Plant Circular RNA Database

Detail information of Solyc04g051490.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g051490.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001415
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 50610487-50614247  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g051490.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc04g051490.2_circ_g.2 Solyc04g051490.2_circ_g.3 Solyc04g051490.2_circ_g.4 Solyc04g051490.2_circ_g.5 						
					
						Support reads
						2
					
						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  
						
							CT-AC							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
						Solyc04g051490.2.1:4

General Information
CircRNA Name	Solyc04g051490.2_circ_g.1
ID in PlantcircBase	sly_circ_001415
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 50610487-50614247 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g051490.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc04g051490.2_circ_g.2 Solyc04g051490.2_circ_g.3 Solyc04g051490.2_circ_g.4 Solyc04g051490.2_circ_g.5
Support reads	2
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	CT-AC 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	Solyc04g051490.2.1:4

			
						 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  
						
							AGACATGACTCATCAATGATTTGCTATTCACAAGGTTGCAAAACTCTTCGGCCTCAAATATGAA
TAATACATATGGAACATCGATAACTTCAGATGAGATcatgggctcttttttatctggttcttgt
ccacgcaatccttgggaataagagaaccatttgcattaacagatagtcttgttaacttgtttct
gtggaaaa

									
								

					

						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
						
							CATGGGCTCTTTTTTATCTGGTTCTTGTCCACGCAATCCTTGGGAATAAGAGAACCATTTGCAT
TAACAGATAGTCTTGTTAACTTGTTTCTGTGGAAAACCAAGAACATCTTAGCAATGACATACGA
AACCATAAACAGTAAGAAATGTTAACTTCTTTATCATCTCTATTTAATCTAGGCAATTGGCCCA
GAGAACGGAAGTCCTGAGGCATCTGCATATTGAAATGTCTCAAGCATCACATCTCATTTGAACC
AAGAGCAGAAAGGACATAAACGACTTTTACCATTCAGCCGAGTATAGTACTCTCTCTGAGGATC
AGTCCCTAGGAAATGAACCAGGACTTTATACTCTTCTATTATAAATTTATAATCTTCAAAAGCA
TTTTGCTTTGATAAGACATAATATCACATTCCTTATCAAGGTCTTACAAATATAAGTATATCTA
TTTCACATTTTACCCCACAGAAAATAAGATATAGATGCCCGCATAAATTATAACACCACTAATA
ATACGGAGTTTATCGCTGAACCAACAGTTGCATTAGCTATTGCAGAGTTGTAAACAGGAAAACC
AAATGTTTTATTAGTTATCCTGTAACATATGTAATTTGGAGTTTCATGTTGCAAACTAAATGTT
AAAATAAGTAATCCATAATTTTTATGTCAGGTTTATTTTCCTCAGGCGTCCAGCCACTAAAATA
GTTATGGTGCTATTATTTCTAAGTATTTCATTTGCTCACTTACAAAAACGGTCTATTACCATTT
GGCACTGCACAAGTTTAGTTGAACTGTATACAACTACAACTCAATCAAAAGCTTGTTAGCATAA
TACCTCGGGACCCCCTAAACTTGGCACCACCTATTCGGTGCACACTTAAACTATTTATTTGTCC
TAATTAACCCTCTATACTTGGCTATTTAGTAGTCTTCACCCCCATGGACAACCTCAACCCAGGG
AGGAGGTGTGATGCACTCGCTGCCATGTGCATATTTTTTGTCCACGTGGTATCATTAATAATAC
GATATATATATATATATATATATATATATATATACCAAACCTTTTAAATTCATTTATTTTCAAA
