Plant Circular RNA Database

Detail information of Solyc04g072290.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc04g072290.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001489
					
						Alias
						4:56912900|56922197
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 59319530-59328827  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g072290.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g072290.2_circ_g.1 Solyc04g072290.2_circ_g.3 						
					
						Support reads
						7
					
						Tissues
						fruit
					
						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
						Solyc04g072290.2.1:15

General Information
CircRNA Name	Solyc04g072290.2_circ_g.2
ID in PlantcircBase	sly_circ_001489
Alias	4:56912900\|56922197
Organism	Solanum lycopersicum
Position	chr4: 59319530-59328827 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g072290.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc04g072290.2_circ_g.1 Solyc04g072290.2_circ_g.3
Support reads	7
Tissues	fruit
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	Solyc04g072290.2.1:15

			
						 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  
						
							ATTTCTGGCACTCAAGTTCACATCTCTTATATTAAGTTCTTTGATTGCTTCTCAGGTTAATTTT
GAGGACACTTGCAAAGGGTTTCTAGAGGTTGCAAAGgttgagcaagctcaaggtggtctgcaat
cactttctttatctcagaagactataaatcagctccgagaaaacttcctttctattgaaaagta
taataatg

						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	ATTTCTGGCACTCAAGTTCACATCTCTTATATTAAGTTCTTTGATTGCTTCTCAGGTTAATTTT GAGGACACTTGCAAAGGGTTTCTAGAGGTTGCAAAGgttgagcaagctcaaggtggtctgcaat cactttctttatctcagaagactataaatcagctccgagaaaacttcctttctattgaaaagta taataatg
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
						0.157340645

Conservation Information
Conserved circRNAs	NA
PMCS	0.157340645

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							59320394-59328824(+)
						
					

						Potential amino acid sequence
						
							MMSISVEASEARDSLRDDKELINTYERLTALDGKRRFALAAAGSHKEEVGRLREYFEDVDRTWE
TFEKTLWAHIANFSKLAKDSPQTLVRAIRVVEMQEILDQQLAEEAAEAEGGGAMASVANPRRNA
KKTTSSKNLTQQKLKAQGKGYKDKCYESIRKSVEARFDKLLDEQDLKTAIEEARVIGEELGEIY
DYVAPCFPPRYEVFQLMVNLYTERFVQWLRKMSDQASNMTNIEILKVTGWVVDYQESLIELGVD
DSLAQVCSESGAMDPLMNAYVERMQATTKKWYLNILEADKVQPPKKTDDGKLYTPAAVDLFRIL
GEQVQIVRENSTDVMLYRIALALIQVMIDFQAAERKRLEEPASEIGLESLCAMINNNLRCYDLA
MELSSSTLEALPQNYAEQVNFEDTCKGFLEVAKVEQAQGGLQSLSLSQKTINQLRENFLSIEKL
CQECQTLIENHDQIKILSNTRNNLNTTLKDVEGMMSISVEASEARDSLRDDKELINTYERLTAL
DGKRRFALAAAGSHKEEVGRLREYFEDVDRTWETFEKTLWAHIANFSKLAKDSPQTLVRAIRVV
EMQEILDQQLAEEAAEAEGGGAMASVANPRRNAKKTTSSKNLTQQKLKAQGKGYKDKCYESIRK
SVEARFDKLLDEQDLKTAIEEARVIGEELGEIYDYVAPCFPPRYEVFQLMVNLYTERFVQWLRK
MSDQASNMTNIEILKVTGWVVDYQESLIELGVDDSLAQVCSESGAMDPLMNAYVERMQATTKKW
YLNILEADKVQPPKKTDDGKLYTPAAVDLFRILGEQVQIVRENSTDVMLYRIALALIQVMIDFQ
AAERKRLEEPASEIGLESLCAMINNNLRCYDLAMELSSSTLEALPQNYAEQVNFEDTCKGFLEV
AKVEQAQGGLQSLSLSQKTINQLRENFLSIEKLCQECQTLIENHDQIKILSNTRNNLNTTLKDV
EGMMSISVEASEARDSLRDDKELINTYERLTALDGKRRFALAAAGSHKEEVGRLREYFEDVDRT
WETFEKTLWAHIANFSKLAKDSPQTLVRAIRVVEMQEILDQQLAEEAAEAEGGGAMASVANPRR
NAKKTTSSKNLTQQKLKAQGKGYKDKCYESIRKSVEARFDKLLDEQDLKTAIEEARVIGEELGE
IYDYVAPCFPPRYEVFQLMVNLYTERFVQWLRKMSDQASNMTNIEILKVTGWVVDYQESLIELG
VDDSLAQVCSESGAMDPLMNAYVERMQATTKKWYLNILEADKVQPPKKTDDGKLYTPAAVDLFR
ILGEQVQIVRENSTDVMLYRIALALIQVMIDFQAAERKRLEEPASEIGLESLCAMINNNLRCYD
LAMELSSSTLEALPQNYAEQVNFEDTCKGFLEVAKVEQAQGGLQSLSLSQKTINQLRENFLSIE
KLCQECQTLIENHDQIKILSNTRNNLNTTLKDVEGMMSISVEASEARDSLRDDKELINTYERLT
ALDGKRRFALAAAGSHKEEVGRLREYFEDVDRTWETFEKTLWAHIANFSKLAKDSPQTLVRAIR
VVEMQEILDQQLAEEAAEAEGGGAMASVANPRRNAKKTTSSKNLTQQKLKAQGKGYKDKCYESI
RKSVEARFDKLLDEQDLKTAIEEARVIGEELGEIYDYVAPCFPPRYEVFQLMVNLYTERFVQWL
RKMSDQASNMTNIEILKVTGWVVDYQESLIELGVDDSLAQVCSESGAMDPLMNAYVERMQATTK
KWYLNILEADKVQPPKKTDDGKLYTPAAVDLFRILGEQVQIVRENSTDVMLYRIALALIQVMID
FQAAERKRLEEPASEIGLESLCAMINNNLRCYDLAMELSSSTLEALPQNYAEQVNFEDTCKGFL
EVAK(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						fruit ripening
					

