Plant Circular RNA Database

Detail information of Solyc03g097350.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g097350.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001087
					
						Alias
						3:53110956|53113895
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 59664353-59667292  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g097350.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g097350.2_circ_g.1 						
					
						Support reads
						2
					
						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  
						
							CT-AC							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
						Solyc03g097350.2.1:8

General Information
CircRNA Name	Solyc03g097350.2_circ_g.2
ID in PlantcircBase	sly_circ_001087
Alias	3:53110956\|53113895
Organism	Solanum lycopersicum
Position	chr3: 59664353-59667292 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g097350.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc03g097350.2_circ_g.1
Support reads	2
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	CT-AC 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	Solyc03g097350.2.1:8

			
						 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  
						
							ACGTCAGGAATCTTTTTGGATTTAATTCTTCAGAGTAAGTGAAATGAGGATTGCAGATGCGGTA
TGTCTCAACGATATCTTTAGTTAACCTTGCCACCAAccaagtattttaatcattctcctcagaa
ggtcaaattctgaagctccagggaacagcggaagtcctagaaataattcagcaacgatgcaacc
aaatgacc

									
								

					

						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: 860
Transcript exons: 59664353-59664475,59665499-59665539,59665617-59665695,59
665779-59665861,59665959-59666028,59666131-59666240,5966
6330-59666483,59667093-59667292
CCAAGTATTTTAATCATTCTCCTCAGAAGGTCAAATTCTGAAGCTCCAGGGAACAGCGGAAGTC
CTAGAAATAATTCAGCAACGATGCAACCAAATGACCACATATCAATAGCAGTGGTATATTGATA
TCCAAGGAGCACTTCAGGTGACCTATAGTACCGACTCTGGATATAAGAGTAAACAGTACGATCC
TCCATGCATGCTGATCCAAAGTCTATAACTTTTATTTCAGCTGGCTTTTCACTAGTGCATAAAA
GAATGTTCTCAGGCTTCAGATCACAGTGAATTATACCAGCATCTTTCATTAGTGCTAATCCACG
CAATATCTGCTTCGAGAACAACTGGACAATGCTCAAAGACAATCCTCTAAAATGGTTCAACTTT
ATAAGCTCATAGAGATTTGTGTCAAGCAGTTCAAAAGCAATGCACAAGTGACGTCGATATACAA
AGTAATCATGGATCCGGACAATATGGTGCTTATCATCAGGGTCATACTTCTTATTTAATGTTGT
CAGGATAGAAACTTCAACAAGTGCTTGTTGATAATATGCTGGTTGATTCTTGATGACCTTAACA
GCAAGAAATGAATTCGATTCTTCAACCCAGCACTTAGCAACCTGGCCAAAAGTTCCATGCCCAA
GCATATCCTTCACTACATACCTTTTCTTTGTGTCCAAATTGACCAACTCAAGATTGACAGAAAG
AATGAGGTCTGAGTTTGCATTATCGTGGCCATCGTTCAACACACCGGCCGATGGGGACGTCAGG
AATCTTTTTGGATTTAATTCTTCAGAGTAAGTGAAATGAGGATTGCAGATGCGGTATGTCTCAA
CGATATCTTTAGTTAACCTTGCCACCAA
						
					

