Plant Circular RNA Database

Detail information of Solyc11g012770.1_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc11g012770.1_circ_g.3
					
						ID in PlantcircBase
						sly_circ_003293
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 5545234-5546917  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc11g012770.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc11g012770.1_circ_g.2 						
					
						Support reads
						NA
					
						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
						Solyc11g012770.1.1:6

General Information
CircRNA Name	Solyc11g012770.1_circ_g.3
ID in PlantcircBase	sly_circ_003293
Alias	NA
Organism	Solanum lycopersicum
Position	chr11: 5545234-5546917 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc11g012770.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc11g012770.1_circ_g.2
Support reads	NA
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	Solyc11g012770.1.1:6

			
						 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  
						
							GGACAAAAAGGTCCATCAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGA
TAACCTCAAAGTCCAAGGCGGACAATTTAAGCTCAGtgcacggcaaaggttgatacaactccca
ctgtggacttgattggttgcagaataaaaatttggtggcccatggataagaagtaagctgctct
taactcga

									
								

					

						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: 475
Transcript exons: 5545234-5545313,5545727-5545778,5545905-5545991,5546101-
5546138,5546618-5546680,5546763-5546917
TGCACGGCAAAGGTTGATACAACTCCCACTGTGGACTTGATTGGTTGCAGAATAAAAATTTGGT
GGCCCATGGATAAGAAATTCTACGAAGGTGTTGTCAAGTCTTTTGACACTCATAAAAGCAAACA
CGTTGTGCTATATGATGATGGTGATGTAGAAGTCCTGCGATTGGAAAAGGAGTGTTGGGAGCTT
GTTGGTGGTGTGCAGAAACCTGTGAAGGGTTCAAATTCCAAAAAGGGTTCAGGCTCCAAGAAAG
AATCTGGAGAGAGGAAAAAAAGAACTCTTGCTGCCTCCAGGCAAAAGAAGGAGACCGATAAGAT
GTCTCCATTATCGCCAGTACGAGGGAAGAGAACTCCAAGGAAGAATTTGAAGTATGGACAAAAA
GGTCCATCAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGATAACCTCAA
AGTCCAAGGCGGACAATTTAAGCTCAG
						
					

						Genomic sequence
						
							TGCACGGCAAAGGTTGATACAACTCCCACTGTGGACTTGATTGGTTGCAGAATAAAAATTTGGT
GGCCCATGGATAAGAAGTAAGCTGCTCTTAACTCGAGAGGAGTAAATGTTCTTTCTAGCTCTTT
TAAGCTATGTGTTGCCTCAGCTATCTTGGAGATCGTTGCTTTCTTTAGTTTTTCCTTGCATGAT
TAAACTTCCTTTTATGTTGATTTTTCTTCAAGCTTGCTGATTGTCTTGGAGCAATACACGTAGT
TATGTTTATATGCACTCTTAACACATCGTGTTCATCATTGTTGCTTCTTTCTCATATCCACTTT
ATTCTTTTGCTCAACTTCTGTTGGTTGTCTTCCATTACAATTGTGGTCATTGGTCATGGGGATG
TTGTTTGCGTTTTCTTCTTTAATCCTTATTCTTGACTCTGGTCTTGTATTTTGGTTAATGTGGT
CTTGAAGATTATTAGGTTAGAGCACTAACTCCAAGTATTTGACAGATTCTACGAAGGTGTTGTC
AAGTCTTTTGACACTCATAAAAGCAAACACGTTGTAAGCTGCATTTCTAGTACAACAATTATTT
ATTTTTTATTACTAAAGTTGATGAACTTCAGCAATTTTTTAATATGTCAACTTCTATTGATTCT
TGGTTATGGTTTGTTATCAATTGTATCAAAGGTGCTATATGATGATGGTGATGTAGAAGTCCTG
CGATTGGAAAAGGAGTGTTGGGAGCTTGTTGGTGGTGTGCAGAAACCTGTGAAGGTATGCTTTT
CCTTATAGTGTTCATCCTCGCAAACTTTTTATTTTTATTCTTGGTATGAACCCATGCATTTTGG
TTTTACTGATTTGTATATTTGAACATTATTTACAGGGTTCAAATTCCAAAAAGGGTTCAGGCTC
CAAGAAAGAGTAAGTGATTCATCTGCTTTAGTAGTCGCTGTAATTTTAAAAATTATTTTTGTGA
TTATCACAATTCCTTTTCTTCTTTTGATAAGTTCTGGGGATTCTGTTTTATATGGTACTTAAAA
TTGAGGAATTGCATTCTTGAGCGTTTGAATTGTGTTGATGGTACTTCTCTTGTTAAATGCTCTG
GATATCATACCTCAGGCTGCATAGTTCTTCTCCCCATTGATGTGGATGGGTAATGGGTTGGTAA
ATAATGATTATTTCTGCCTTTATTGTTCAGACTATTATCAAGTGTTGATGACTAGCTTAATTCT
TTTCTAATCTTGATTTTTTGACGCCTTTCACGAAAGAACTGTTAACTTTGCATAATGTGGCTCC
TTTTTAAGTTTCATGCATTATGATGCTACCTGAGCCTTGTGTATTAGCATCATAGACGAATTAT
GAGTAGCTTTAACCTCCCCGTCTTCATTTAATGACTGCAGATCTGGAGAGAGGAAAAAAAGAAC
TCTTGCTGCCTCCAGGCAAAAGAAGGAGACCGATAAGATGTGAGCTTGATTCTTTAACTTGATT
GCACATAATTTTTTTGTGTATTTCCTATTTGCCTTATGCGTGTTGTTTTACTGACAGGTCTCCA
TTATCGCCAGTACGAGGGAAGAGAACTCCAAGGAAGAATTTGAAGTATGGACAAAAAGGTCCAT
CAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGATAACCTCAAAGTCCAA
GGCGGACAATTTAAGCTCAG
						