			
		

Functional Information
Coding potential	Y
Potential coding position	59320394-59328824(+)
Potential amino acid sequence	MMSISVEASEARDSLRDDKELINTYERLTALDGKRRFALAAAGSHKEEVGRLREYFEDVDRTWE TFEKTLWAHIANFSKLAKDSPQTLVRAIRVVEMQEILDQQLAEEAAEAEGGGAMASVANPRRNA KKTTSSKNLTQQKLKAQGKGYKDKCYESIRKSVEARFDKLLDEQDLKTAIEEARVIGEELGEIY DYVAPCFPPRYEVFQLMVNLYTERFVQWLRKMSDQASNMTNIEILKVTGWVVDYQESLIELGVD DSLAQVCSESGAMDPLMNAYVERMQATTKKWYLNILEADKVQPPKKTDDGKLYTPAAVDLFRIL GEQVQIVRENSTDVMLYRIALALIQVMIDFQAAERKRLEEPASEIGLESLCAMINNNLRCYDLA MELSSSTLEALPQNYAEQVNFEDTCKGFLEVAKVEQAQGGLQSLSLSQKTINQLRENFLSIEKL CQECQTLIENHDQIKILSNTRNNLNTTLKDVEGMMSISVEASEARDSLRDDKELINTYERLTAL DGKRRFALAAAGSHKEEVGRLREYFEDVDRTWETFEKTLWAHIANFSKLAKDSPQTLVRAIRVV EMQEILDQQLAEEAAEAEGGGAMASVANPRRNAKKTTSSKNLTQQKLKAQGKGYKDKCYESIRK SVEARFDKLLDEQDLKTAIEEARVIGEELGEIYDYVAPCFPPRYEVFQLMVNLYTERFVQWLRK MSDQASNMTNIEILKVTGWVVDYQESLIELGVDDSLAQVCSESGAMDPLMNAYVERMQATTKKW YLNILEADKVQPPKKTDDGKLYTPAAVDLFRILGEQVQIVRENSTDVMLYRIALALIQVMIDFQ AAERKRLEEPASEIGLESLCAMINNNLRCYDLAMELSSSTLEALPQNYAEQVNFEDTCKGFLEV AKVEQAQGGLQSLSLSQKTINQLRENFLSIEKLCQECQTLIENHDQIKILSNTRNNLNTTLKDV EGMMSISVEASEARDSLRDDKELINTYERLTALDGKRRFALAAAGSHKEEVGRLREYFEDVDRT WETFEKTLWAHIANFSKLAKDSPQTLVRAIRVVEMQEILDQQLAEEAAEAEGGGAMASVANPRR NAKKTTSSKNLTQQKLKAQGKGYKDKCYESIRKSVEARFDKLLDEQDLKTAIEEARVIGEELGE IYDYVAPCFPPRYEVFQLMVNLYTERFVQWLRKMSDQASNMTNIEILKVTGWVVDYQESLIELG VDDSLAQVCSESGAMDPLMNAYVERMQATTKKWYLNILEADKVQPPKKTDDGKLYTPAAVDLFR ILGEQVQIVRENSTDVMLYRIALALIQVMIDFQAAERKRLEEPASEIGLESLCAMINNNLRCYD LAMELSSSTLEALPQNYAEQVNFEDTCKGFLEVAKVEQAQGGLQSLSLSQKTINQLRENFLSIE KLCQECQTLIENHDQIKILSNTRNNLNTTLKDVEGMMSISVEASEARDSLRDDKELINTYERLT ALDGKRRFALAAAGSHKEEVGRLREYFEDVDRTWETFEKTLWAHIANFSKLAKDSPQTLVRAIR VVEMQEILDQQLAEEAAEAEGGGAMASVANPRRNAKKTTSSKNLTQQKLKAQGKGYKDKCYESI RKSVEARFDKLLDEQDLKTAIEEARVIGEELGEIYDYVAPCFPPRYEVFQLMVNLYTERFVQWL RKMSDQASNMTNIEILKVTGWVVDYQESLIELGVDDSLAQVCSESGAMDPLMNAYVERMQATTK KWYLNILEADKVQPPKKTDDGKLYTPAAVDLFRILGEQVQIVRENSTDVMLYRIALALIQVMID FQAAERKRLEEPASEIGLESLCAMINNNLRCYDLAMELSSSTLEALPQNYAEQVNFEDTCKGFL EVAK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc04g072290.2_circ_g.2

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