Plant Circular RNA Database

Detail information of Solyc09g018060.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc09g018060.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_002828
					
						Alias
						9:12713068|12714300
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 12713068-12714300  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc09g018060.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc09g018060.2_circ_g.1 Solyc09g018060.2_circ_g.2 Solyc09g018060.2_circ_g.3 						
					
						Support reads
						19
					
						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
						Solyc09g018060.2.1:3

General Information
CircRNA Name	Solyc09g018060.2_circ_g.4
ID in PlantcircBase	sly_circ_002828
Alias	9:12713068\|12714300
Organism	Solanum lycopersicum
Position	chr9: 12713068-12714300 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc09g018060.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc09g018060.2_circ_g.1 Solyc09g018060.2_circ_g.2 Solyc09g018060.2_circ_g.3
Support reads	19
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	Solyc09g018060.2.1:3

			
						 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: TTGGAAGGAAAAGAAAAATGATAC
 R: TGACAGCAGAAACTGGGACATA
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: TTGGAAGGAAAAGAAAAATGATAC R: TGACAGCAGAAACTGGGACATA 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  
						
							CATAACAACTTCCCGAACAAAACGGCCTTCAAGTGCAGATCTTTCTTCTGAGGTGTTACCACCA
TTAAGAACTTTTATTGCAACAATTTGATCACCATACctcaggtgccatccaccggtatgtccca
gtttctgctgtcatcatctctgtaagggtctcttcccttgctaacccaaaatcagcaagcttca
cagacttc

									
								

					

						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: 454
Transcript exons: 12713068-12713192,12713710-12713905,12714168-12714300
CTCAGGTGCCATCCACCGGTATGTCCCAGTTTCTGCTGTCATCATCTCTGTAAGGGTCTCTTCC
CTTGCTAACCCAAAATCAGCAAGCTTCACAGACTTCTGATTGGCCGTGAGCAGCAAATTGTCAG
GTTTTAGATCTCTATGTATAATGCCATTGGCATGTAAACATTCCATGGCCCGAGCAATGTCAAG
AGCATAATTTATGGCGACGTGTAGGTCAAGCACGTTTGGTCGAATGCTGACTAAGTACTTCCGA
AGAGACATTCCAGGCAGTAGCTCTGAAACTATAACCATCAAAGGATCCTTGCAAGCTCCAATAA
ATTTTACAAGATTCTCATGTTTTACTCTTGACATCATAACAACTTCCCGAACAAAACGGCCTTC
AAGTGCAGATCTTTCTTCTGAGGTGTTACCACCATTAAGAACTTTTATTGCAACAATTTGATCA
CCATAC
						
					

						Genomic sequence
						
							CTCAGGTGCCATCCACCGGTATGTCCCAGTTTCTGCTGTCATCATCTCTGTAAGGGTCTCTTCC
CTTGCTAACCCAAAATCAGCAAGCTTCACAGACTTCTGATTGGCCGTGAGCAGCAAATTGTCTG
CATGAATGACATTTCACATGTGCTCTTTCTTAGACATGAGAAGATTAAAAAAGAATGCACATTA
ATGAATTCAATAGGGAAGGTAAACAGCTGGTGATGCCAACTTAAGAATATACTCCAAGTTAGCA
GCATGAATTGAACCACACATCAAGGGAAAATATCAACTAAATATGAGTTTGATATCCTCTGTTG
GCTTTACTACATTTGAGATTCTTTTTACAAGAATTAAAAAAGTGAGATAGCAAGCGATGAAGTG
ATAGGTGGAGCCAGAAATGTATACCACAATGTCTGCACTAATAACCTCTTCCTTCAATGGTATT
TAGATTACTGACCATAGTAGAGCCAACATAAATTTTAAGATAACCCAGAAAAAAGAACTCTTCC
AGCGGTAAAATATTGATGGATAAAAGAATTTAGTCCAAAAAACATAATATTTGGCCTGTTTAAC
ATTTCAATGAAAAACTACATTAACAAAAAGAAGAAATTCTTCTACAGTCGGCTAGCCAAGTGGT
ACCAGGTTTTAGATCTCTATGTATAATGCCATTGGCATGTAAACATTCCATGGCCCGAGCAATG
TCAAGAGCATAATTTATGGCGACGTGTAGGTCAAGCACGTTTGGTCGAATGCTGACTAAGTACT
TCCGAAGAGACATTCCAGGCAGTAGCTCTGAAACTATAACCATCAAAGGATCCTTGCAAGCTCC
AATAAACTGCAAACATGAACCATCATGTGAACTGGGCCAAAAATGTAAAAGGTTTAGCACCAGT
TACATAATAGGCAAAGGAACATGAACTAACTACAGAACGTAAATAACCGTGTATGTGAATATTT
ACTAGCTAACACCTTATTGACTGCTAAACTTAACCAAAAAAAACTGTTCAAAGGAAGTTAAACA
CAACACTTTGAAAAGATAATCAGAATATTAATTTGGAGTTGAAGGAACTTGGAAGGAAAAGAAA
AATGATACTTACTTTTACAAGATTCTCATGTTTTACTCTTGACATCATAACAACTTCCCGAACA
AAACGGCCTTCAAGTGCAGATCTTTCTTCTGAGGTGTTACCACCATTAAGAACTTTTATTGCAA
CAATTTGATCACCATAC
						