					

			
		

Sequences
Splice junction sequence	GGACAAAAAGGTCCATCAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGA TAACCTCAAAGTCCAAGGCGGACAATTTAAGCTCAGtgcacggcaaaggttgatacaactccca ctgtggacttgattggttgcagaataaaaatttggtggcccatggataagaagtaagctgctct taactcga
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: 475 Transcript exons: 5545234-5545313,5545727-5545778,5545905-5545991,5546101- 5546138,5546618-5546680,5546763-5546917 TGCACGGCAAAGGTTGATACAACTCCCACTGTGGACTTGATTGGTTGCAGAATAAAAATTTGGT GGCCCATGGATAAGAAATTCTACGAAGGTGTTGTCAAGTCTTTTGACACTCATAAAAGCAAACA CGTTGTGCTATATGATGATGGTGATGTAGAAGTCCTGCGATTGGAAAAGGAGTGTTGGGAGCTT GTTGGTGGTGTGCAGAAACCTGTGAAGGGTTCAAATTCCAAAAAGGGTTCAGGCTCCAAGAAAG AATCTGGAGAGAGGAAAAAAAGAACTCTTGCTGCCTCCAGGCAAAAGAAGGAGACCGATAAGAT GTCTCCATTATCGCCAGTACGAGGGAAGAGAACTCCAAGGAAGAATTTGAAGTATGGACAAAAA GGTCCATCAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGATAACCTCAA AGTCCAAGGCGGACAATTTAAGCTCAG
Genomic sequence	TGCACGGCAAAGGTTGATACAACTCCCACTGTGGACTTGATTGGTTGCAGAATAAAAATTTGGT GGCCCATGGATAAGAAGTAAGCTGCTCTTAACTCGAGAGGAGTAAATGTTCTTTCTAGCTCTTT TAAGCTATGTGTTGCCTCAGCTATCTTGGAGATCGTTGCTTTCTTTAGTTTTTCCTTGCATGAT TAAACTTCCTTTTATGTTGATTTTTCTTCAAGCTTGCTGATTGTCTTGGAGCAATACACGTAGT TATGTTTATATGCACTCTTAACACATCGTGTTCATCATTGTTGCTTCTTTCTCATATCCACTTT ATTCTTTTGCTCAACTTCTGTTGGTTGTCTTCCATTACAATTGTGGTCATTGGTCATGGGGATG TTGTTTGCGTTTTCTTCTTTAATCCTTATTCTTGACTCTGGTCTTGTATTTTGGTTAATGTGGT CTTGAAGATTATTAGGTTAGAGCACTAACTCCAAGTATTTGACAGATTCTACGAAGGTGTTGTC AAGTCTTTTGACACTCATAAAAGCAAACACGTTGTAAGCTGCATTTCTAGTACAACAATTATTT ATTTTTTATTACTAAAGTTGATGAACTTCAGCAATTTTTTAATATGTCAACTTCTATTGATTCT TGGTTATGGTTTGTTATCAATTGTATCAAAGGTGCTATATGATGATGGTGATGTAGAAGTCCTG CGATTGGAAAAGGAGTGTTGGGAGCTTGTTGGTGGTGTGCAGAAACCTGTGAAGGTATGCTTTT CCTTATAGTGTTCATCCTCGCAAACTTTTTATTTTTATTCTTGGTATGAACCCATGCATTTTGG TTTTACTGATTTGTATATTTGAACATTATTTACAGGGTTCAAATTCCAAAAAGGGTTCAGGCTC CAAGAAAGAGTAAGTGATTCATCTGCTTTAGTAGTCGCTGTAATTTTAAAAATTATTTTTGTGA TTATCACAATTCCTTTTCTTCTTTTGATAAGTTCTGGGGATTCTGTTTTATATGGTACTTAAAA TTGAGGAATTGCATTCTTGAGCGTTTGAATTGTGTTGATGGTACTTCTCTTGTTAAATGCTCTG GATATCATACCTCAGGCTGCATAGTTCTTCTCCCCATTGATGTGGATGGGTAATGGGTTGGTAA ATAATGATTATTTCTGCCTTTATTGTTCAGACTATTATCAAGTGTTGATGACTAGCTTAATTCT TTTCTAATCTTGATTTTTTGACGCCTTTCACGAAAGAACTGTTAACTTTGCATAATGTGGCTCC TTTTTAAGTTTCATGCATTATGATGCTACCTGAGCCTTGTGTATTAGCATCATAGACGAATTAT GAGTAGCTTTAACCTCCCCGTCTTCATTTAATGACTGCAGATCTGGAGAGAGGAAAAAAAGAAC TCTTGCTGCCTCCAGGCAAAAGAAGGAGACCGATAAGATGTGAGCTTGATTCTTTAACTTGATT GCACATAATTTTTTTGTGTATTTCCTATTTGCCTTATGCGTGTTGTTTTACTGACAGGTCTCCA TTATCGCCAGTACGAGGGAAGAGAACTCCAAGGAAGAATTTGAAGTATGGACAAAAAGGTCCAT CAAAATCTTCTTTGAGCAGAAGAAGCCTGCTTTTAGGCAAGCCGTTGATAACCTCAAAGTCCAA GGCGGACAATTTAAGCTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.338821505