						Genomic sequence
						
							CCAAGTATTTTAATCATTCTCCTCAGAAGGTCAAATTCTGAAGCTCCAGGGAACAGCGGAAGTC
CTAGAAATAATTCAGCAACGATGCAACCAAATGACCACATATCAATAGCAGTGGTATATCTGAG
GAAGGATTAAGGTATACGATACATAAAAAATCCAAATAAAAAGGTACAATACTACATGGAAATA
AAATAGCATTTGTGATTGTCCCAGTATGATAAAAGACTGCAAAAATAGAACTTCACGTAGCTGG
TGTCTCACGAACAGCCATGTGAAGGGGAGCAATCATTTGTAGTGGATGTGCACTATGTGAGAGA
CACAATGAGGATGCCAAACATCTTTTTATTCACTGCAGTTATGCTAGATAGAATGGGATTTTGT
TCTGAAAACCGCTGGGATTAACTGGAAAATACCGAGGATGACAACAGAACTACTCCAATTCTGG
TAATCAAAAGGTTTGGGTAAGACAAAGATGAAAACATGGAATACTTTCCCTTCGAGAGTATGGT
GGACCATTTGGAAGGAAAGGAATGTAAGGATTTTTTAAAGCAAACCAGAATCTGTAGTTAGTAC
CAAGTACAGGCGTTTATCCCAACTACTTTTTGGGTGTAACGAGGCAACTGCAAATGATAGAGAC
CGTGATAGATTTTTTGAGCTCATTACACAAAACGTAATGGAGCTACCCCATGTAAATCCCCCAA
ATCACCTTCTGATTGCTGGACTTTTAATACAAAGCTTTATTAACTATCAAAAATAAACTTTTGA
TGCCCTTACTAGGGACAAAAGCTGCTCTTTTTGAACATCATAACAAAATTTAACAACATTTCCA
AAACTGATGAACTTCATAGTTGCAGAGGGTTAAGGGAGGACTTCTCCTATCATTTTTATCTAAT
TAGAGAAAGCCCACCTGATAGTTTGTGATTCTGCTGGCAAACTTTAAGATGAAGGTTGGAAAGC
ATTCAAATCATATTGCCACAAGAAGCTGAATGAAGAAACACTTCTAACTGAAAAACTACGGAAG
TTACTACAAAAAGTTTCCCCACACAATGATACAAGCAGTCAAATTCGGTGCAGCCTCCTGCAGG
CACTCATATAAGAAACGATGAACAGAAAGTAAGATCAAACTAAATAACTCAAGGATACTGATAT
CCAAGGAGCACTTCAGGTGACCTATAGTACCGACTCTGCATAAGAAGATATTAGTAAATTAAGA
GATATTAGAGCAATCAAGTAAACTTTAATAGAAAGAAGCAACAATGACCTGGATATAAGAGTAA
ACAGTACGATCCTCCATGCATGCTGATCCAAAGTCTATAACTTTTATTTCAGCTGGCTTTTCAC
TGACAAGATGCAAGAAACTAAGTGAAATGAAAAGTTAGTGAAGCAAAATGATATCTCCAACATT
GGTATCAGAGAAGCTTGCCTAGTGCATAAAAGAATGTTCTCAGGCTTCAGATCACAGTGAATTA