AGTAAATAAGCAGAAACCAATTCTTGTTTTCAATGAACTACCTCCTCTGTGCACTGTTCACTTT
TACGTGTCCACTATTCCCAAAAATAGATTTTCACTTTCGAATGTCACTTTTTACCTATCAAGAG
AAAACAATTATTATTTTTTCATGGTTTACCCTTAATGTTAATACTTATTCCCCGAATCATTTTT
CAAGATCTAATACAAAACATCAATAAATAGGGATAGTGTGGTAAAACAACAATGTCAATCATTG
TTTTCTTAATGGGTGTGCCAAGTTCAAATGAGACAAGTATAAGTGAAAGGAGGGAGTACAAGCT
TAGCATTGTTGAATGAAATCATCATACCACCTGCCCACTCATCCAGAAAGGAAAGGAAAAAATT
TAACCAACTATTTTCCTCCTGAAAGCAACATACTCACTCCATTCACTTTTCACTTGTCCAATTT
GGACGTTGTACAACCCTTACGAAACAATGATTAACAGAAGTATCGACTATTATTCCACAATACC
CATATTAATTGATGTTTAGTCTTAAGGTTTAGGGAAATGATTTAGATAAGAAATAATTAATGTT
AAGGTTAAGACATGGAAAAAAATATATGTTTTTGTCTTAATATGTTAATAGTGACAAGTAAAAA
TGAAAATCTATTTTTAGTATAATGGACAGGTAAAAGTGAATGAAGGGAGTAATAAACAACAGAC
CCAATCTTTCCTAATTAAGAAGTTTAGTAGACAAAAGGTAGTAGCATACAGAACTCCAAAAATT
CACTATTCAGTAGGTATTAATCAATAAACTAGCCCAATTTTTTAATTACAAAATACTACAAGCC
CGACACATTGATATTATATAGATGGTCGCGTATATGGCAATTGTCCAAAAATACGAATTCACTG
AAATATAAATATGACATACCTAAACTGACAAGAAGCTAAGCTGCAAGTCAGCCCAGCTACATGT
TCAGCTAATTCAGCTTCATCAACACAGTGCCTAGAATGCACCTTAACAAAGTTAATTGTTAATT
TTGACAGAACCTGCCAAAGAAAAGAGAAACTCAATACCCAAGGAATAGCACCAAAATTTCAAGC
TTACACTAATAACATTCTTAATTATTTCCAATAAACTATGTCGCCGGACTCTTCAAAATATCGA
CGGTTGCGTGCAGGATACTCAAAAATTAGAGTATTTTGAAGAATCTGACACAGGTGTGGTAACA
ATTTTGGAGAGTCCGAGCAACATAGCCAATAATAACGAGAACCAGTGTTGCAACAACCTCCTCT
ATAAGTGGTCGTTTCCAACCAGTATGATTGGCAGGGTCCTTGTATTGTCCTTGTTCCCTATCAC
CAATAGCAGTAACAGTTATAAGATACTGTAGAAAATTAAATATATTTCTTTTGTCTTAAGCATC
TTGAAGCTTTGACCAGTTGTTTCTTTGAGCTATACATGAAAGTCATTTGGTTGAACATAGAGGA
TTTGGGACAGAAAAAGTGCTTAGACTTGCCAAAATACGATGTCAAAAGCAAATATATTGACAAG
CCAACCTTTTAGGGGCACACAGAATTCCACCAACAAAAAAGAAAATAAATATATGCCCAAGATT
AAAATGTTCTATGTTACATGGATTCCATTCCAAGTATCAAATATGCTATGTATGACAATTACGT
TCTGTAATCAGCAAATAATTTGTGTATTAAGAAGGATTATGAAATACACATATCCAAGTCATAG
CAACTCAACAAGCTCATGTACCAGAGGAGTTGTCTAACAAATCAAATTTGAACTGCTGCATTTC
TCTGTAAACTTCTAAAATAAAGCAAATAAAAATAAACTTCCAGTTAGAATTATTTCAGCTAATT
TTTTATACCCTGGCTTCAATAAATAAACTAACATGCTGCTACTTTTTTACAACCGAGAAATCCC
AGAGGGACTCTGCTACTTATTATTTCTTTCTTGAAAGAAGAACAATTCTTTCTTGAAACAAGAA
CAATTTGATACTAAGCACATGGTCTGAAAGCATAACAATAGAAAACCACAAGAAACCTAGAAGG
TGCATCGTCATTGTACTTGATACAATTTGCACCTCAAAGCTTTCATTCCATCTTACTTAACATT
CAACAAAAAAAAAATGAACAACTAACTGTTAAATTCATGATCTGTCGCAACTTGATTTCATCTC
TCAAGCATGTCACACACGAACAGAACACTGAAAAATAAAAGGCACCTATAACAGAAAGTTCTAT
AAATGGAGAACAGATGTACTGAACAATCCAATGGTCAAATTCAGGATCTTCTATCATACGTGAA
AAAGGTTGAAAAAGAAAATTACGGCAACAACAGAGGTCTAAAAATAGAGAACAGAGAAAATTTA
TGTGTCAGAAAATAAATTAACAAACTTAACAATAACAACAACTACACCTCAATACCAAGCTAGT
CAGAAAATTTGCTGAACTTAAAGTGAAAAAGAGTTGAGATGGACAAAAATGAAGTTACCGTCAA
CCTTTTGTTGATATATGCCAAAAGCTTGTTTGTGAGATAACAAACTGTATGAAGAGGATAAAGG
CGTTGGACACGGGAGACATGACTCATCAATGATTTGCTATTCACAAGGTTGCAAAACTCTTCGG
CCTCAAATATGAATAATACATATGGAACATCGATAACTTCAGATGAGAT
						
					

			
		

