Plant Circular RNA Database

Detail information of Solyc03g026350.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g026350.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000938
					
						Alias
						3:8165331|8166401
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 3785197-3786267  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g026350.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc03g026350.2_circ_g.1 						
					
						Support reads
						19/28
					
						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
						Solyc03g026350.2.1:5

General Information
CircRNA Name	Solyc03g026350.2_circ_g.2
ID in PlantcircBase	sly_circ_000938
Alias	3:8165331\|8166401
Organism	Solanum lycopersicum
Position	chr3: 3785197-3786267 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g026350.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc03g026350.2_circ_g.1
Support reads	19/28
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	Solyc03g026350.2.1:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: TGTGTTGATGATTGTGCTTGTTT
 R: TATGCGTGTCTATGTATGGGATG
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	Yes 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	F: TGTGTTGATGATTGTGCTTGTTT R: TATGCGTGTCTATGTATGGGATG 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  
						
							TTATCCAATCATGTGTTGATGATTGTGCTTGTTTTTATAGGTCTGGGCTGCTAATGATAGTGGG
AACTTGGAGGTTACATATACTCATCAAGAGGATTGTtgtgcaggggttgtcaattttgatggtg
aagtaggttctatgctgagtgaaggcccatggatttttgtgggtttaactaatcttgtcaaggt
gaattgtc

									
								

					

						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: 516
Transcript exons: 3785197-3785286,3785477-3785578,3785703-3785846,3786004-
3786123,3786208-3786267
TGTGCAGGGGTTGTCAATTTTGATGGTGAAGTAGGTTCTATGCTGAGTGAAGGCCCATGGATTT
TTGTGGGTTTAACTAATCTTGTCAAGGCATGGAATACTCAAACAGGAACTGACCTCAGTCTTAA
TGGGCCAGTTGGACAAGTCTATGCTCTTGTTGTTGGCAATGATATGCTCCTTGCTGGTACGGAG
GATGGTATATTGGCATGGAAATATAATGGGAGCACCAATAATTTTGATCCAATCAAAGCATTGA
CAGGACACAGCCATCATGTGGTATCACTGGTCGTTGGAGCTAATAGACTATATTCTGGTTCCAT
GGACAATTCAATAAGAGTGTGGAACCTTGAAACATTAGAGTGCTTACAGATCTTGACAGATCAT
ACAAGTGTTGTTATGTCTGTTCTATGCTGGGATCAGTTTCTTTTATCATGTTCACTGGACAAAA
CGATAAAGGTCTGGGCTGCTAATGATAGTGGGAACTTGGAGGTTACATATACTCATCAAGAGGA
TTGT
						
					

						Genomic sequence
						
							TGTGCAGGGGTTGTCAATTTTGATGGTGAAGTAGGTTCTATGCTGAGTGAAGGCCCATGGATTT
TTGTGGGTTTAACTAATCTTGTCAAGGTGAATTGTCAAACAGAATTATTTTATTATCTTTCTTT
TTTTGCTTGCAGTTCATCTCTCTCTCTCTCTCTCTCTCCATACTTTGGGCATCCCATACATAGA
CACGCATATCTATTTACGAATACGTTCAACACTCTTAATATAGTGAATTCCATTCCTTACGTCA
CGGATGTGTCTGATAACTTTGCAGGCATGGAATACTCAAACAGGAACTGACCTCAGTCTTAATG
GGCCAGTTGGACAAGTCTATGCTCTTGTTGTTGGCAATGATATGCTCCTTGCTGGTACGGAGGT
AAGTGTGTATGGTTAGTTATATGTTTACGAAATAAAGGAAAAGAAGAAGATTGTATGTAACATA
AGTGCATGCCTATACAACCTGGTCTTTCAGTCTATAAATTAACTGGAAAGTACTGCAGGATGGT
ATATTGGCATGGAAATATAATGGGAGCACCAATAATTTTGATCCAATCAAAGCATTGACAGGAC
ACAGCCATCATGTGGTATCACTGGTCGTTGGAGCTAATAGACTATATTCTGGTTCCATGGACAA
TTCAATAAGAGTAAGTTGGTCAGAGAGCGATGTGGATTCTCTTGTCACTTTATGTTTCTCTATT
TCCTCTCGATATGTAGAGAAAGTTAGGGATATAGAGTTCTGCATTTTGACCTAGACTTTGCAGT
TGCTACTGTTTTTCCTTACTGTTGCTATTGTGTCTTCAGGTGTGGAACCTTGAAACATTAGAGT
GCTTACAGATCTTGACAGATCATACAAGTGTTGTTATGTCTGTTCTATGCTGGGATCAGTTTCT
TTTATCATGTTCACTGGACAAAACGATAAAGGTTTATGTTTGTTCTTTTTCTTGAAAAATTTAG
CTCTCTTAAGCTTATCCAATCATGTGTTGATGATTGTGCTTGTTTTTATAGGTCTGGGCTGCTA
ATGATAGTGGGAACTTGGAGGTTACATATACTCATCAAGAGGATTGT
						
					

			
		

