Plant Circular RNA Database

Detail information of Solyc01g086710.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g086710.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000230
					
						Alias
						1:73420514|73422655, SL3.0ch01:81535690|81537831
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 81659714-81661855  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g086710.2						
					
						Parent gene annotation
						
							DNA-directed RNA polymerase subunit beta
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc01g086710.2_circ_g.1 Solyc01g086710.2_circ_g.3 						
					
						Support reads
						3
					
						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
						Solyc01g086710.2.1:6

General Information
CircRNA Name	Solyc01g086710.2_circ_g.2
ID in PlantcircBase	sly_circ_000230
Alias	1:73420514\|73422655, SL3.0ch01:81535690\|81537831
Organism	Solanum lycopersicum
Position	chr1: 81659714-81661855 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g086710.2
Parent gene annotation	DNA-directed RNA polymerase subunit beta
Parent gene strand	+
Alternative splicing	Solyc01g086710.2_circ_g.1 Solyc01g086710.2_circ_g.3
Support reads	3
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	Solyc01g086710.2.1:6

			
						 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  
						
							TGAATTGTCTTCTTGTATGATGTCTGAGACATGCTTCTTGCTATCTGCTTGCAGGATACAAGGA
AGGGAATACTTGCTTCCTGTTGGTATCATCTTAAAGtgtagacaagctaaaatttcatattcag
gaaagtttttggtggatatctgtttccagtatggtgatggagctgtaatccgggagaaatttaa
ttttggac

									
								

					

						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
						
							TGTAGACAAGCTAAAATTTCATATTCAGGAAAGTTTTTGGTGGATATCTGTTTCCAGTATGGTG
ATGGAGCTGTAATCCGGGAGAAATTTAATTTTGGACAGTTCCCTATCATGTTGAAGGTGAGTTT
TATACTTCCCTAAGTTTCAGCTAATTTCTGCTGAAAATGTTGCAAGTTGAGAAAAAGAAAATAG
ACATGAGGGGATAGTCACAAAAAAGAATCCGATGATGGACCCCTTTAAAGTGATTCTGATCATT
ACATGTGTTTTAAGACAACATCTATAAGTTACAGAGGTTTAAAAAAGTAAGCACTTAATCGTTG
AACCACCAATACAAAATGTGTTGCCTCCTTTTTTCCTTTTTAATGACAGTACTATTGTTAATGC
ATGTATGACCTTTATTTGTTCATTTTACTTCTTTTAGTCAAAGCTATGTCACTTGAGAGGTGCT
GATGACTCCAAGAAGTTAGTTGCTTACAAGGAAGAGCCATCAGAAATGGGCGGGTGAGAGCTGA
AATTCTTATGATCAATCTCTTTATCCCTATTCTATTCAGCTCCTTTTCTCTGCTAGTTTTGGGT
GTCCTGCCTTTTTCCATTAGGAGTTATAAAACTTCTGAAGAATCTGTCATATTTTGTAACTCAG
AAATATTTGTTGGGTGTGTTCACAGATATTTCATTCTGAAAGGGCTTGAGAGAGTTATTCGTCT
TATAATTTTGCCAAAGCGAAACTATGTGAGTCTTCCTTGCTTATTTGTTCTCTGTCTATGACGA
AGTTTTGACACTTCTATCATTTACCCTGGTTTTTCTCTACATTATGTTTTACTCCACTGGAATA
TTCTTTTCATGTGATTCATTGGTTTCATTTAACATTTCATTATAGCCAACAAGTATGGCACGGA
ATTCATTTCGTGATAGGCGAGAAGGATATTCTGATAAAGCTGTTGTTATAAGGTTCTTTCTCCT
CACTCTTACTTGATGACTTGTTCATGTAGCAAAGTTGCGTTTGGTTATGCTTTGGTGCTTGTTT
TTTTAAAAGAGATGCTATCTTGCTTGTGATTGTTCCTGAAGACTCTGTCTTACATGTCTGCCGA
AATGAATATCGTCTCTGAATAAGGGTATTCTCAAGAACTTTGTGTACTAGAATTTTTTTAGAGA
TTCTTGTGCTGACAAATATCATAAAAAAGAAAGCAAGCAACGTGCTATGCACTTTCTAGCTTTT
TAAAACATCAAGTAAAATAACTGTGCAGGCGGAAGGAAGGGGTAGGAGAATGAAGAGGTGAGAT
CCTATTCCGTCATGCTGATATGGTTGGTTGAATTGTTAGTCTTTCCTCTTCTGATAGGGTTTCA
GTGGTAACTACTTAAAGATTACATCTACAGTAATTGTTTTGATCTTGAAGACTGCCAAAAAAAA
TTCATTTTAAGGACAGAAAAGTACAAAACAATTGTTTTACATTTATTGTGATCCAAGGAAAATT
TCGTCTAGGACTTGTATATTTTACCAATGAACAATCAGTACATTTAAATCGTTCATATATCAGT
TAAAATTACTAAAGCTGATTTGAGGTTGCCTGATTGACCATATTGATTTTCTGACTCACGGGAG
GAGAGAGTTGTATATTTTACGAATGAACAATCAGTACACATTAAATCTTTTATATATCAGTGAA
AATTACTAAAGCTGATTTGAGGTTGCCTGATTAACCATATTGATTTTTCTGATTCAAGGGAGGA
GAGAGTTTTGGGTAAGATTGATGCTTTCTGAATACTTCTTTGCTATCTGCTATACAGGAAGAAC
CTTTGGCTTATTTAGTCAGCGAAAATAAATTAGGATGCAAAAAATGTCAATGTCTTTCCTGTCT
GTTAATGATACTGCTTCAGCTCTTCTTTAATTATGGGGCTCACATGTGTTTTGGGGCAATACTA
ATCATCTACTTGGACTCAGATGTGTAAGGGAAGATCAATCTGCAGTCTCACTTAAATTGTATTA
TCTAAACAATGGAAGTGCAAGACTTGGATTCTGGTGAGGAACTAAAACTTAGCATGATTGAATT
GTCTTCTTGTATGATGTCTGAGACATGCTTCTTGCTATCTGCTTGCAGGATACAAGGAAGGGAA
TACTTGCTTCCTGTTGGTATCATCTTAAAG
						
