Plant Circular RNA Database

Detail information of AT5G56290_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G56290_circ_g.3
					
						ID in PlantcircBase
						ath_circ_044369
					
						Alias
						Ath_circ_FC3828
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 22787060-22789132  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT5G56290						
					
						Parent gene annotation
						
							Peroxisome biogenesis protein 5
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G56290_circ_g.1 AT5G56290_circ_g.2 AT5G56290_circ_g.4 AT5G56290_circ_g.5 AT5G56290_circ_g.6 AT5G56290_circ_g.7 AT5G56290_circ_g.8 AT5G56290_circ_g.9 AT5G56290_circ_g.10 						
					
						Support reads
						7
					
						Tissues
						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
						AT5G56290.1:5

General Information
CircRNA Name	AT5G56290_circ_g.3
ID in PlantcircBase	ath_circ_044369
Alias	Ath_circ_FC3828
Organism	Arabidpsis thaliana
Position	chr5: 22787060-22789132 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT5G56290
Parent gene annotation	Peroxisome biogenesis protein 5
Parent gene strand	+
Alternative splicing	AT5G56290_circ_g.1 AT5G56290_circ_g.2 AT5G56290_circ_g.4 AT5G56290_circ_g.5 AT5G56290_circ_g.6 AT5G56290_circ_g.7 AT5G56290_circ_g.8 AT5G56290_circ_g.9 AT5G56290_circ_g.10
Support reads	7
Tissues	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	AT5G56290.1:5

			
						 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  
						
							AAGCCAAATGAGAAGTATGGATATGCAAAATATAGCTGCAATGGAGCAGACTCGTAAGCTTGCC
CATACACTATCTCAAGATGGGAATCCGAAATTTCAGgaaaggctcaaggagatacctaatgcaa
accggtcaggtcctcggccacaattttactctgaagaccaacagataaggtcacttcctggttc
tgagttag

									
								

					

						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
						
							GAAAGGCTCAAGGAGATACCTAATGCAAACCGGTCAGGTCCTCGGCCACAATTTTACTCTGAAG
ACCAACAGATAAGGTCACTTCCTGGTTCTGAGTTAGATCAGCCACTTCTGCAACCGGGTGCTCA
GGTTAATGTTGTGGAAAGTTTTGGTTTTACAATGGTAGTATTGACTCTGATTATCTAGCCTCTG
TGATGGCTGATGGGTTTGCAATTTTTACATTAGGGGTCAGAGTTCTTCCGTGGTTTTCGCTCTG
TTGATCAGAATGGTTTGGGTGCAGCTTGGGATGAGGTACAGCAAGGTGGACCTATGCCTCCAAT
GGGACCTATGTTTGAGCCAGTTCAGCCTACATTTGAAGGTTTGTGATTTGATCTATACCACTTT
TATTTAATCCCGGATACAAAACGGTTAGATGTAGTGGTTTTGATATTGAATAAAAGGTAGTATA
TATTTTCACATATTCATCTTGAATCGAGAAGTACATAACATTATTTTTGTAGGAAGAGAAGTTA
ACACTGAAAGTGTTAGTTAGTAATTTAGTATAGCGACATGAAATAAATAGTGTGGTCATTTCTT
TCCATGAGTCCTATTTCTCCTGAATGACACGTTGAATATTCATAGCTCTGTCTTAGTTATATAG
CCTAATGTCGAGTGAGGCATTTTTCGTTTGCTTGCTTGATTAGTTTTTCCATTGCTTATATATT
GCAGGACCCCCACAGAGAGTTTTATCAAACTTTCTGCATTCATTTGTTGAGAGTAGCCGTGGTG
GTATTCCATTTCGTCCAGCACCTGTTCCAGTTCTAGGATTGTCACAAAGTGACAAACAATGTAT
ACGTGATCGTAGTAGCATAATGGCCCGGCATTTTTTTGCCGATAGGGGAGAGGAATTTATTAAT
TCTCAGGTTTGCCATTTATCTGATAGTGTTCTGTAGCTGCAACATTGTGTTATATGCTTTCAAC
TTAGGTTTTAAGGGTCGAGTATATACTTAATATTTTGGTGTTATATCATTCATGCCCATTGCCC
TTTTGAAATCAAGATCTATTCAATTATATAACGAAGTGTAATTACAAGAAAGTTCAGGTCCACT
CTCCTTCATCTTGAGTTTAAATCAAAATGTAACATTTTGGAATGCAACGAGGTAGCACTGTCAC
TGTCATATATCACAATCATCTGTGGGTCAGGGCTTTTGTTTGGGAATTATAGCTGTTGTTTTAC
TTGGTAATTGTTCCTATCTAGTATGGATTTCTCGAGACCATGCCAGCTGTGCAGTATAGTTAAG
CCTTTTGTTTGTTGCCGATGGCCTAAGCCGTTTTCTCTTCTCCATGTCGTTGGCTGAATATTTT
GTTCGGCATTGTTTTTCAAGGTAAACGCATTATTGTCATCTTTAGATATTGATGATGGGATACA
AGCTCGAGGTCATGTTCCCGGGAGATTTCGGGAGCTAGATGATTACTGGAATGAGTCTCAAGCT
GTTGTGAAACCTAATTTACATCCTGCTGACAATTGGGCGGCTGAATTTAACCAACATGGGATGG
ATCATGGTGGTCCTGATTCATGGGTCCAGTCTTTTGAGCAACAACATGGTGTGAATGGGTGGGC
TACTGAGTTCGAGCAGGTAACTAGCATAAATAGCTATATGATAGAAACTTTTTCCTTCAGTTGT
TTGAAACTTCTCTTTGATTGCCCATCCCAAACATATGTTTATAAGCTTTCAATGAGTATCAAAG
ACATTATGAGGGCATTTATTTTGGTAGTGTAGACTTTGATTTCGATAGTCACTAGGGCATAGTT
GTTCACAAGCCTGAATCTGTTGTGACTTTTTTTATGCTGTATTAGTCATCAGTGTTTGAGTCGC
ATTTGATATCCCAACAGCTTGGCTTTCTGATAATTTATCATGTTCTTCTGAAAATATTTGGCGC
CTCATCCTTTTTATTTTCTTGAACTTTCTAAAGGGTCAATCTCAATTGATGTCAAGCCAAATGA
GAAGTATGGATATGCAAAATATAGCTGCAATGGAGCAGACTCGTAAGCTTGCCCATACACTATC
TCAAGATGGGAATCCGAAATTTCAG
						
