Plant Circular RNA Database

Detail information of Solyc11g017170.1_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc11g017170.1_circ_g.3
					
						ID in PlantcircBase
						sly_circ_003322
					
						Alias
						11:7981451|7983985
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 7981451-7983985  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc11g017170.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc11g017170.1_circ_g.1 Solyc11g017170.1_circ_g.2 						
					
						Support reads
						10
					
						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
						Solyc11g017170.1.1:5

General Information
CircRNA Name	Solyc11g017170.1_circ_g.3
ID in PlantcircBase	sly_circ_003322
Alias	11:7981451\|7983985
Organism	Solanum lycopersicum
Position	chr11: 7981451-7983985 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc11g017170.1
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc11g017170.1_circ_g.1 Solyc11g017170.1_circ_g.2
Support reads	10
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	Solyc11g017170.1.1:5

			
						 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  
						
							TGAAATTGTACTTAAGCATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACAGCT
ATATGTTGTCGTGTTACTCCATCCCAAAAGGCACAGgacagcaaacacgcatctttgctgaagc
tgtggaacaatatgctcagcttggtctgcgaacattatgtttggcatggcgtgatttagaagaa
gaagaata

									
								

					

						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: 596
Transcript exons: 7981451-7981605,7981766-7981846,7982027-7982147,7982282-
7982388,7983854-7983985
GACAGCAAACACGCATCTTTGCTGAAGCTGTGGAACAATATGCTCAGCTTGGTCTGCGAACATT
ATGTTTGGCATGGCGTGATTTAGAAGAAGAAGAATATCATGAATGGTCATTATTGTTTAAAGAG
GCTAATAGTTCATTGGTTGATAGAGAGTGGAGAGTAGCTGAAGTCTGCCAAAGAATAGAGCAGG
GCTTTGAGATTATTGGAGTTGCAGCAATTGAAGATCGTCTTCAGGATGCTGTACCTGAAACAAT
TGAGACACTCAGGAAGGCTGGAATAAACTTTTGGATGCTGACTGGCGACAAACAGAATACGGCG
ATACAGATTGCACGTTCATGTAATTTTGTTTCTCCTGAACCTAAAGGTCAGCTTCTGCTGATTA
ATGGGAGAACTGAAGATGAAGTAGGTCAAAGTCTGGAGAGAGTGCTTCTTACAATGAGAATCAC
AAATGCAGAACCTAAGGATGTTGCTTTTGTTGTGGATGGTTGGGCTCTTGAAATTGTACTTAAG
CATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACAGCTATATGTTGTCGTGTTA
CTCCATCCCAAAAGGCACAG
						
					