Sequences
Splice junction sequence	TTATCCAATCATGTGTTGATGATTGTGCTTGTTTTTATAGGTCTGGGCTGCTAATGATAGTGGG AACTTGGAGGTTACATATACTCATCAAGAGGATTGTtgtgcaggggttgtcaattttgatggtg aagtaggttctatgctgagtgaaggcccatggatttttgtgggtttaactaatcttgtcaaggt gaattgtc
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: 516 Transcript exons: 3785197-3785286,3785477-3785578,3785703-3785846,3786004- 3786123,3786208-3786267 TGTGCAGGGGTTGTCAATTTTGATGGTGAAGTAGGTTCTATGCTGAGTGAAGGCCCATGGATTT TTGTGGGTTTAACTAATCTTGTCAAGGCATGGAATACTCAAACAGGAACTGACCTCAGTCTTAA TGGGCCAGTTGGACAAGTCTATGCTCTTGTTGTTGGCAATGATATGCTCCTTGCTGGTACGGAG GATGGTATATTGGCATGGAAATATAATGGGAGCACCAATAATTTTGATCCAATCAAAGCATTGA CAGGACACAGCCATCATGTGGTATCACTGGTCGTTGGAGCTAATAGACTATATTCTGGTTCCAT GGACAATTCAATAAGAGTGTGGAACCTTGAAACATTAGAGTGCTTACAGATCTTGACAGATCAT ACAAGTGTTGTTATGTCTGTTCTATGCTGGGATCAGTTTCTTTTATCATGTTCACTGGACAAAA CGATAAAGGTCTGGGCTGCTAATGATAGTGGGAACTTGGAGGTTACATATACTCATCAAGAGGA TTGT
Genomic sequence	TGTGCAGGGGTTGTCAATTTTGATGGTGAAGTAGGTTCTATGCTGAGTGAAGGCCCATGGATTT TTGTGGGTTTAACTAATCTTGTCAAGGTGAATTGTCAAACAGAATTATTTTATTATCTTTCTTT TTTTGCTTGCAGTTCATCTCTCTCTCTCTCTCTCTCTCCATACTTTGGGCATCCCATACATAGA CACGCATATCTATTTACGAATACGTTCAACACTCTTAATATAGTGAATTCCATTCCTTACGTCA CGGATGTGTCTGATAACTTTGCAGGCATGGAATACTCAAACAGGAACTGACCTCAGTCTTAATG GGCCAGTTGGACAAGTCTATGCTCTTGTTGTTGGCAATGATATGCTCCTTGCTGGTACGGAGGT AAGTGTGTATGGTTAGTTATATGTTTACGAAATAAAGGAAAAGAAGAAGATTGTATGTAACATA AGTGCATGCCTATACAACCTGGTCTTTCAGTCTATAAATTAACTGGAAAGTACTGCAGGATGGT ATATTGGCATGGAAATATAATGGGAGCACCAATAATTTTGATCCAATCAAAGCATTGACAGGAC ACAGCCATCATGTGGTATCACTGGTCGTTGGAGCTAATAGACTATATTCTGGTTCCATGGACAA TTCAATAAGAGTAAGTTGGTCAGAGAGCGATGTGGATTCTCTTGTCACTTTATGTTTCTCTATT TCCTCTCGATATGTAGAGAAAGTTAGGGATATAGAGTTCTGCATTTTGACCTAGACTTTGCAGT TGCTACTGTTTTTCCTTACTGTTGCTATTGTGTCTTCAGGTGTGGAACCTTGAAACATTAGAGT GCTTACAGATCTTGACAGATCATACAAGTGTTGTTATGTCTGTTCTATGCTGGGATCAGTTTCT TTTATCATGTTCACTGGACAAAACGATAAAGGTTTATGTTTGTTCTTTTTCTTGAAAAATTTAG CTCTCTTAAGCTTATCCAATCATGTGTTGATGATTGTGCTTGTTTTTATAGGTCTGGGCTGCTA ATGATAGTGGGAACTTGGAGGTTACATATACTCATCAAGAGGATTGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.382161929

Conservation Information
Conserved circRNAs	NA
PMCS	0.382161929

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3785237-3786264(+)
3786222-3785227(+)
						
						Potential amino acid sequence
						
							MLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYNGSTN
NFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLCWDQF
LLSCSLDKTIKVWAANDSGNLEVTYTHQEDCCAGVVNFDGEVGSMLSEGPWIFVGLTNLVKAWN
TQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYNGSTNNFDPIKALTGHSHHVVSLVV
GANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLCWDQFLLSCSLDKTIKVWAANDSGN
LEVTYTHQEDCCAGVVNFDGEVGSMLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALV
VGNDMLLAGTEDGILAWKYNGSTNNFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLE
TLECLQILTDHTSVVMSVLCWDQFLLSCSLDKTIKVWAANDSGNLEVTYTHQEDCCAGVVNFDG
EVGSMLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYN
GSTNNFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLC
WDQFLLSCSLDKTIKVWAANDSGNLEVTYTHQEDC(+)
MIVGTWRLHILIKRIVVQGLSILMVK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	3785237-3786264(+) 3786222-3785227(+)
Potential amino acid sequence	MLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYNGSTN NFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLCWDQF LLSCSLDKTIKVWAANDSGNLEVTYTHQEDCCAGVVNFDGEVGSMLSEGPWIFVGLTNLVKAWN TQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYNGSTNNFDPIKALTGHSHHVVSLVV GANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLCWDQFLLSCSLDKTIKVWAANDSGN LEVTYTHQEDCCAGVVNFDGEVGSMLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALV VGNDMLLAGTEDGILAWKYNGSTNNFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLE TLECLQILTDHTSVVMSVLCWDQFLLSCSLDKTIKVWAANDSGNLEVTYTHQEDCCAGVVNFDG EVGSMLSEGPWIFVGLTNLVKAWNTQTGTDLSLNGPVGQVYALVVGNDMLLAGTEDGILAWKYN GSTNNFDPIKALTGHSHHVVSLVVGANRLYSGSMDNSIRVWNLETLECLQILTDHTSVVMSVLC WDQFLLSCSLDKTIKVWAANDSGNLEVTYTHQEDC(+) MIVGTWRLHILIKRIVVQGLSILMVK*(+)
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 Solyc03g026350.2_circ_g.2

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