Plant Circular RNA Database

Detail information of Solyc04g080020.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g080020.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001565
					
						Alias
						4:61912034|61913566
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 64318664-64320196  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, circseq_cup
					
						Parent gene
						
							Solyc04g080020.2						
					
						Parent gene annotation
						
							Lysophospholipid acyltransferase LPEAT1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						8/16
					
						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
						Solyc04g080020.2.1:3

General Information
CircRNA Name	Solyc04g080020.2_circ_g.1
ID in PlantcircBase	sly_circ_001565
Alias	4:61912034\|61913566
Organism	Solanum lycopersicum
Position	chr4: 64318664-64320196 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI, circseq_cup
Parent gene	Solyc04g080020.2
Parent gene annotation	Lysophospholipid acyltransferase LPEAT1
Parent gene strand	+
Alternative splicing	NA
Support reads	8/16
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	Solyc04g080020.2.1:3

			
						 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  
						
							GTGCGGATTGATGATCTCATTCCTCTGGTCATGCAGGGTAATTTGTTACTTTCAGATATTGGTT
TGGCAGAGAAGCGAGTATATCATGCTGCTCTCAATGagggcacaaccacaaatggtgattttct
ccttccattcaagagtggcgcatttctctcaggggctccagtgcaacctgtgatactaagatat
ccgtacca

									
								

					

						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: 339
Transcript exons: 64318664-64318797,64319431-64319571,64320133-64320196
AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC
TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA
TCTGGGGCTCGGCATGTGATTCTCCTTCTCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGT
TACCTGTTTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCG
GAGGTTGATGGCTCATGAGGGTAATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTA
TATCATGCTGCTCTCAATG
Transcript length: 339
Transcript exons: 64318664-64320196
AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC
TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA
TCTGGGGCTCGGCATGTGATTCTCCTTCCCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGT
TACCTGTTTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCG
GAGGTTGATGGCTCATGAGGGTAATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTA
TATCATGCTGCTCTCAATG
						
					

						Genomic sequence
						
							AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC
TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA
TCTGGGGTAAGTATTTGATAATTTGAAGCTTGCTTTGTCGTTTTAGGGACACTCTGTCATATGG
TAGTACTCCATCTTCAGTGAATGATTCAGTTTCATAATACTGTGCTTGTTACAGATACAGGCTA
ATATTCATGCTCCCTCCTAACACCAATGATTGTCTTTTTTGTTCATCTTAAAACATGTTATGTT
TCTTGTTTTGGTTTTAAGAATTATCATTTTCTTGCATTCAGGCATGTATTAATTGTTTTCCTGC
TTTTGTGCAAATGTATACTACATTATAATTTTCCTGTTCTGACAGTTAGTGTAACAGAATACAG
ATACGGATCATAGAATCGTACTACTTTGTCGGGATCTTGATTTCTTTACCACAAAATAGACAAA
TGATAGATTTTTAGCTGAACCTTATGGCACCAAGTTAGCGTTACAGCAAGGAAAATTTAGTATC
AAATACCTGAATATTTGTTCTGATAGATGAATCTGATAGCACAAAAGTTCTTGTATGCATCTCA
TTATATGGTCAACTGGTTACATTTATAATAATTGTTCATAGTAATCAGTGTTATACTGTTAAAT
AAAGTCATGAATTCTATGAGACTGGTTCTTTTTCTTAGGATGAAAATGCAATTCCTTTTGCAGG
CTCGGCATGTGATTCTCCTTCTCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGTTACCTGT
TTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCGGAGGTTG
ATGGCTCATGAGGTATGTTTTGGATGCAATTTTACCTTAATGACAAGCTCAATCTTCATATTTG
CAGAGTAGGAACATGAAGTAAATCTGGAGACCTGTTAGAAATACGATTTGCTAGTTTTATGCCC
CTCTCCCCCACTACAATTAGAGGAACATACTTCATAGTTCATTGACCATTTTGTAAGAATGAAA
TTTCATTCAATGCTTCCTGCTCATAAGATGTGGTTTTGTAGAAAGTGGATATATTTCTCTGCAA
TCTGGAGATGGCAAGCTATGTCCTCTATTGAGCTTACGTTGAAATTTTCTTTAGAAATGTTGTT
TAGAAAAAAGGAGTCCTTCACAACCCATTATTTCTGTGCTCTTATGTTTGTATTCCTTGAAAGT
AAGAGCAAAATATCATGATCTTTGCACTGCAAACAACAGATGCTTATCTTTATAAAAGTAGTAT
TCTTTTTACCTCCCCTTGTGTTCTCCCTACGCATGCAAAGTAAATAAATGAATCTATTACAGGG
TAATTTCAATCCTCTGTATACTTGTGTGCGGATTGATGATCTCATTCCTCTGGTCATGCAGGGT
AATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTATATCATGCTGCTCTCAATG
						
					

			
		