						Genomic sequence
						
							GACAGCAAACACGCATCTTTGCTGAAGCTGTGGAACAATATGCTCAGCTTGGTCTGCGAACATT
ATGTTTGGCATGGCGTGATTTAGAAGAAGAAGAATATCATGAATGGTCATTATTGTTTAAAGAG
GCTAATAGTTCATTGGTTGATAGAGAGGTAAGAAATTATTTTCTATGGTTCATGCGTGCTACTA
TTGACTTTTTTCTTTTAGCAAAGCTTAGATCACCTGCGTTATGTATACCTTCTGCTCTGGCTCT
CTGTTGGGTGTTACTGAAGTTTTCAGTTGACTGATTGATCTTATACTTGTATGCCACAGTGGAG
AGTAGCTGAAGTCTGCCAAAGAATAGAGCAGGGCTTTGAGATTATTGGAGTTGCAGCAATTGAA
GATCGTCTTCAGGTGAGACCGTCTTCTCTAAAAAAAATTTAAAAAATTCTTGATAAGGCTTGCT
TGCTGTCTTGACACAATTCTTGCATCTTCACGTAGATGCTCCTTTTAGAATTCTACATTATTGT
ACCTTGGTCAATGGATTTCGTAATCTTACTTTTCACTTGTATATATACACACATATTTATCCAG
GATGCTGTACCTGAAACAATTGAGACACTCAGGAAGGCTGGAATAAACTTTTGGATGCTGACTG
GCGACAAACAGAATACGGCGATACAGATTGCACGTTCATGTAATTTTGTTTCTCCTGGTATGCC
CTGTTGATTTTTTTCTCCTTCTGTTACCTTTTTTCTTTTTAGTTTGTGCTTTCTTGTACAATGT
ATTGTCGACAAAAGATGTTTTCTTCTTAAAAATTTGTCAAGAGACTGATTGACATCTTTGCAGA
ACCTAAAGGTCAGCTTCTGCTGATTAATGGGAGAACTGAAGATGAAGTAGGTCAAAGTCTGGAG
AGAGTGCTTCTTACAATGAGAATCACAAATGCAGAACCTAAGGTATGTTGAATTAAATGCATGT
CTATGTTGACGAGTGTTCTATTTTGTTAACTGGAAATACAAATTCTTTCATTTCTATCAGATCC
TATCAGCTGCTTAGCTAAGACAATAAGTGTTTGCTTGGCTGCCACTTCTATTATCTCCTTCTGT
AAAAGATAAACAGAGATGCTGAAATGATTGCATATTCCAAATTCCAGCCATATTTGCATTTCAG
TTATTTTAGATCTGGAAAATATGAGCTTGTTTTCTTGACCATTGTGCTTGATGTTGACATAGGA
TATAAACTTGCTTTTGGGTTTCTGTTTGTACCTTTTTAGTAGTGGATGAATTAATATATGCATC
TTTGATACTCCCTCCGTCCGGAATTGTTTGTCATGGTTTCTATTTTTAGAGTCAAAATTGTAAA
AACTTTGAGTAACATTTTAAGATGTATTTTTTCATCATATTAATATGCAAAAAATTCTAATTTA
TAGTACTTTTCATGTAGTTTTAGAATGTCTAATTTTTTGTTTAAAATATAGAATTAATGTGATC
TAATTTACCTTTGAAAATTAGTCAAATTGACTTTCGATAAGCGCAACATGACAAACAATTCCGG
ACGGAGGGAGTATCTGCTTTTGGGACAATATAATTTGTAAGTGAAGCTAAATGTTGTAAAATTG
TCAGGCTGAGCTCTGAATTTGGATTACTTGAAAAGGATCATAATTTGTTAGTGATATCCTTAGA
ATTAATTGTGTCTGCCTTAATAAAGCTATGTCTTGAGTGGGTTAAAAATAACATGATCATACAC
AGAGAAGTTCACAAGGATTATACATCAACTCTCAGTTTGAAGTGTAATGGCTACAGTCACGGGG
AGATGAAAGTGTTTCCTGCCTTCTGTTTTTGTGATAGACTCTATTGTTTAATAAGGAGACTCTA
AAATCATAGAAGTGTTTCTTCGCATTGATTTTTTTTTGATAACCAAAAAGGAATTAAGAATTAA
CATGGCAAGAGCCACCTGATCCCAAGACATAGCTGAACAAAGGTGCATGCTATTGTGTCTTTGG
AATATTTGGATGACTTATTTCAGTAAAGGCACATCTTATCCATGATGGTCAGGTGAAACACTAA
AAATGGGAGCCCGGTGCACTAAGCATCACTATACCTGGGGCCTGGAGATGGGCCTGACCATATT
AGGTATTAGGTCTATTATATGAAGTCCTATTTCCACAGCTTGAACCTGTCACCTGTTCCAGTTT
TTTATTTTTTTCCGTTTGTTTATAACATCCTTTCTGTATGCCTACTCTAAGGCACTATCTTGTA
AATCTCAAAATTATACTTTCAGAGAGGGAGGAAACAGAAGAACAAGAAAACTTACCTTCCCTCC
AAGATCTCTGAAATAACACTTATGATGGAATGGGTGGTACTTATTCTTATAGATGTTCCTCTTT
CATGATACATGACTCTTAGTTTTTATATCTGGCAGGATGTTGCTTTTGTTGTGGATGGTTGGGC
TCTTGAAATTGTACTTAAGCATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACA
GCTATATGTTGTCGTGTTACTCCATCCCAAAAGGCACAG
						
					

			
		

