9 AT5G38470.2:9

			
						 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  
						
							CATTTCATTCGATGCCACCAGGAATGTTATGGAACAGTTGGAAGCAGCAATGCCACAAGCTGTT
ACCGTTACACCTGAAGAGCGTGAAGCCATTGAACGGaccaaggcttctccaagtggggcatcaa
ccgcatctgcaccagcacctagtgctacacaggtgaataaaagttcttatgtaatatggttatg
gtttctat

									
								

					

						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
						
							ACCAAGGCTTCTCCAAGTGGGGCATCAACCGCATCTGCACCAGCACCTAGTGCTACACAGGTGA
ATAAAAGTTCTTATGTAATATGGTTATGGTTTCTATTTGTAAGTGACAACAAAATAGTATATCT
AGATAACAGTTTTGTCTAATAGAATTGCTTGGATTTTCTGTAACAGCCACAGACAGTAGCTACA
CCTCAGGTTTCTGCTCCTACTGCCTCAGTGTAAGTTGCCTTCCTCTGGCATTGATTTACCTCCT
TTTGAAAGAGAAATTGTCAGCTTCTTATGTAGTTGCCGGTTTGCTGATTCTCTGTTCTTTTTAC
TTGCGTTCTCAGTCCAGTTCCTACAAGTGGAACTGCAACCGCTGCAGCTCCAGCTACTGCTGCT
TCGTAAGAACTTTTCAGAAGTATACTATATTCATTTTCGAATATCTGTTCATTGATTGTGTAAA
TGTTGCCCACTTTCTTGGTTGAAACAGGGTTCAGACAGATGTGTATGGTCAAGCAGCATCAAAC
CTTGTTGCTGGAACTACTTTAGAGTCCACTGTTCAGCAAATTCTTGATATGGGTGGAGGTAGTT
GGGACCGTGACACTGTTGTTCGTGCTCTGAGAGCTGCGTTCAACAATCCTGAAAGAGCTGTTGA
ATACCTGTACTCGGTATGATTCATTCCACTTCTTGATTTTACGTTTTTCTTTGATATATTGTAT
CTACCTTTGATTTGCGGTTTGCCAGAATTTAAGCAACATTTGCTCTTGAACTTTTGGTTGATAC
ATTTCAGGGTATCCCTGCTCAAGCTGAAATCCCACCAGTTGCTCAAGCCCCAGCTACTGGGGAA
CAGGCAGCCAATCCTCTAGCACAGCCCCAACAAGCAGCAGCTCCAGCAGCTGCAACTGGTGGTC
CAAACGCAAATCCATTAAACCTGTTCCCCCAGGTAGGGTTTTTAAACTGGTGAACCGATTTCAT
TTGCTCGTTTTCCCTTGTGAATTTGTTTTATTGACATCCACTCTTATCTGTCTCTATCCAGGGC
ATGCCCGCTGCAGATGCTGGTGCTGGAGCTGGTAATCTTGATTTCCTGCGTAACAGTCAACAGG
TATTTTCAATTTCTTTTCCATTCGAGAACGGAAATCTTCATTTCTCTCCTCTTATGTCATTTGC
AATTCTTTTGCCTTTTCATAGTTCCAAGCCTTGCGAGCTATGGTACAAGCAAACCCACAAATTC
TACAGGTAAAATTTTTAACCTCTTATTCTTTATTTGGTAGGTTATATGATATTGATTTCCCACT
TATACTGTTTCGTTTTGCAGCCTATGCTTCAGGAGCTCGGTAAACAAAACCCCCAGCTTGTGCG
ACTAATTCAAGAGCACCAGGCTGACTTCCTACGCTTGATAAACGAACCTGTCGAGGGAGAAGAG
TGGGTTTAATATCATGATTCTCCTTTACGTTTTCATTTTATTCTTTTTTCTCAATAAAGCATGT
AATCTGACATTTCATTCGATGCCACCAGGAATGTTATGGAACAGTTGGAAGCAGCAATGCCACA
AGCTGTTACCGTTACACCTGAAGAGCGTGAAGCCATTGAACGG
						
					

			
		