Sequences
Splice junction sequence	AGACATGACTCATCAATGATTTGCTATTCACAAGGTTGCAAAACTCTTCGGCCTCAAATATGAA TAATACATATGGAACATCGATAACTTCAGATGAGATcatgggctcttttttatctggttcttgt ccacgcaatccttgggaataagagaaccatttgcattaacagatagtcttgttaacttgtttct gtggaaaa
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	CATGGGCTCTTTTTTATCTGGTTCTTGTCCACGCAATCCTTGGGAATAAGAGAACCATTTGCAT TAACAGATAGTCTTGTTAACTTGTTTCTGTGGAAAACCAAGAACATCTTAGCAATGACATACGA AACCATAAACAGTAAGAAATGTTAACTTCTTTATCATCTCTATTTAATCTAGGCAATTGGCCCA GAGAACGGAAGTCCTGAGGCATCTGCATATTGAAATGTCTCAAGCATCACATCTCATTTGAACC AAGAGCAGAAAGGACATAAACGACTTTTACCATTCAGCCGAGTATAGTACTCTCTCTGAGGATC AGTCCCTAGGAAATGAACCAGGACTTTATACTCTTCTATTATAAATTTATAATCTTCAAAAGCA TTTTGCTTTGATAAGACATAATATCACATTCCTTATCAAGGTCTTACAAATATAAGTATATCTA TTTCACATTTTACCCCACAGAAAATAAGATATAGATGCCCGCATAAATTATAACACCACTAATA ATACGGAGTTTATCGCTGAACCAACAGTTGCATTAGCTATTGCAGAGTTGTAAACAGGAAAACC AAATGTTTTATTAGTTATCCTGTAACATATGTAATTTGGAGTTTCATGTTGCAAACTAAATGTT AAAATAAGTAATCCATAATTTTTATGTCAGGTTTATTTTCCTCAGGCGTCCAGCCACTAAAATA GTTATGGTGCTATTATTTCTAAGTATTTCATTTGCTCACTTACAAAAACGGTCTATTACCATTT GGCACTGCACAAGTTTAGTTGAACTGTATACAACTACAACTCAATCAAAAGCTTGTTAGCATAA TACCTCGGGACCCCCTAAACTTGGCACCACCTATTCGGTGCACACTTAAACTATTTATTTGTCC TAATTAACCCTCTATACTTGGCTATTTAGTAGTCTTCACCCCCATGGACAACCTCAACCCAGGG AGGAGGTGTGATGCACTCGCTGCCATGTGCATATTTTTTGTCCACGTGGTATCATTAATAATAC GATATATATATATATATATATATATATATATATACCAAACCTTTTAAATTCATTTATTTTCAAA AGTAAATAAGCAGAAACCAATTCTTGTTTTCAATGAACTACCTCCTCTGTGCACTGTTCACTTT TACGTGTCCACTATTCCCAAAAATAGATTTTCACTTTCGAATGTCACTTTTTACCTATCAAGAG AAAACAATTATTATTTTTTCATGGTTTACCCTTAATGTTAATACTTATTCCCCGAATCATTTTT CAAGATCTAATACAAAACATCAATAAATAGGGATAGTGTGGTAAAACAACAATGTCAATCATTG TTTTCTTAATGGGTGTGCCAAGTTCAAATGAGACAAGTATAAGTGAAAGGAGGGAGTACAAGCT TAGCATTGTTGAATGAAATCATCATACCACCTGCCCACTCATCCAGAAAGGAAAGGAAAAAATT TAACCAACTATTTTCCTCCTGAAAGCAACATACTCACTCCATTCACTTTTCACTTGTCCAATTT GGACGTTGTACAACCCTTACGAAACAATGATTAACAGAAGTATCGACTATTATTCCACAATACC CATATTAATTGATGTTTAGTCTTAAGGTTTAGGGAAATGATTTAGATAAGAAATAATTAATGTT AAGGTTAAGACATGGAAAAAAATATATGTTTTTGTCTTAATATGTTAATAGTGACAAGTAAAAA TGAAAATCTATTTTTAGTATAATGGACAGGTAAAAGTGAATGAAGGGAGTAATAAACAACAGAC CCAATCTTTCCTAATTAAGAAGTTTAGTAGACAAAAGGTAGTAGCATACAGAACTCCAAAAATT CACTATTCAGTAGGTATTAATCAATAAACTAGCCCAATTTTTTAATTACAAAATACTACAAGCC CGACACATTGATATTATATAGATGGTCGCGTATATGGCAATTGTCCAAAAATACGAATTCACTG AAATATAAATATGACATACCTAAACTGACAAGAAGCTAAGCTGCAAGTCAGCCCAGCTACATGT TCAGCTAATTCAGCTTCATCAACACAGTGCCTAGAATGCACCTTAACAAAGTTAATTGTTAATT TTGACAGAACCTGCCAAAGAAAAGAGAAACTCAATACCCAAGGAATAGCACCAAAATTTCAAGC TTACACTAATAACATTCTTAATTATTTCCAATAAACTATGTCGCCGGACTCTTCAAAATATCGA CGGTTGCGTGCAGGATACTCAAAAATTAGAGTATTTTGAAGAATCTGACACAGGTGTGGTAACA ATTTTGGAGAGTCCGAGCAACATAGCCAATAATAACGAGAACCAGTGTTGCAACAACCTCCTCT ATAAGTGGTCGTTTCCAACCAGTATGATTGGCAGGGTCCTTGTATTGTCCTTGTTCCCTATCAC CAATAGCAGTAACAGTTATAAGATACTGTAGAAAATTAAATATATTTCTTTTGTCTTAAGCATC TTGAAGCTTTGACCAGTTGTTTCTTTGAGCTATACATGAAAGTCATTTGGTTGAACATAGAGGA TTTGGGACAGAAAAAGTGCTTAGACTTGCCAAAATACGATGTCAAAAGCAAATATATTGACAAG CCAACCTTTTAGGGGCACACAGAATTCCACCAACAAAAAAGAAAATAAATATATGCCCAAGATT AAAATGTTCTATGTTACATGGATTCCATTCCAAGTATCAAATATGCTATGTATGACAATTACGT TCTGTAATCAGCAAATAATTTGTGTATTAAGAAGGATTATGAAATACACATATCCAAGTCATAG CAACTCAACAAGCTCATGTACCAGAGGAGTTGTCTAACAAATCAAATTTGAACTGCTGCATTTC TCTGTAAACTTCTAAAATAAAGCAAATAAAAATAAACTTCCAGTTAGAATTATTTCAGCTAATT TTTTATACCCTGGCTTCAATAAATAAACTAACATGCTGCTACTTTTTTACAACCGAGAAATCCC AGAGGGACTCTGCTACTTATTATTTCTTTCTTGAAAGAAGAACAATTCTTTCTTGAAACAAGAA CAATTTGATACTAAGCACATGGTCTGAAAGCATAACAATAGAAAACCACAAGAAACCTAGAAGG TGCATCGTCATTGTACTTGATACAATTTGCACCTCAAAGCTTTCATTCCATCTTACTTAACATT CAACAAAAAAAAAATGAACAACTAACTGTTAAATTCATGATCTGTCGCAACTTGATTTCATCTC TCAAGCATGTCACACACGAACAGAACACTGAAAAATAAAAGGCACCTATAACAGAAAGTTCTAT AAATGGAGAACAGATGTACTGAACAATCCAATGGTCAAATTCAGGATCTTCTATCATACGTGAA AAAGGTTGAAAAAGAAAATTACGGCAACAACAGAGGTCTAAAAATAGAGAACAGAGAAAATTTA TGTGTCAGAAAATAAATTAACAAACTTAACAATAACAACAACTACACCTCAATACCAAGCTAGT CAGAAAATTTGCTGAACTTAAAGTGAAAAAGAGTTGAGATGGACAAAAATGAAGTTACCGTCAA CCTTTTGTTGATATATGCCAAAAGCTTGTTTGTGAGATAACAAACTGTATGAAGAGGATAAAGG CGTTGGACACGGGAGACATGACTCATCAATGATTTGCTATTCACAAGGTTGCAAAACTCTTCGG CCTCAAATATGAATAATACATATGGAACATCGATAACTTCAGATGAGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139384594