TACCAGCATCTTTCATTAGTGCTAATCCACGCAATATCTATACACAACGGTAAGGCAAACATAT
TACAAACTTTATTACACAAACAGATGTGGTCACCATCAGAAGTTCTATGTTCAGACCAGCAACC
AATTACCTGCTTCGAGAACAACTGGACAATGCTCAAAGACAATCCTCTAAAATGGTTCAACTTT
ATAAGCTCATAGCTGGAAAAAATAAGAAATTTAAATAAATCAGAATGTTGAGTCTGTAATACAT
TGCAGATAGTCACACGAAACATTTTAAAATGCTGCTTCTCCAGAACTTACAGATTTGTGTCAAG
CAGTTCAAAAGCAATGCACAAGTGACGTCGATATACAAAGTAATCATGGATCCGGACAATATGG
TGCTTATCATCAGGGTCATACTTCTTATTTAACTGGAAAAAGAAAAAGGAAGGGAGCTAATGAT
ATCCGCATCAACTTTACAGACAGCACTGAAAATACAAAACCAGCTGAGTAATTTTACTGTTGTC
AGGATAGAAACTTCAACAAGTGCTTGTTGATAATATGCTGGTTGATTCTTGATGACCTTAACAG
CAAGAAATGAATTCGATTCTTCAACCCAGCACTTAGCAACCTGGCCAAAAGTTCCATGCCCAAG
CATATCCTTCACTACATACCTGTATACAGTGAAAACAGTACAAAATAGTCAAATTTGTGACAAA
GTGAGAGGATTTACAGGAAACAATGACTAGAATGAAGTATGCAGGTGTGAAAGAAAAAAAAACT
TCACTGGTCATTAAATTGTTTCATGGAAAAAATCATAAAAAGGACTGCCCGCTGAGTATAAAAG
AACTTCAGACTCATCACACAGCAACACATTTACTCATAACTAAAGAGAGAAGCATGATCATTCA
AGTCGTTAAGTAGATAATCAAATATTTGTTTTCTTTCTTATGTAATCTAATCTTGGAAAAATAT
TTCAGATACATTTTTTCTTTTACTTTTTTCAGGCGGTTTAGCCTGCAAAGGAAAAGCAGTGTCA
CACAAAATAAAGTGCACTTGACCAAAAAGTACATAAAAGCATACACAGCAAAGAAGTATTCAAT
TGCTATAATGAGACAACTAGTAGCAAAATATCCAATTTACCCAAATTAGATACTTCTGAAGTGT
AAAGTATAAAAAGAACCCCACCTCTCTAAAGCTTTTGCATATCAACCCTCTCAAAGGGCAATTA
GGACCCAAAAATACATGACAGAAAAATGTGTAACAGGGAAGACATTACCAACCTTTTCTTTGTG
TCCAAATTGACCAACTCAAGATTGACAGAAAGAATGAGGTCTGAGTTTGCATTATCGTGGCCAT
CGTTCAACACACCGGCCGATGGGGACGTCAGGAATCTTTTTGGATTTAATTCTTCAGAGTAAGT
GAAATGAGGATTGCAGATGCGGTATGTCTCAACGATATCTTTAGTTAACCTTGCCACCAA
						