Sequences
Splice junction sequence	CATTTCATTCGATGCCACCAGGAATGTTATGGAACAGTTGGAAGCAGCAATGCCACAAGCTGTT ACCGTTACACCTGAAGAGCGTGAAGCCATTGAACGGaccaaggcttctccaagtggggcatcaa ccgcatctgcaccagcacctagtgctacacaggtgaataaaagttcttatgtaatatggttatg gtttctat
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	ACCAAGGCTTCTCCAAGTGGGGCATCAACCGCATCTGCACCAGCACCTAGTGCTACACAGGTGA ATAAAAGTTCTTATGTAATATGGTTATGGTTTCTATTTGTAAGTGACAACAAAATAGTATATCT AGATAACAGTTTTGTCTAATAGAATTGCTTGGATTTTCTGTAACAGCCACAGACAGTAGCTACA CCTCAGGTTTCTGCTCCTACTGCCTCAGTGTAAGTTGCCTTCCTCTGGCATTGATTTACCTCCT TTTGAAAGAGAAATTGTCAGCTTCTTATGTAGTTGCCGGTTTGCTGATTCTCTGTTCTTTTTAC TTGCGTTCTCAGTCCAGTTCCTACAAGTGGAACTGCAACCGCTGCAGCTCCAGCTACTGCTGCT TCGTAAGAACTTTTCAGAAGTATACTATATTCATTTTCGAATATCTGTTCATTGATTGTGTAAA TGTTGCCCACTTTCTTGGTTGAAACAGGGTTCAGACAGATGTGTATGGTCAAGCAGCATCAAAC CTTGTTGCTGGAACTACTTTAGAGTCCACTGTTCAGCAAATTCTTGATATGGGTGGAGGTAGTT GGGACCGTGACACTGTTGTTCGTGCTCTGAGAGCTGCGTTCAACAATCCTGAAAGAGCTGTTGA ATACCTGTACTCGGTATGATTCATTCCACTTCTTGATTTTACGTTTTTCTTTGATATATTGTAT CTACCTTTGATTTGCGGTTTGCCAGAATTTAAGCAACATTTGCTCTTGAACTTTTGGTTGATAC ATTTCAGGGTATCCCTGCTCAAGCTGAAATCCCACCAGTTGCTCAAGCCCCAGCTACTGGGGAA CAGGCAGCCAATCCTCTAGCACAGCCCCAACAAGCAGCAGCTCCAGCAGCTGCAACTGGTGGTC CAAACGCAAATCCATTAAACCTGTTCCCCCAGGTAGGGTTTTTAAACTGGTGAACCGATTTCAT TTGCTCGTTTTCCCTTGTGAATTTGTTTTATTGACATCCACTCTTATCTGTCTCTATCCAGGGC ATGCCCGCTGCAGATGCTGGTGCTGGAGCTGGTAATCTTGATTTCCTGCGTAACAGTCAACAGG TATTTTCAATTTCTTTTCCATTCGAGAACGGAAATCTTCATTTCTCTCCTCTTATGTCATTTGC AATTCTTTTGCCTTTTCATAGTTCCAAGCCTTGCGAGCTATGGTACAAGCAAACCCACAAATTC TACAGGTAAAATTTTTAACCTCTTATTCTTTATTTGGTAGGTTATATGATATTGATTTCCCACT TATACTGTTTCGTTTTGCAGCCTATGCTTCAGGAGCTCGGTAAACAAAACCCCCAGCTTGTGCG ACTAATTCAAGAGCACCAGGCTGACTTCCTACGCTTGATAAACGAACCTGTCGAGGGAGAAGAG TGGGTTTAATATCATGATTCTCCTTTACGTTTTCATTTTATTCTTTTTTCTCAATAAAGCATGT AATCTGACATTTCATTCGATGCCACCAGGAATGTTATGGAACAGTTGGAAGCAGCAATGCCACA AGCTGTTACCGTTACACCTGAAGAGCGTGAAGCCATTGAACGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.153830501

Conservation Information
Conserved circRNAs	NA
PMCS	0.153830501

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							15406255-15407270(+)
						
						Potential amino acid sequence
						
							MGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQPQQAAA
PAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQILQPMLQELGK
QNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEEREAIERTKASPSGAST
ASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASNLVAGTTLE
STVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPL
AQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQILQ
PMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEEREAIERTK
ASPSGASTASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASN
LVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPAT
GEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMV
QANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEE
REAIERTKASPSGASTASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTD
VYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIP
PVAQAPATGEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQ
FQALRAMVQANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQ
AVTVTPEEREAIER(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	15406255-15407270(+)
Potential amino acid sequence	MGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPLAQPQQAAA PAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQILQPMLQELGK QNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEEREAIERTKASPSGAST ASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASNLVAGTTLE STVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPATGEQAANPL AQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMVQANPQILQ PMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEEREAIERTK ASPSGASTASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTDVYGQAASN LVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIPPVAQAPAT GEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQFQALRAMV QANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQAVTVTPEE REAIERTKASPSGASTASAPAPSATQPQTVATPQVSAPTASVPVPTSGTATAAAPATAASVQTD VYGQAASNLVAGTTLESTVQQILDMGGGSWDRDTVVRALRAAFNNPERAVEYLYSGIPAQAEIP PVAQAPATGEQAANPLAQPQQAAAPAAATGGPNANPLNLFPQGMPAADAGAGAGNLDFLRNSQQ FQALRAMVQANPQILQPMLQELGKQNPQLVRLIQEHQADFLRLINEPVEGEENVMEQLEAAMPQ AVTVTPEEREAIER(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G38470_circ_g.3

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