Plant Circular RNA Database

Detail information of Solyc06g051030.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc06g051030.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001941
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 34132538-34134190  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc06g051030.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						9
					
						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
						Solyc06g051030.2.1:4

General Information
CircRNA Name	Solyc06g051030.2_circ_g.1
ID in PlantcircBase	sly_circ_001941
Alias	NA
Organism	Solanum lycopersicum
Position	chr6: 34132538-34134190 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc06g051030.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	NA
Support reads	9
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	Solyc06g051030.2.1:4

			
						 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  
						
							GAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAACCAAGCTACGAGACCCCA
ACCTTTGTCACTTCCCTATGGGAGAATGATATTAAGgtttggcactgttaagattcagggagag
agtggagagagatccatttggggctttgctgaattggaaagatggtgatggagtggaaaatcca
tgtacttg

									
								

					

						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: 496
Transcript exons: 34132538-34132676,34133595-34133666,34133829-34133972,34
134050-34134190
GTTTGGCACTGTTAAGATTCAGGGAGAGAGTGGAGAGAGATCCATTTGGGGCTTTGCTGAATTG
GAAAGATGGTGATGGAGTGGAAAATCCATGTACTTGGTTTGGAGTTGGGTGCTTTAATGGGAAT
GTTGTGTCTCTAGACTTGAGAGATCTCCATCTATGTGGTACCATAGGTCCTGATCTCGCGCGCT
TGGTTCACTTGAAGTTTATAATCTTACGTAACAATTCCTTTACTGGGTTCATACCTGATGAGAT
TGCAAAGCTAAAAGAATTGGAGATTCTGGACCTGGGATCTAATAACTTTAGCCAGCCGCTGCCT
TCTGAGCTTTGCAATAATCCCTCTCTGGAAATTATCTTATCAGACAAAAATGAGCTGTTTAGCA
GCATATTTCCTGGAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAACCAAGC
TACGAGACCCCAACCTTTGTCACTTCCCTATGGGAGAATGATATTAAG
						
					

						Genomic sequence
						
							GTTTGGCACTGTTAAGATTCAGGGAGAGAGTGGAGAGAGATCCATTTGGGGCTTTGCTGAATTG
GAAAGATGGTGATGGAGTGGAAAATCCATGTACTTGGTTTGGAGTTGGGTGCTTTAATGGGAAT
GTTGTGTCTCTGTAAGTACTAAAAATTGCTCTTTTCTCTTCTTATTTGGTTCTGCAGAAGTCTT
CTTTTTCAATTTTGATCTGGTTGGCTTATATAGATGAATCTAAATTTGGTCTCTGTTTGAATTC
TGAAACTTTTGTTCCATGAGTTGGTGGTGATTCCAGTATGTGTCTGATCAAAAAACAGATAAAT
GAGAAGCTTTTGGCACCGATTCCTGTTGAAGATCTGTTCATGGAGTGTAGCTAATTTTGTTATT
GTAAAGAGAGAGCTATTGTAAAATTTGATTTTCGTTACTCAATTGTTTGAGAGGCTAAGCACAA
TCTTATAATATGTTGTGATCAAAATAATTAAACATAGTCTCGAGAATGGATGTAAATAAGTTGA
TTTCTAAATTCAGAATGATGAAGCATCTGACCGTGCCTCTAATGGAAGGGAGATCTGGAAAACC
CGTGCTCCTCTAGAAAGGGCAAACATGGAGTTAGATATAGTACCAAGATATAAATTTCATCAGA
GATCAAATAAAAGGAGTCAAATTTTACACACTACCTTCGATGTCAACTTCCTCCAGTTTATTTA
TTTTTTTCAAATAAATGTAAACCAGATAATTAGAGCTACATGTATAACGTGATCTCTTTGTTTC
TTGATCTGATACTTGATTCTATATTTCTATGAAGTAACCAGGAGTTGAATTTTGTAAAGGGTAA
TTATATCATAGCTAGCATATATCCGTCCCTAGCTAACTTTAAAAACACATTTTTACTGTATCCA
TTTTCATAAATGCAATAATTTTCGTACACAATTATCTCCATTTATTATCATGAATATAATTTTC
AAGTCGGTGAGTAGCATAGTGTCTAAGTTGAATTTGCTATTGTAAAAATTATCTATGATACTGA
TGTTCTAACCTGTGTTTTTTTATCTACTCACAGAGACTTGAGAGATCTCCATCTATGTGGTACC
ATAGGTCCTGATCTCGCGCGCTTGGTTCACTTGAAGTTTATGTATGTGCACGTTTAAACTAGAT
GTCTTCATTTTCCTAGTCGCTGTTATTACAAACTCTATATTTAAGTCTTCTTCGTTTTATTAGT
CGCTGTCATTACAAACTCTATATTTAAGTCTTTCTCTTTAAGATAATTGGCAACTCACTGGAGA
CTTCTTTACAGAATCTTACGTAACAATTCCTTTACTGGGTTCATACCTGATGAGATTGCAAAGC
TAAAAGAATTGGAGATTCTGGACCTGGGATCTAATAACTTTAGCCAGCCGCTGCCTTCTGAGCT
TTGCAATAATCCCTCTCTGGAAATTATGTGAGTTCAAACAGAGGTGGTGTCATTTTCTAATTTT
ACCTCCTTGTTCCCTTACTTACAGAGTTACACTAATGCAGCTTATCAGACAAAAATGAGCTGTT
TAGCAGCATATTTCCTGGAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAAC
CAAGCTACGAGACCCCAACCTTTGTCACTTCCCTATGGGAGAATGATATTAAG
						
