Plant Circular RNA Database

Detail information of Solyc05g056590.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc05g056590.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001844
					
						Alias
						5:65004393|65010005
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 65858043-65863655  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc05g056590.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc05g056590.2_circ_igg.1 Solyc05g056590.2_circ_igg.2 Solyc05g056590.2_circ_g.1 Solyc05g056590.2_circ_g.2 						
					
						Support reads
						4/5
					
						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
						Solyc05g056590.2.1:9

General Information
CircRNA Name	Solyc05g056590.2_circ_g.3
ID in PlantcircBase	sly_circ_001844
Alias	5:65004393\|65010005
Organism	Solanum lycopersicum
Position	chr5: 65858043-65863655 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc05g056590.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc05g056590.2_circ_igg.1 Solyc05g056590.2_circ_igg.2 Solyc05g056590.2_circ_g.1 Solyc05g056590.2_circ_g.2
Support reads	4/5
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	Solyc05g056590.2.1:9

			
						 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  
						
							CAGACGGGTGATTGGCTTGAAAATATTATGAAAGTCATAAATCTTATTTTGTTGTCTTGACAGG
TATCCTGTGGTTGGAAGCATACAGCAGCAATTTCTGaagctgatacggtactgtctatacccaa
taaagttgaatgcttgaatggagtcacaatcaaaatcatttccctaggtttcgaacactcaatt
gctgtaac

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CAGACGGGTGATTGGCTTGAAAATATTATGAAAGTCATAAATCTTATTTTGTTGTCTTGACAGG TATCCTGTGGTTGGAAGCATACAGCAGCAATTTCTGaagctgatacggtactgtctatacccaa taaagttgaatgcttgaatggagtcacaatcaaaatcatttccctaggtttcgaacactcaatt gctgtaac
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.16724755

Conservation Information
Conserved circRNAs	NA
PMCS	0.16724755

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							65858929-65863652(+)
65858111-65863171(-)
						
						Potential amino acid sequence
						
							MLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEKAACGGYHTCVITGGGE
LYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAISEADTVLSIPNKVECL
NGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIKSDSEYTPRLIKELEGL
KVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEKAACGGYHT
CVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAISEADTVLS
IPNKVECLNGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIKSDSEYTPR
LIKELEGLKVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEK
AACGGYHTCVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAI
SEADTVLSIPNKVECLNGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIK
SDSEYTPRLIKELEGLKVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVV
DGLPYAEKAACGGYHTCVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSC
GWKHTAAIS(+)
MILIVTPFKHSTLLGIDSTVSASEIAAVCFQPQDTSETECLKNGPSTLSGK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	65858929-65863652(+) 65858111-65863171(-)
Potential amino acid sequence	MLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEKAACGGYHTCVITGGGE LYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAISEADTVLSIPNKVECL NGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIKSDSEYTPRLIKELEGL KVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEKAACGGYHT CVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAISEADTVLS IPNKVECLNGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIKSDSEYTPR LIKELEGLKVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVVDGLPYAEK AACGGYHTCVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSCGWKHTAAI SEADTVLSIPNKVECLNGVTIKIISLGFEHSIAVTDKGETLSWGGGQSGRLGHGHQSGIFGLIK SDSEYTPRLIKELEGLKVKNASAGMLHSVCISATENGSVHIFGERANKKLGFSEASNCSLPSVV DGLPYAEKAACGGYHTCVITGGGELYVWGTNENGCLGIGSTDVAHLPERVEGPFLRHSVSEVSC GWKHTAAIS(+) MILIVTPFKHSTLLGIDSTVSASEIAAVCFQPQDTSETECLKNGPSTLSGK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

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

circRNA

Detail information of Solyc05g056590.2_circ_g.3

Address

Any questions?

Supported by