Conservation Information
Conserved circRNAs	NA
PMCS	0.139384594

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							50614208-50610532(+)
50614242-50610557(+)
50610491-50610488(-)
						
						Potential amino acid sequence
						
							MNNTYGTSITSDEIMGSFLSGSCPRNPWE*(+)
MRSWALFYLVLVHAILGNKRTICINR*(+)
MISSEVIDVPYVLFIFEAEEFCNLVNSKSLMSHVSRVQRLYPLHTVCYLTNKLLAYINKREQGQ
YKDPANHTGWKRPLIEEVLSKLTINFVKVHSRHCVDEAELAEHVAGLTCSLASCQFRNKLTRLS
VNANGSLIPKDCVDKNQIKKSP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	50614208-50610532(+) 50614242-50610557(+) 50610491-50610488(-)
Potential amino acid sequence	MNNTYGTSITSDEIMGSFLSGSCPRNPWE(+) MRSWALFYLVLVHAILGNKRTICINR(+) MISSEVIDVPYVLFIFEAEEFCNLVNSKSLMSHVSRVQRLYPLHTVCYLTNKLLAYINKREQGQ YKDPANHTGWKRPLIEEVLSKLTINFVKVHSRHCVDEAELAEHVAGLTCSLASCQFRNKLTRLS VNANGSLIPKDCVDKNQIKKSP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g051490.2_circ_g.1

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