					

			
		

Sequences
Splice junction sequence	GAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAACCAAGCTACGAGACCCCA ACCTTTGTCACTTCCCTATGGGAGAATGATATTAAGgtttggcactgttaagattcagggagag agtggagagagatccatttggggctttgctgaattggaaagatggtgatggagtggaaaatcca tgtacttg
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: 496 Transcript exons: 34132538-34132676,34133595-34133666,34133829-34133972,34 134050-34134190 GTTTGGCACTGTTAAGATTCAGGGAGAGAGTGGAGAGAGATCCATTTGGGGCTTTGCTGAATTG GAAAGATGGTGATGGAGTGGAAAATCCATGTACTTGGTTTGGAGTTGGGTGCTTTAATGGGAAT GTTGTGTCTCTAGACTTGAGAGATCTCCATCTATGTGGTACCATAGGTCCTGATCTCGCGCGCT TGGTTCACTTGAAGTTTATAATCTTACGTAACAATTCCTTTACTGGGTTCATACCTGATGAGAT TGCAAAGCTAAAAGAATTGGAGATTCTGGACCTGGGATCTAATAACTTTAGCCAGCCGCTGCCT TCTGAGCTTTGCAATAATCCCTCTCTGGAAATTATCTTATCAGACAAAAATGAGCTGTTTAGCA GCATATTTCCTGGAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAACCAAGC TACGAGACCCCAACCTTTGTCACTTCCCTATGGGAGAATGATATTAAG
Genomic sequence	GTTTGGCACTGTTAAGATTCAGGGAGAGAGTGGAGAGAGATCCATTTGGGGCTTTGCTGAATTG GAAAGATGGTGATGGAGTGGAAAATCCATGTACTTGGTTTGGAGTTGGGTGCTTTAATGGGAAT GTTGTGTCTCTGTAAGTACTAAAAATTGCTCTTTTCTCTTCTTATTTGGTTCTGCAGAAGTCTT CTTTTTCAATTTTGATCTGGTTGGCTTATATAGATGAATCTAAATTTGGTCTCTGTTTGAATTC TGAAACTTTTGTTCCATGAGTTGGTGGTGATTCCAGTATGTGTCTGATCAAAAAACAGATAAAT GAGAAGCTTTTGGCACCGATTCCTGTTGAAGATCTGTTCATGGAGTGTAGCTAATTTTGTTATT GTAAAGAGAGAGCTATTGTAAAATTTGATTTTCGTTACTCAATTGTTTGAGAGGCTAAGCACAA TCTTATAATATGTTGTGATCAAAATAATTAAACATAGTCTCGAGAATGGATGTAAATAAGTTGA TTTCTAAATTCAGAATGATGAAGCATCTGACCGTGCCTCTAATGGAAGGGAGATCTGGAAAACC CGTGCTCCTCTAGAAAGGGCAAACATGGAGTTAGATATAGTACCAAGATATAAATTTCATCAGA GATCAAATAAAAGGAGTCAAATTTTACACACTACCTTCGATGTCAACTTCCTCCAGTTTATTTA