					

			
		

Sequences
Splice junction sequence	TGAATTGTCTTCTTGTATGATGTCTGAGACATGCTTCTTGCTATCTGCTTGCAGGATACAAGGA AGGGAATACTTGCTTCCTGTTGGTATCATCTTAAAGtgtagacaagctaaaatttcatattcag gaaagtttttggtggatatctgtttccagtatggtgatggagctgtaatccgggagaaatttaa ttttggac
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	TGTAGACAAGCTAAAATTTCATATTCAGGAAAGTTTTTGGTGGATATCTGTTTCCAGTATGGTG ATGGAGCTGTAATCCGGGAGAAATTTAATTTTGGACAGTTCCCTATCATGTTGAAGGTGAGTTT TATACTTCCCTAAGTTTCAGCTAATTTCTGCTGAAAATGTTGCAAGTTGAGAAAAAGAAAATAG ACATGAGGGGATAGTCACAAAAAAGAATCCGATGATGGACCCCTTTAAAGTGATTCTGATCATT ACATGTGTTTTAAGACAACATCTATAAGTTACAGAGGTTTAAAAAAGTAAGCACTTAATCGTTG AACCACCAATACAAAATGTGTTGCCTCCTTTTTTCCTTTTTAATGACAGTACTATTGTTAATGC ATGTATGACCTTTATTTGTTCATTTTACTTCTTTTAGTCAAAGCTATGTCACTTGAGAGGTGCT GATGACTCCAAGAAGTTAGTTGCTTACAAGGAAGAGCCATCAGAAATGGGCGGGTGAGAGCTGA AATTCTTATGATCAATCTCTTTATCCCTATTCTATTCAGCTCCTTTTCTCTGCTAGTTTTGGGT GTCCTGCCTTTTTCCATTAGGAGTTATAAAACTTCTGAAGAATCTGTCATATTTTGTAACTCAG AAATATTTGTTGGGTGTGTTCACAGATATTTCATTCTGAAAGGGCTTGAGAGAGTTATTCGTCT TATAATTTTGCCAAAGCGAAACTATGTGAGTCTTCCTTGCTTATTTGTTCTCTGTCTATGACGA AGTTTTGACACTTCTATCATTTACCCTGGTTTTTCTCTACATTATGTTTTACTCCACTGGAATA TTCTTTTCATGTGATTCATTGGTTTCATTTAACATTTCATTATAGCCAACAAGTATGGCACGGA ATTCATTTCGTGATAGGCGAGAAGGATATTCTGATAAAGCTGTTGTTATAAGGTTCTTTCTCCT CACTCTTACTTGATGACTTGTTCATGTAGCAAAGTTGCGTTTGGTTATGCTTTGGTGCTTGTTT TTTTAAAAGAGATGCTATCTTGCTTGTGATTGTTCCTGAAGACTCTGTCTTACATGTCTGCCGA AATGAATATCGTCTCTGAATAAGGGTATTCTCAAGAACTTTGTGTACTAGAATTTTTTTAGAGA TTCTTGTGCTGACAAATATCATAAAAAAGAAAGCAAGCAACGTGCTATGCACTTTCTAGCTTTT TAAAACATCAAGTAAAATAACTGTGCAGGCGGAAGGAAGGGGTAGGAGAATGAAGAGGTGAGAT CCTATTCCGTCATGCTGATATGGTTGGTTGAATTGTTAGTCTTTCCTCTTCTGATAGGGTTTCA GTGGTAACTACTTAAAGATTACATCTACAGTAATTGTTTTGATCTTGAAGACTGCCAAAAAAAA TTCATTTTAAGGACAGAAAAGTACAAAACAATTGTTTTACATTTATTGTGATCCAAGGAAAATT TCGTCTAGGACTTGTATATTTTACCAATGAACAATCAGTACATTTAAATCGTTCATATATCAGT TAAAATTACTAAAGCTGATTTGAGGTTGCCTGATTGACCATATTGATTTTCTGACTCACGGGAG GAGAGAGTTGTATATTTTACGAATGAACAATCAGTACACATTAAATCTTTTATATATCAGTGAA AATTACTAAAGCTGATTTGAGGTTGCCTGATTAACCATATTGATTTTTCTGATTCAAGGGAGGA GAGAGTTTTGGGTAAGATTGATGCTTTCTGAATACTTCTTTGCTATCTGCTATACAGGAAGAAC CTTTGGCTTATTTAGTCAGCGAAAATAAATTAGGATGCAAAAAATGTCAATGTCTTTCCTGTCT GTTAATGATACTGCTTCAGCTCTTCTTTAATTATGGGGCTCACATGTGTTTTGGGGCAATACTA ATCATCTACTTGGACTCAGATGTGTAAGGGAAGATCAATCTGCAGTCTCACTTAAATTGTATTA TCTAAACAATGGAAGTGCAAGACTTGGATTCTGGTGAGGAACTAAAACTTAGCATGATTGAATT GTCTTCTTGTATGATGTCTGAGACATGCTTCTTGCTATCTGCTTGCAGGATACAAGGAAGGGAA TACTTGCTTCCTGTTGGTATCATCTTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.151565013