Sequences
Splice junction sequence	TGAAATTGTACTTAAGCATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACAGCT ATATGTTGTCGTGTTACTCCATCCCAAAAGGCACAGgacagcaaacacgcatctttgctgaagc tgtggaacaatatgctcagcttggtctgcgaacattatgtttggcatggcgtgatttagaagaa gaagaata
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: 596 Transcript exons: 7981451-7981605,7981766-7981846,7982027-7982147,7982282- 7982388,7983854-7983985 GACAGCAAACACGCATCTTTGCTGAAGCTGTGGAACAATATGCTCAGCTTGGTCTGCGAACATT ATGTTTGGCATGGCGTGATTTAGAAGAAGAAGAATATCATGAATGGTCATTATTGTTTAAAGAG GCTAATAGTTCATTGGTTGATAGAGAGTGGAGAGTAGCTGAAGTCTGCCAAAGAATAGAGCAGG GCTTTGAGATTATTGGAGTTGCAGCAATTGAAGATCGTCTTCAGGATGCTGTACCTGAAACAAT TGAGACACTCAGGAAGGCTGGAATAAACTTTTGGATGCTGACTGGCGACAAACAGAATACGGCG ATACAGATTGCACGTTCATGTAATTTTGTTTCTCCTGAACCTAAAGGTCAGCTTCTGCTGATTA ATGGGAGAACTGAAGATGAAGTAGGTCAAAGTCTGGAGAGAGTGCTTCTTACAATGAGAATCAC AAATGCAGAACCTAAGGATGTTGCTTTTGTTGTGGATGGTTGGGCTCTTGAAATTGTACTTAAG CATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACAGCTATATGTTGTCGTGTTA CTCCATCCCAAAAGGCACAG
Genomic sequence	GACAGCAAACACGCATCTTTGCTGAAGCTGTGGAACAATATGCTCAGCTTGGTCTGCGAACATT ATGTTTGGCATGGCGTGATTTAGAAGAAGAAGAATATCATGAATGGTCATTATTGTTTAAAGAG GCTAATAGTTCATTGGTTGATAGAGAGGTAAGAAATTATTTTCTATGGTTCATGCGTGCTACTA TTGACTTTTTTCTTTTAGCAAAGCTTAGATCACCTGCGTTATGTATACCTTCTGCTCTGGCTCT CTGTTGGGTGTTACTGAAGTTTTCAGTTGACTGATTGATCTTATACTTGTATGCCACAGTGGAG AGTAGCTGAAGTCTGCCAAAGAATAGAGCAGGGCTTTGAGATTATTGGAGTTGCAGCAATTGAA GATCGTCTTCAGGTGAGACCGTCTTCTCTAAAAAAAATTTAAAAAATTCTTGATAAGGCTTGCT TGCTGTCTTGACACAATTCTTGCATCTTCACGTAGATGCTCCTTTTAGAATTCTACATTATTGT ACCTTGGTCAATGGATTTCGTAATCTTACTTTTCACTTGTATATATACACACATATTTATCCAG GATGCTGTACCTGAAACAATTGAGACACTCAGGAAGGCTGGAATAAACTTTTGGATGCTGACTG GCGACAAACAGAATACGGCGATACAGATTGCACGTTCATGTAATTTTGTTTCTCCTGGTATGCC CTGTTGATTTTTTTCTCCTTCTGTTACCTTTTTTCTTTTTAGTTTGTGCTTTCTTGTACAATGT ATTGTCGACAAAAGATGTTTTCTTCTTAAAAATTTGTCAAGAGACTGATTGACATCTTTGCAGA ACCTAAAGGTCAGCTTCTGCTGATTAATGGGAGAACTGAAGATGAAGTAGGTCAAAGTCTGGAG AGAGTGCTTCTTACAATGAGAATCACAAATGCAGAACCTAAGGTATGTTGAATTAAATGCATGT CTATGTTGACGAGTGTTCTATTTTGTTAACTGGAAATACAAATTCTTTCATTTCTATCAGATCC TATCAGCTGCTTAGCTAAGACAATAAGTGTTTGCTTGGCTGCCACTTCTATTATCTCCTTCTGT AAAAGATAAACAGAGATGCTGAAATGATTGCATATTCCAAATTCCAGCCATATTTGCATTTCAG TTATTTTAGATCTGGAAAATATGAGCTTGTTTTCTTGACCATTGTGCTTGATGTTGACATAGGA TATAAACTTGCTTTTGGGTTTCTGTTTGTACCTTTTTAGTAGTGGATGAATTAATATATGCATC TTTGATACTCCCTCCGTCCGGAATTGTTTGTCATGGTTTCTATTTTTAGAGTCAAAATTGTAAA AACTTTGAGTAACATTTTAAGATGTATTTTTTCATCATATTAATATGCAAAAAATTCTAATTTA TAGTACTTTTCATGTAGTTTTAGAATGTCTAATTTTTTGTTTAAAATATAGAATTAATGTGATC TAATTTACCTTTGAAAATTAGTCAAATTGACTTTCGATAAGCGCAACATGACAAACAATTCCGG ACGGAGGGAGTATCTGCTTTTGGGACAATATAATTTGTAAGTGAAGCTAAATGTTGTAAAATTG TCAGGCTGAGCTCTGAATTTGGATTACTTGAAAAGGATCATAATTTGTTAGTGATATCCTTAGA ATTAATTGTGTCTGCCTTAATAAAGCTATGTCTTGAGTGGGTTAAAAATAACATGATCATACAC AGAGAAGTTCACAAGGATTATACATCAACTCTCAGTTTGAAGTGTAATGGCTACAGTCACGGGG AGATGAAAGTGTTTCCTGCCTTCTGTTTTTGTGATAGACTCTATTGTTTAATAAGGAGACTCTA AAATCATAGAAGTGTTTCTTCGCATTGATTTTTTTTTGATAACCAAAAAGGAATTAAGAATTAA CATGGCAAGAGCCACCTGATCCCAAGACATAGCTGAACAAAGGTGCATGCTATTGTGTCTTTGG AATATTTGGATGACTTATTTCAGTAAAGGCACATCTTATCCATGATGGTCAGGTGAAACACTAA AAATGGGAGCCCGGTGCACTAAGCATCACTATACCTGGGGCCTGGAGATGGGCCTGACCATATT AGGTATTAGGTCTATTATATGAAGTCCTATTTCCACAGCTTGAACCTGTCACCTGTTCCAGTTT TTTATTTTTTTCCGTTTGTTTATAACATCCTTTCTGTATGCCTACTCTAAGGCACTATCTTGTA AATCTCAAAATTATACTTTCAGAGAGGGAGGAAACAGAAGAACAAGAAAACTTACCTTCCCTCC AAGATCTCTGAAATAACACTTATGATGGAATGGGTGGTACTTATTCTTATAGATGTTCCTCTTT CATGATACATGACTCTTAGTTTTTATATCTGGCAGGATGTTGCTTTTGTTGTGGATGGTTGGGC TCTTGAAATTGTACTTAAGCATTATCGGAAGGCATTCACAGAACTTGCTATATTGTCAAGAACA GCTATATGTTGTCGTGTTACTCCATCCCAAAAGGCACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.491754517