					

			
		

Sequences
Splice junction sequence	AAGCCAAATGAGAAGTATGGATATGCAAAATATAGCTGCAATGGAGCAGACTCGTAAGCTTGCC CATACACTATCTCAAGATGGGAATCCGAAATTTCAGgaaaggctcaaggagatacctaatgcaa accggtcaggtcctcggccacaattttactctgaagaccaacagataaggtcacttcctggttc tgagttag
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	GAAAGGCTCAAGGAGATACCTAATGCAAACCGGTCAGGTCCTCGGCCACAATTTTACTCTGAAG ACCAACAGATAAGGTCACTTCCTGGTTCTGAGTTAGATCAGCCACTTCTGCAACCGGGTGCTCA GGTTAATGTTGTGGAAAGTTTTGGTTTTACAATGGTAGTATTGACTCTGATTATCTAGCCTCTG TGATGGCTGATGGGTTTGCAATTTTTACATTAGGGGTCAGAGTTCTTCCGTGGTTTTCGCTCTG TTGATCAGAATGGTTTGGGTGCAGCTTGGGATGAGGTACAGCAAGGTGGACCTATGCCTCCAAT GGGACCTATGTTTGAGCCAGTTCAGCCTACATTTGAAGGTTTGTGATTTGATCTATACCACTTT TATTTAATCCCGGATACAAAACGGTTAGATGTAGTGGTTTTGATATTGAATAAAAGGTAGTATA TATTTTCACATATTCATCTTGAATCGAGAAGTACATAACATTATTTTTGTAGGAAGAGAAGTTA ACACTGAAAGTGTTAGTTAGTAATTTAGTATAGCGACATGAAATAAATAGTGTGGTCATTTCTT TCCATGAGTCCTATTTCTCCTGAATGACACGTTGAATATTCATAGCTCTGTCTTAGTTATATAG CCTAATGTCGAGTGAGGCATTTTTCGTTTGCTTGCTTGATTAGTTTTTCCATTGCTTATATATT GCAGGACCCCCACAGAGAGTTTTATCAAACTTTCTGCATTCATTTGTTGAGAGTAGCCGTGGTG GTATTCCATTTCGTCCAGCACCTGTTCCAGTTCTAGGATTGTCACAAAGTGACAAACAATGTAT ACGTGATCGTAGTAGCATAATGGCCCGGCATTTTTTTGCCGATAGGGGAGAGGAATTTATTAAT TCTCAGGTTTGCCATTTATCTGATAGTGTTCTGTAGCTGCAACATTGTGTTATATGCTTTCAAC TTAGGTTTTAAGGGTCGAGTATATACTTAATATTTTGGTGTTATATCATTCATGCCCATTGCCC TTTTGAAATCAAGATCTATTCAATTATATAACGAAGTGTAATTACAAGAAAGTTCAGGTCCACT CTCCTTCATCTTGAGTTTAAATCAAAATGTAACATTTTGGAATGCAACGAGGTAGCACTGTCAC TGTCATATATCACAATCATCTGTGGGTCAGGGCTTTTGTTTGGGAATTATAGCTGTTGTTTTAC TTGGTAATTGTTCCTATCTAGTATGGATTTCTCGAGACCATGCCAGCTGTGCAGTATAGTTAAG CCTTTTGTTTGTTGCCGATGGCCTAAGCCGTTTTCTCTTCTCCATGTCGTTGGCTGAATATTTT GTTCGGCATTGTTTTTCAAGGTAAACGCATTATTGTCATCTTTAGATATTGATGATGGGATACA AGCTCGAGGTCATGTTCCCGGGAGATTTCGGGAGCTAGATGATTACTGGAATGAGTCTCAAGCT GTTGTGAAACCTAATTTACATCCTGCTGACAATTGGGCGGCTGAATTTAACCAACATGGGATGG ATCATGGTGGTCCTGATTCATGGGTCCAGTCTTTTGAGCAACAACATGGTGTGAATGGGTGGGC TACTGAGTTCGAGCAGGTAACTAGCATAAATAGCTATATGATAGAAACTTTTTCCTTCAGTTGT TTGAAACTTCTCTTTGATTGCCCATCCCAAACATATGTTTATAAGCTTTCAATGAGTATCAAAG ACATTATGAGGGCATTTATTTTGGTAGTGTAGACTTTGATTTCGATAGTCACTAGGGCATAGTT GTTCACAAGCCTGAATCTGTTGTGACTTTTTTTATGCTGTATTAGTCATCAGTGTTTGAGTCGC ATTTGATATCCCAACAGCTTGGCTTTCTGATAATTTATCATGTTCTTCTGAAAATATTTGGCGC CTCATCCTTTTTATTTTCTTGAACTTTCTAAAGGGTCAATCTCAATTGATGTCAAGCCAAATGA GAAGTATGGATATGCAAAATATAGCTGCAATGGAGCAGACTCGTAAGCTTGCCCATACACTATC TCAAGATGGGAATCCGAAATTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.133786762