Conservation Information
Conserved circRNAs	NA
PMCS	0.151565013

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							81659826-81661852(+)
81659828-81661697(-)
						
						Potential amino acid sequence
						
							MLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPTSMARNSFRDRR
EGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILKCRQAKISYSGKF
LVDICFQYGDGAVIREKFNFGQFPIMLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLER
VIRLIILPKRNYPTSMARNSFRDRREGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQ
GREYLLPVGIILKCRQAKISYSGKFLVDICFQYGDGAVIREKFNFGQFPIMLKSKLCHLRGADD
SKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPTSMARNSFRDRREGYSDKAVVIRCVR
EDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILKCRQAKISYSGKFLVDICFQYGDGAVI
REKFNFGQFPIMLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPT
SMARNSFRDRREGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILK(
+)
MIGNCPKLNFSRITAPSPYWKQISTKNFPEYEILACLHFKMIPTGSKYSLPCIQNPSLALPLFR
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to low-temperature stress (acting as miRNA sponges); fruit ripening

Functional Information
Coding potential	Y
Potential coding position	81659826-81661852(+) 81659828-81661697(-)
Potential amino acid sequence	MLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPTSMARNSFRDRR EGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILKCRQAKISYSGKF LVDICFQYGDGAVIREKFNFGQFPIMLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLER VIRLIILPKRNYPTSMARNSFRDRREGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQ GREYLLPVGIILKCRQAKISYSGKFLVDICFQYGDGAVIREKFNFGQFPIMLKSKLCHLRGADD SKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPTSMARNSFRDRREGYSDKAVVIRCVR EDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILKCRQAKISYSGKFLVDICFQYGDGAVI REKFNFGQFPIMLKSKLCHLRGADDSKKLVAYKEEPSEMGGYFILKGLERVIRLIILPKRNYPT SMARNSFRDRREGYSDKAVVIRCVREDQSAVSLKLYYLNNGSARLGFWIQGREYLLPVGIILK( +) MIGNCPKLNFSRITAPSPYWKQISTKNFPEYEILACLHFKMIPTGSKYSLPCIQNPSLALPLFR *(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to low-temperature stress (acting as miRNA sponges); fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018;Yang et al., 2020

circRNA

Detail information of Solyc01g086710.2_circ_g.2

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