					

			
		

Sequences
Splice junction sequence	ACGTCAGGAATCTTTTTGGATTTAATTCTTCAGAGTAAGTGAAATGAGGATTGCAGATGCGGTA TGTCTCAACGATATCTTTAGTTAACCTTGCCACCAAccaagtattttaatcattctcctcagaa ggtcaaattctgaagctccagggaacagcggaagtcctagaaataattcagcaacgatgcaacc aaatgacc
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: 860 Transcript exons: 59664353-59664475,59665499-59665539,59665617-59665695,59 665779-59665861,59665959-59666028,59666131-59666240,5966 6330-59666483,59667093-59667292 CCAAGTATTTTAATCATTCTCCTCAGAAGGTCAAATTCTGAAGCTCCAGGGAACAGCGGAAGTC CTAGAAATAATTCAGCAACGATGCAACCAAATGACCACATATCAATAGCAGTGGTATATTGATA TCCAAGGAGCACTTCAGGTGACCTATAGTACCGACTCTGGATATAAGAGTAAACAGTACGATCC TCCATGCATGCTGATCCAAAGTCTATAACTTTTATTTCAGCTGGCTTTTCACTAGTGCATAAAA GAATGTTCTCAGGCTTCAGATCACAGTGAATTATACCAGCATCTTTCATTAGTGCTAATCCACG CAATATCTGCTTCGAGAACAACTGGACAATGCTCAAAGACAATCCTCTAAAATGGTTCAACTTT ATAAGCTCATAGAGATTTGTGTCAAGCAGTTCAAAAGCAATGCACAAGTGACGTCGATATACAA AGTAATCATGGATCCGGACAATATGGTGCTTATCATCAGGGTCATACTTCTTATTTAATGTTGT CAGGATAGAAACTTCAACAAGTGCTTGTTGATAATATGCTGGTTGATTCTTGATGACCTTAACA GCAAGAAATGAATTCGATTCTTCAACCCAGCACTTAGCAACCTGGCCAAAAGTTCCATGCCCAA GCATATCCTTCACTACATACCTTTTCTTTGTGTCCAAATTGACCAACTCAAGATTGACAGAAAG AATGAGGTCTGAGTTTGCATTATCGTGGCCATCGTTCAACACACCGGCCGATGGGGACGTCAGG AATCTTTTTGGATTTAATTCTTCAGAGTAAGTGAAATGAGGATTGCAGATGCGGTATGTCTCAA CGATATCTTTAGTTAACCTTGCCACCAA
Genomic sequence	CCAAGTATTTTAATCATTCTCCTCAGAAGGTCAAATTCTGAAGCTCCAGGGAACAGCGGAAGTC CTAGAAATAATTCAGCAACGATGCAACCAAATGACCACATATCAATAGCAGTGGTATATCTGAG GAAGGATTAAGGTATACGATACATAAAAAATCCAAATAAAAAGGTACAATACTACATGGAAATA AAATAGCATTTGTGATTGTCCCAGTATGATAAAAGACTGCAAAAATAGAACTTCACGTAGCTGG TGTCTCACGAACAGCCATGTGAAGGGGAGCAATCATTTGTAGTGGATGTGCACTATGTGAGAGA CACAATGAGGATGCCAAACATCTTTTTATTCACTGCAGTTATGCTAGATAGAATGGGATTTTGT TCTGAAAACCGCTGGGATTAACTGGAAAATACCGAGGATGACAACAGAACTACTCCAATTCTGG TAATCAAAAGGTTTGGGTAAGACAAAGATGAAAACATGGAATACTTTCCCTTCGAGAGTATGGT GGACCATTTGGAAGGAAAGGAATGTAAGGATTTTTTAAAGCAAACCAGAATCTGTAGTTAGTAC CAAGTACAGGCGTTTATCCCAACTACTTTTTGGGTGTAACGAGGCAACTGCAAATGATAGAGAC CGTGATAGATTTTTTGAGCTCATTACACAAAACGTAATGGAGCTACCCCATGTAAATCCCCCAA ATCACCTTCTGATTGCTGGACTTTTAATACAAAGCTTTATTAACTATCAAAAATAAACTTTTGA TGCCCTTACTAGGGACAAAAGCTGCTCTTTTTGAACATCATAACAAAATTTAACAACATTTCCA AAACTGATGAACTTCATAGTTGCAGAGGGTTAAGGGAGGACTTCTCCTATCATTTTTATCTAAT TAGAGAAAGCCCACCTGATAGTTTGTGATTCTGCTGGCAAACTTTAAGATGAAGGTTGGAAAGC ATTCAAATCATATTGCCACAAGAAGCTGAATGAAGAAACACTTCTAACTGAAAAACTACGGAAG TTACTACAAAAAGTTTCCCCACACAATGATACAAGCAGTCAAATTCGGTGCAGCCTCCTGCAGG CACTCATATAAGAAACGATGAACAGAAAGTAAGATCAAACTAAATAACTCAAGGATACTGATAT CCAAGGAGCACTTCAGGTGACCTATAGTACCGACTCTGCATAAGAAGATATTAGTAAATTAAGA GATATTAGAGCAATCAAGTAAACTTTAATAGAAAGAAGCAACAATGACCTGGATATAAGAGTAA