Sequences
Splice junction sequence	GTGCGGATTGATGATCTCATTCCTCTGGTCATGCAGGGTAATTTGTTACTTTCAGATATTGGTT TGGCAGAGAAGCGAGTATATCATGCTGCTCTCAATGagggcacaaccacaaatggtgattttct ccttccattcaagagtggcgcatttctctcaggggctccagtgcaacctgtgatactaagatat ccgtacca
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: 339 Transcript exons: 64318664-64318797,64319431-64319571,64320133-64320196 AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA TCTGGGGCTCGGCATGTGATTCTCCTTCTCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGT TACCTGTTTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCG GAGGTTGATGGCTCATGAGGGTAATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTA TATCATGCTGCTCTCAATG Transcript length: 339 Transcript exons: 64318664-64320196 AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA TCTGGGGCTCGGCATGTGATTCTCCTTCCCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGT TACCTGTTTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCG GAGGTTGATGGCTCATGAGGGTAATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTA TATCATGCTGCTCTCAATG
Genomic sequence	AGGGCACAACCACAAATGGTGATTTTCTCCTTCCATTCAAGAGTGGCGCATTTCTCTCAGGGGC TCCAGTGCAACCTGTGATACTAAGATATCCGTACCAGAGATTAAGTCCTGCATGGGACTCTATA TCTGGGGTAAGTATTTGATAATTTGAAGCTTGCTTTGTCGTTTTAGGGACACTCTGTCATATGG TAGTACTCCATCTTCAGTGAATGATTCAGTTTCATAATACTGTGCTTGTTACAGATACAGGCTA ATATTCATGCTCCCTCCTAACACCAATGATTGTCTTTTTTGTTCATCTTAAAACATGTTATGTT TCTTGTTTTGGTTTTAAGAATTATCATTTTCTTGCATTCAGGCATGTATTAATTGTTTTCCTGC TTTTGTGCAAATGTATACTACATTATAATTTTCCTGTTCTGACAGTTAGTGTAACAGAATACAG ATACGGATCATAGAATCGTACTACTTTGTCGGGATCTTGATTTCTTTACCACAAAATAGACAAA TGATAGATTTTTAGCTGAACCTTATGGCACCAAGTTAGCGTTACAGCAAGGAAAATTTAGTATC AAATACCTGAATATTTGTTCTGATAGATGAATCTGATAGCACAAAAGTTCTTGTATGCATCTCA TTATATGGTCAACTGGTTACATTTATAATAATTGTTCATAGTAATCAGTGTTATACTGTTAAAT AAAGTCATGAATTCTATGAGACTGGTTCTTTTTCTTAGGATGAAAATGCAATTCCTTTTGCAGG CTCGGCATGTGATTCTCCTTCTCTGTCAATTTGTAAATTACGTGGAGGCAACCTGGTTACCTGT TTACTACCCTTCTCAGCAAGAAAAGGATGACCCTAGACTTTATGCTGAGAATGTTCGGAGGTTG ATGGCTCATGAGGTATGTTTTGGATGCAATTTTACCTTAATGACAAGCTCAATCTTCATATTTG CAGAGTAGGAACATGAAGTAAATCTGGAGACCTGTTAGAAATACGATTTGCTAGTTTTATGCCC CTCTCCCCCACTACAATTAGAGGAACATACTTCATAGTTCATTGACCATTTTGTAAGAATGAAA TTTCATTCAATGCTTCCTGCTCATAAGATGTGGTTTTGTAGAAAGTGGATATATTTCTCTGCAA TCTGGAGATGGCAAGCTATGTCCTCTATTGAGCTTACGTTGAAATTTTCTTTAGAAATGTTGTT TAGAAAAAAGGAGTCCTTCACAACCCATTATTTCTGTGCTCTTATGTTTGTATTCCTTGAAAGT AAGAGCAAAATATCATGATCTTTGCACTGCAAACAACAGATGCTTATCTTTATAAAAGTAGTAT TCTTTTTACCTCCCCTTGTGTTCTCCCTACGCATGCAAAGTAAATAAATGAATCTATTACAGGG TAATTTCAATCCTCTGTATACTTGTGTGCGGATTGATGATCTCATTCCTCTGGTCATGCAGGGT AATTTGTTACTTTCAGATATTGGTTTGGCAGAGAAGCGAGTATATCATGCTGCTCTCAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.38631437

Conservation Information
Conserved circRNAs	NA
PMCS	0.38631437

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							64319568-64318741(+)
64319561-64320193(+)
						
						Potential amino acid sequence
						
							MRVICYFQILVWQRSEYIMLLSMRAQPQMVIFSFHSRVAHFSQGLQCNL*(+)
MAHEGNLLLSDIGLAEKRVYHAALNEGTTTNGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPA
WDSISGARHVILLLCQFVNYVEATWLPVYYPSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLA
EKRVYHAALNEGTTTNGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPAWDSISGARHVILLLC
QFVNYVEATWLPVYYPSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLAEKRVYHAALNEGTTT
NGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPAWDSISGARHVILLLCQFVNYVEATWLPVYY
PSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLAEKRVYHAALN(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to chilling stress

Functional Information
Coding potential	Y
Potential coding position	64319568-64318741(+) 64319561-64320193(+)
Potential amino acid sequence	MRVICYFQILVWQRSEYIMLLSMRAQPQMVIFSFHSRVAHFSQGLQCNL*(+) MAHEGNLLLSDIGLAEKRVYHAALNEGTTTNGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPA WDSISGARHVILLLCQFVNYVEATWLPVYYPSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLA EKRVYHAALNEGTTTNGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPAWDSISGARHVILLLC QFVNYVEATWLPVYYPSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLAEKRVYHAALNEGTTT NGDFLLPFKSGAFLSGAPVQPVILRYPYQRLSPAWDSISGARHVILLLCQFVNYVEATWLPVYY PSQQEKDDPRLYAENVRRLMAHEGNLLLSDIGLAEKRVYHAALN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to chilling stress

			
						 Other Information
					
						References
						Zuo et al., 2016; Yin et al., 2018

circRNA

Detail information of Solyc04g080020.2_circ_g.1

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