Conservation Information
Conserved circRNAs	NA
PMCS	0.133786762

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22787369-22789129(+)
						
						Potential amino acid sequence
						
							MPPMGPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSI
MARHFFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADN
WAAEFNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKL
AHTLSQDGNPKFQERLKEIPNANRSGPRPQFYSEDQQIRSLPGSELDQPLLQPGAQGSEFFRGF
RSVDQNGLGAAWDEVQQGGPMPPMGPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAP
VPVLGLSQSDKQCIRDRSSIMARHFFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFREL
DDYWNESQAVVKPNLHPADNWAAEFNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMS
SQMRSMDMQNIAAMEQTRKLAHTLSQDGNPKFQERLKEIPNANRSGPRPQFYSEDQQIRSLPGS
ELDQPLLQPGAQGSEFFRGFRSVDQNGLGAAWDEVQQGGPMPPMGPMFEPVQPTFEGPPQRVLS
NFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSIMARHFFADRGEEFINSQVNALLSS
LDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADNWAAEFNQHGMDHGGPDSWVQSFEQ
QHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKLAHTLSQDGNPKFQERLKEIPNANR
SGPRPQFYSEDQQIRSLPGSELDQPLLQPGAQGSEFFRGFRSVDQNGLGAAWDEVQQGGPMPPM
GPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSIMARH
FFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADNWAAE
FNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKLAHTL
SQDGNPKFQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22787369-22789129(+)
Potential amino acid sequence	MPPMGPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSI MARHFFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADN WAAEFNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKL AHTLSQDGNPKFQERLKEIPNANRSGPRPQFYSEDQQIRSLPGSELDQPLLQPGAQGSEFFRGF RSVDQNGLGAAWDEVQQGGPMPPMGPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAP VPVLGLSQSDKQCIRDRSSIMARHFFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFREL DDYWNESQAVVKPNLHPADNWAAEFNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMS SQMRSMDMQNIAAMEQTRKLAHTLSQDGNPKFQERLKEIPNANRSGPRPQFYSEDQQIRSLPGS ELDQPLLQPGAQGSEFFRGFRSVDQNGLGAAWDEVQQGGPMPPMGPMFEPVQPTFEGPPQRVLS NFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSIMARHFFADRGEEFINSQVNALLSS LDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADNWAAEFNQHGMDHGGPDSWVQSFEQ QHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKLAHTLSQDGNPKFQERLKEIPNANR SGPRPQFYSEDQQIRSLPGSELDQPLLQPGAQGSEFFRGFRSVDQNGLGAAWDEVQQGGPMPPM GPMFEPVQPTFEGPPQRVLSNFLHSFVESSRGGIPFRPAPVPVLGLSQSDKQCIRDRSSIMARH FFADRGEEFINSQVNALLSSLDIDDGIQARGHVPGRFRELDDYWNESQAVVKPNLHPADNWAAE FNQHGMDHGGPDSWVQSFEQQHGVNGWATEFEQGQSQLMSSQMRSMDMQNIAAMEQTRKLAHTL SQDGNPKFQ(+)
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 AT5G56290_circ_g.3

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