ACAGTACGATCCTCCATGCATGCTGATCCAAAGTCTATAACTTTTATTTCAGCTGGCTTTTCAC TGACAAGATGCAAGAAACTAAGTGAAATGAAAAGTTAGTGAAGCAAAATGATATCTCCAACATT GGTATCAGAGAAGCTTGCCTAGTGCATAAAAGAATGTTCTCAGGCTTCAGATCACAGTGAATTA TACCAGCATCTTTCATTAGTGCTAATCCACGCAATATCTATACACAACGGTAAGGCAAACATAT TACAAACTTTATTACACAAACAGATGTGGTCACCATCAGAAGTTCTATGTTCAGACCAGCAACC AATTACCTGCTTCGAGAACAACTGGACAATGCTCAAAGACAATCCTCTAAAATGGTTCAACTTT ATAAGCTCATAGCTGGAAAAAATAAGAAATTTAAATAAATCAGAATGTTGAGTCTGTAATACAT TGCAGATAGTCACACGAAACATTTTAAAATGCTGCTTCTCCAGAACTTACAGATTTGTGTCAAG CAGTTCAAAAGCAATGCACAAGTGACGTCGATATACAAAGTAATCATGGATCCGGACAATATGG TGCTTATCATCAGGGTCATACTTCTTATTTAACTGGAAAAAGAAAAAGGAAGGGAGCTAATGAT ATCCGCATCAACTTTACAGACAGCACTGAAAATACAAAACCAGCTGAGTAATTTTACTGTTGTC AGGATAGAAACTTCAACAAGTGCTTGTTGATAATATGCTGGTTGATTCTTGATGACCTTAACAG CAAGAAATGAATTCGATTCTTCAACCCAGCACTTAGCAACCTGGCCAAAAGTTCCATGCCCAAG CATATCCTTCACTACATACCTGTATACAGTGAAAACAGTACAAAATAGTCAAATTTGTGACAAA GTGAGAGGATTTACAGGAAACAATGACTAGAATGAAGTATGCAGGTGTGAAAGAAAAAAAAACT TCACTGGTCATTAAATTGTTTCATGGAAAAAATCATAAAAAGGACTGCCCGCTGAGTATAAAAG AACTTCAGACTCATCACACAGCAACACATTTACTCATAACTAAAGAGAGAAGCATGATCATTCA AGTCGTTAAGTAGATAATCAAATATTTGTTTTCTTTCTTATGTAATCTAATCTTGGAAAAATAT TTCAGATACATTTTTTCTTTTACTTTTTTCAGGCGGTTTAGCCTGCAAAGGAAAAGCAGTGTCA CACAAAATAAAGTGCACTTGACCAAAAAGTACATAAAAGCATACACAGCAAAGAAGTATTCAAT TGCTATAATGAGACAACTAGTAGCAAAATATCCAATTTACCCAAATTAGATACTTCTGAAGTGT AAAGTATAAAAAGAACCCCACCTCTCTAAAGCTTTTGCATATCAACCCTCTCAAAGGGCAATTA GGACCCAAAAATACATGACAGAAAAATGTGTAACAGGGAAGACATTACCAACCTTTTCTTTGTG TCCAAATTGACCAACTCAAGATTGACAGAAAGAATGAGGTCTGAGTTTGCATTATCGTGGCCAT CGTTCAACACACCGGCCGATGGGGACGTCAGGAATCTTTTTGGATTTAATTCTTCAGAGTAAGT GAAATGAGGATTGCAGATGCGGTATGTCTCAACGATATCTTTAGTTAACCTTGCCACCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.570565289

Conservation Information
Conserved circRNAs	NA
PMCS	0.570565289

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							59666469-59667279(-)
						
						Potential amino acid sequence
						
							MLGHGTFGQVAKCWVEESNSFLAVKVIKNQPAYYQQALVEVSILTTLNKKYDPDDKHHIVRIHD
YFVYRRHLCIAFELLDTNLYELIKLNHFRGLSLSIVQLFSKQILRGLALMKDAGIIHCDLKPEN
ILLCTSEKPAEIKVIDFGSACMEDRTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELF
LGLPLFPGASEFDLLRRMIKILGWWQG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	59666469-59667279(-)
Potential amino acid sequence	MLGHGTFGQVAKCWVEESNSFLAVKVIKNQPAYYQQALVEVSILTTLNKKYDPDDKHHIVRIHD YFVYRRHLCIAFELLDTNLYELIKLNHFRGLSLSIVQLFSKQILRGLALMKDAGIIHCDLKPEN ILLCTSEKPAEIKVIDFGSACMEDRTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELF LGLPLFPGASEFDLLRRMIKILGWWQG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc03g097350.2_circ_g.2

Address

Any questions?

Supported by