TTTTTTTCAAATAAATGTAAACCAGATAATTAGAGCTACATGTATAACGTGATCTCTTTGTTTC TTGATCTGATACTTGATTCTATATTTCTATGAAGTAACCAGGAGTTGAATTTTGTAAAGGGTAA TTATATCATAGCTAGCATATATCCGTCCCTAGCTAACTTTAAAAACACATTTTTACTGTATCCA TTTTCATAAATGCAATAATTTTCGTACACAATTATCTCCATTTATTATCATGAATATAATTTTC AAGTCGGTGAGTAGCATAGTGTCTAAGTTGAATTTGCTATTGTAAAAATTATCTATGATACTGA TGTTCTAACCTGTGTTTTTTTATCTACTCACAGAGACTTGAGAGATCTCCATCTATGTGGTACC ATAGGTCCTGATCTCGCGCGCTTGGTTCACTTGAAGTTTATGTATGTGCACGTTTAAACTAGAT GTCTTCATTTTCCTAGTCGCTGTTATTACAAACTCTATATTTAAGTCTTCTTCGTTTTATTAGT CGCTGTCATTACAAACTCTATATTTAAGTCTTTCTCTTTAAGATAATTGGCAACTCACTGGAGA CTTCTTTACAGAATCTTACGTAACAATTCCTTTACTGGGTTCATACCTGATGAGATTGCAAAGC TAAAAGAATTGGAGATTCTGGACCTGGGATCTAATAACTTTAGCCAGCCGCTGCCTTCTGAGCT TTGCAATAATCCCTCTCTGGAAATTATGTGAGTTCAAACAGAGGTGGTGTCATTTTCTAATTTT ACCTCCTTGTTCCCTTACTTACAGAGTTACACTAATGCAGCTTATCAGACAAAAATGAGCTGTT TAGCAGCATATTTCCTGGAAGCGATAAACTTGAAATGGTCCCAGATGTCCAAGAAAATAACAAC CAAGCTACGAGACCCCAACCTTTGTCACTTCCCTATGGGAGAATGATATTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.35137161

Conservation Information
Conserved circRNAs	NA
PMCS	0.35137161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34134109-34132610(+)
34133629-34134188(-)
						
						Potential amino acid sequence
						
							MVPDVQENNNQATRPQPLSLPYGRMILRFGTVKIQGESGERSIWGFAELERW*(+)
MVPHRWRSLKSRDTTFPLKHPTPNQVHGFSTPSPSFQFSKAPNGSLSTLSLNLNSAKP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34134109-34132610(+) 34133629-34134188(-)
Potential amino acid sequence	MVPDVQENNNQATRPQPLSLPYGRMILRFGTVKIQGESGERSIWGFAELERW(+) MVPHRWRSLKSRDTTFPLKHPTPNQVHGFSTPSPSFQFSKAPNGSLSTLSLNLNSAKP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc06g051030.2_circ_g.1

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