Conservation Information
Conserved circRNAs	NA
PMCS	0.491754517

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7982376-7981472(+)
7983953-7981534(+)
7982082-7981534(+)
7981566-7983940(-)
						
						Potential amino acid sequence
						
							MQNLRMLLLLWMVGLLKLYLSIIGRHSQNLLYCQEQLYVVVLLHPKRHRTANTHLC*(+)
MLSCYSIPKGTGQQTRIFAEAVEQYAQLGLRTLCLAWRDLEEEEYHEWSLLFKEANSSLVDREW
RVAEVCQRIEQGFEIIGVAAIEDRLQDAVPETIETLRKAGINFWMLTGDKQNTAIQIARSCNFV
SPEPKGQLLLINGRTEDEVGQSLERVLLTMRITNAEPKDVAFVVDGWALEIVLKHYRKAFTELA
ILSRTAICCRVTPSQKAQDSKHASLLKLWNNMLSLVCEHYVWHGVI*(+)
MLTGDKQNTAIQIARSCNFVSPEPKGQLLLINGRTEDEVGQSLERVLLTMRITNAEPKDVAFVV
DGWALEIVLKHYRKAFTELAILSRTAICCRVTPSQKAQDSKHASLLKLWNNMLSLVCEHYVWHG
VI*(+)
MTIHDILLLLNHAMPNIMFADQAEHIVPQLQQRCVFAVLCLLGWSNTTTYSCS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7982376-7981472(+) 7983953-7981534(+) 7982082-7981534(+) 7981566-7983940(-)
Potential amino acid sequence	MQNLRMLLLLWMVGLLKLYLSIIGRHSQNLLYCQEQLYVVVLLHPKRHRTANTHLC(+) MLSCYSIPKGTGQQTRIFAEAVEQYAQLGLRTLCLAWRDLEEEEYHEWSLLFKEANSSLVDREW RVAEVCQRIEQGFEIIGVAAIEDRLQDAVPETIETLRKAGINFWMLTGDKQNTAIQIARSCNFV SPEPKGQLLLINGRTEDEVGQSLERVLLTMRITNAEPKDVAFVVDGWALEIVLKHYRKAFTELA ILSRTAICCRVTPSQKAQDSKHASLLKLWNNMLSLVCEHYVWHGVI(+) MLTGDKQNTAIQIARSCNFVSPEPKGQLLLINGRTEDEVGQSLERVLLTMRITNAEPKDVAFVV DGWALEIVLKHYRKAFTELAILSRTAICCRVTPSQKAQDSKHASLLKLWNNMLSLVCEHYVWHG VI(+) MTIHDILLLLNHAMPNIMFADQAEHIVPQLQQRCVFAVLCLLGWSNTTTYSCS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017; Yin et al., 2018

circRNA

Detail information of Solyc11g017170.1_circ_g.3

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