					

			
		

Sequences
Splice junction sequence	CATAACAACTTCCCGAACAAAACGGCCTTCAAGTGCAGATCTTTCTTCTGAGGTGTTACCACCA TTAAGAACTTTTATTGCAACAATTTGATCACCATACctcaggtgccatccaccggtatgtccca gtttctgctgtcatcatctctgtaagggtctcttcccttgctaacccaaaatcagcaagcttca cagacttc
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: 454 Transcript exons: 12713068-12713192,12713710-12713905,12714168-12714300 CTCAGGTGCCATCCACCGGTATGTCCCAGTTTCTGCTGTCATCATCTCTGTAAGGGTCTCTTCC CTTGCTAACCCAAAATCAGCAAGCTTCACAGACTTCTGATTGGCCGTGAGCAGCAAATTGTCAG GTTTTAGATCTCTATGTATAATGCCATTGGCATGTAAACATTCCATGGCCCGAGCAATGTCAAG AGCATAATTTATGGCGACGTGTAGGTCAAGCACGTTTGGTCGAATGCTGACTAAGTACTTCCGA AGAGACATTCCAGGCAGTAGCTCTGAAACTATAACCATCAAAGGATCCTTGCAAGCTCCAATAA ATTTTACAAGATTCTCATGTTTTACTCTTGACATCATAACAACTTCCCGAACAAAACGGCCTTC AAGTGCAGATCTTTCTTCTGAGGTGTTACCACCATTAAGAACTTTTATTGCAACAATTTGATCA CCATAC
Genomic sequence	CTCAGGTGCCATCCACCGGTATGTCCCAGTTTCTGCTGTCATCATCTCTGTAAGGGTCTCTTCC CTTGCTAACCCAAAATCAGCAAGCTTCACAGACTTCTGATTGGCCGTGAGCAGCAAATTGTCTG CATGAATGACATTTCACATGTGCTCTTTCTTAGACATGAGAAGATTAAAAAAGAATGCACATTA ATGAATTCAATAGGGAAGGTAAACAGCTGGTGATGCCAACTTAAGAATATACTCCAAGTTAGCA GCATGAATTGAACCACACATCAAGGGAAAATATCAACTAAATATGAGTTTGATATCCTCTGTTG GCTTTACTACATTTGAGATTCTTTTTACAAGAATTAAAAAAGTGAGATAGCAAGCGATGAAGTG ATAGGTGGAGCCAGAAATGTATACCACAATGTCTGCACTAATAACCTCTTCCTTCAATGGTATT TAGATTACTGACCATAGTAGAGCCAACATAAATTTTAAGATAACCCAGAAAAAAGAACTCTTCC AGCGGTAAAATATTGATGGATAAAAGAATTTAGTCCAAAAAACATAATATTTGGCCTGTTTAAC ATTTCAATGAAAAACTACATTAACAAAAAGAAGAAATTCTTCTACAGTCGGCTAGCCAAGTGGT ACCAGGTTTTAGATCTCTATGTATAATGCCATTGGCATGTAAACATTCCATGGCCCGAGCAATG TCAAGAGCATAATTTATGGCGACGTGTAGGTCAAGCACGTTTGGTCGAATGCTGACTAAGTACT TCCGAAGAGACATTCCAGGCAGTAGCTCTGAAACTATAACCATCAAAGGATCCTTGCAAGCTCC AATAAACTGCAAACATGAACCATCATGTGAACTGGGCCAAAAATGTAAAAGGTTTAGCACCAGT TACATAATAGGCAAAGGAACATGAACTAACTACAGAACGTAAATAACCGTGTATGTGAATATTT ACTAGCTAACACCTTATTGACTGCTAAACTTAACCAAAAAAAACTGTTCAAAGGAAGTTAAACA CAACACTTTGAAAAGATAATCAGAATATTAATTTGGAGTTGAAGGAACTTGGAAGGAAAAGAAA AATGATACTTACTTTTACAAGATTCTCATGTTTTACTCTTGACATCATAACAACTTCCCGAACA AAACGGCCTTCAAGTGCAGATCTTTCTTCTGAGGTGTTACCACCATTAAGAACTTTTATTGCAA CAATTTGATCACCATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.618383885

Conservation Information
Conserved circRNAs	NA
PMCS	0.618383885

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12714205-12714294(-)
						
						Potential amino acid sequence
						
							MMSRVKHENLVKFIGACKDPLMVIVSELLPGMSLRKYLVSIRPNVLDLHVAINYALDIARAMEC
LHANGIIHRDLKPDNLLLTANQKSVKLADFGLAREETLTEMMTAETGTYRWMAPEVW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12714205-12714294(-)
Potential amino acid sequence	MMSRVKHENLVKFIGACKDPLMVIVSELLPGMSLRKYLVSIRPNVLDLHVAINYALDIARAMEC LHANGIIHRDLKPDNLLLTANQKSVKLADFGLAREETLTEMMTAETGTYRWMAPEVW*(-)
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 Solyc09g018060.2_circ_g.4

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