Conservation Information
Conserved circRNAs	NA
PMCS	0.338821505

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5545304-5545247(+)
5545765-5545746(-)
5545306-5546916(-)
						
						Potential amino acid sequence
						
							MDKKFYEGVVKSFDTHKSKHVVLYDDGDVEVLRLEKECWELVGGVQKPVKGSNSKKGSGSKKES
GERKKRTLAASRQKKETDKMSPLSPVRGKRTPRKNLKYGQKGPSKSSLSRRSLLLGKPLITSKS
KADNLSSVHGKG*(+)
MSVKRLDNTFVEFLIHGPPNFYSATNQVHSGSCINLCRALSLNCPPWTLRLSTACLKAGFFCSK
KILMDLFVHTSNSSLEFSSLVLAIMETSYRSPSFAWRQQEFFFSSLQILSWSLNPFWNLNPSQV
SAHHQQAPNTPFPIAGLLHHHHHIAQRVCFYECQKT*(-)
MGHQIFILQPIKSTVGVVSTFAVH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5545304-5545247(+) 5545765-5545746(-) 5545306-5546916(-)
Potential amino acid sequence	MDKKFYEGVVKSFDTHKSKHVVLYDDGDVEVLRLEKECWELVGGVQKPVKGSNSKKGSGSKKES GERKKRTLAASRQKKETDKMSPLSPVRGKRTPRKNLKYGQKGPSKSSLSRRSLLLGKPLITSKS KADNLSSVHGKG(+) MSVKRLDNTFVEFLIHGPPNFYSATNQVHSGSCINLCRALSLNCPPWTLRLSTACLKAGFFCSK KILMDLFVHTSNSSLEFSSLVLAIMETSYRSPSFAWRQQEFFFSSLQILSWSLNPFWNLNPSQV SAHHQQAPNTPFPIAGLLHHHHHIAQRVCFYECQKT(-) MGHQIFILQPIKSTVGVVSTFAVH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc11g012770.1_circ_g.3

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