Plant Circular RNA Database

Detail information of Solyc07g043420.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc07g043420.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_002327
					
						Alias
						7:54503614|54503828, Slcirc106
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 57180114-57180328  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI, circseq_cup
					
						Parent gene
						
							Solyc07g043420.2						
					
						Parent gene annotation
						
							Putative uncharacterized protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc07g043420.2_circ_g.1 Solyc07g043420.2_circ_g.2 Solyc07g043420.2_circ_g.4 Solyc07g043420.2_circ_g.5 Solyc07g043420.2_circ_g.6 Solyc07g043420.2_circ_g.7 Solyc07g043420.2_circ_g.8 Solyc07g043420.2_circ_g.9 Solyc07g043420.2_circ_g.10 Solyc07g043420.2_circ_g.11 						
					
						Support reads
						22/134
					
						Tissues
						fruit/leaf
					
						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
						Solyc07g043420.2.1:1

General Information
CircRNA Name	Solyc07g043420.2_circ_g.3
ID in PlantcircBase	sly_circ_002327
Alias	7:54503614\|54503828, Slcirc106
Organism	Solanum lycopersicum
Position	chr7: 57180114-57180328 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	CIRI, circseq_cup
Parent gene	Solyc07g043420.2
Parent gene annotation	Putative uncharacterized protein
Parent gene strand	+
Alternative splicing	Solyc07g043420.2_circ_g.1 Solyc07g043420.2_circ_g.2 Solyc07g043420.2_circ_g.4 Solyc07g043420.2_circ_g.5 Solyc07g043420.2_circ_g.6 Solyc07g043420.2_circ_g.7 Solyc07g043420.2_circ_g.8 Solyc07g043420.2_circ_g.9 Solyc07g043420.2_circ_g.10 Solyc07g043420.2_circ_g.11
Support reads	22/134
Tissues	fruit/leaf
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	Solyc07g043420.2.1:1

			
						 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  
						
							CAGTATTCCAGTCATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGAT
CTGTTGAAAGCTTTTGAAGAATATGGGTTTTTTCAGattgattgtcaatggcggatcttctctc
gaactggtcaagcacattagaagcagttcctaaaagtcattgcatcccagagcatgaaagacca
tcagatcc

						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: 215
Transcript exons: 57180114-57180328
ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG
TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC
ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT
TTGAAGAATATGGGTTTTTTCAG
Transcript length: 215
Transcript exons: 57180114-57180328
ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG
TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC
ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT
TTGAAGAATATGGTTTTTTTCAG
						
						Genomic sequence
						
							ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG
TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC
ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT
TTGAAGAATATGGGTTTTTTCAG

Sequences
Splice junction sequence	CAGTATTCCAGTCATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGAT CTGTTGAAAGCTTTTGAAGAATATGGGTTTTTTCAGattgattgtcaatggcggatcttctctc gaactggtcaagcacattagaagcagttcctaaaagtcattgcatcccagagcatgaaagacca tcagatcc
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: 215 Transcript exons: 57180114-57180328 ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT TTGAAGAATATGGGTTTTTTCAG Transcript length: 215 Transcript exons: 57180114-57180328 ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT TTGAAGAATATGGTTTTTTTCAG
Genomic sequence	ATTGATTGTCAATGGCGGATCTTCTCTCGAACTGGTCAAGCACATTAGAAGCAGTTCCTAAAAG TCATTGCATCCCAGAGCATGAAAGACCATCAGATCCAGTTGAAATTGGCGACAGTATTCCAGTC ATTGATTTGGGAAAAGCTAATGGTGAAGAACGAAGTGTTGTTGTTAAAGATCTGTTGAAAGCTT TTGAAGAATATGGGTTTTTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.890905082

Conservation Information
Conserved circRNAs	NA
PMCS	0.890905082

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							57180316-57180171(+)
57180126-57180158(+)
57180160-57180208(-)
						
						Potential amino acid sequence
						
							MGFFRLIVNGGSSLELVKHIRSSS*(+)
MADLLSNWSSTLEAVPKSHCIPEHERPSDPVEIGDSIPVIDLGKANGEERSVVVKDLLKAFEEY
GFFQIDCQWRIFSRTGQAH*(+)
MCLTSSREDPPLTINLKKPIFFKSFQQIFNNNTSFFTISFSQINDWNTVANFNWI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	57180316-57180171(+) 57180126-57180158(+) 57180160-57180208(-)
Potential amino acid sequence	MGFFRLIVNGGSSLELVKHIRSSS(+) MADLLSNWSSTLEAVPKSHCIPEHERPSDPVEIGDSIPVIDLGKANGEERSVVVKDLLKAFEEY GFFQIDCQWRIFSRTGQAH(+) MCLTSSREDPPLTINLKKPIFFKSFQQIFNNNTSFFTISFSQINDWNTVANFNWI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc07g043420.2_circ_g.3

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