Plant Circular RNA Database

Detail information of Solyc01g080200.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g080200.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000189
					
						Alias
						1:71920117|71921148, Slcirc017
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 79409311-79410342  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g080200.2						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 33A
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g080200.2_circ_g.1 						
					
						Support reads
						13/139
					
						Tissues
						fruit/leaf
					
						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
						Solyc01g080200.2.1:3

General Information
CircRNA Name	Solyc01g080200.2_circ_g.2
ID in PlantcircBase	sly_circ_000189
Alias	1:71920117\|71921148, Slcirc017
Organism	Solanum lycopersicum
Position	chr1: 79409311-79410342 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g080200.2
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 33A
Parent gene strand	-
Alternative splicing	Solyc01g080200.2_circ_g.1
Support reads	13/139
Tissues	fruit/leaf
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	Solyc01g080200.2.1:3

			
						 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: CTGGAGGAGACAATAATCTGG
 R: GGAATAGCACCAGTGGACTG
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: CTGGAGGAGACAATAATCTGG R: GGAATAGCACCAGTGGACTG 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  
						
							TTCAAGCGTCCATTCACGTAACCAGGCCAAAAATAAGCAGAAGTGTCCAGCAAATTTCTGGCAA
TGCAAGCCTCAACTATCAAGTGATGCAGGTTACCAGcatgccgtgaagggagaaaatctgaaca
cagtccactggtgctattccaacgagtaagacatttaacattggagcgtagcctattaaatggc
tatcttta

									
								

					

						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: 488
Transcript exons: 79409311-79409472,79409614-79409728,79410132-79410342
CATGCCGTGAAGGGAGAAAATCTGAACACAGTCCACTGGTGCTATTCCAACGAGTAAGACATTT
AACATTGGAGCGTAGCCTATTAAATGGCTATCTTTACCAGAATAGTCAGTAGGAACTGGAGGAG
ACAATAATCTGGTTATGAAATTGACGGTATGTTCCTGTATATTCCAACCACGAATCAGTGAGGC
TCCACAAAGAATGGTAGCAGCAGCTATCTTCTCATCATCTTCTCCTTTGACCGCCATCTCGAAA
ATCTTCTCAAGCTCTGCTAAACTTGAAGCTGGAGCAGAAACCAAAGCATTAATAATAGCGGGAG
TCAACGGGGCCCCCTTCATAAATGATGACCAACCAGGCACTTGAGTTGGCATACTGTGCGCTAA
CTGGTTCAAGCGTCCATTCACGTAACCAGGCCAAAAATAAGCAGAAGTGTCCAGCAAATTTCTG
GCAATGCAAGCCTCAACTATCAAGTGATGCAGGTTACCAG
						
					

						Genomic sequence
						
							CATGCCGTGAAGGGAGAAAATCTGAACACAGTCCACTGGTGCTATTCCAACGAGTAAGACATTT
AACATTGGAGCGTAGCCTATTAAATGGCTATCTTTACCAGAATAGTCAGTAGGAACTGGAGGAG
ACAATAATCTGGTTATGAAATTGACGGTATGTTCCTGCGTGATCACAACCAAAAGGAAGAACCA
CATTATTTCTTCGCAAGAACAATTTAATGATACTTTTAGTAATGGGTATCAGGATCGTAATGCT
CTAAACAAAAGAATTTCCTTTGCTGAAGCAAACTATTTGTTTATTACCTGTATATTCCAACCAC
GAATCAGTGAGGCTCCACAAAGAATGGTAGCAGCAGCTATCTTCTCATCATCTTCTCCTTTGAC
CGCCATCTCGAAAATCTTCTCAAGCTCTGCTAAACTTCCATTAAATCCATGAGCTTAAATTAAG
TTGCTTTTTACCCTTGGTTAAATCAATTAAAAAGAGCATCTGATATACTTTGCTTCAGGAAAGA
AAAAAGCAACTCAAGACCAGGCTACCATCATGGAATACTAGAATAGATTTTGACTATTATCTGT
CTTTACTGCAATTAGGAGTCATTGCCTAGGATAGGAGGACTACTATGTATAACTCTATCATCAG
CCCTTTCCACGAATATACAAACAGTCAATTGTTGTTTCAGTACTGCAAGCTCCAATTGTTACAG
AGTTTTGATGCTCAGATAAGTTACAACATAAACTTGGTTTTTTTTTCTTGACTTAATCACTGAA
GTGTAGACATTTTAGGGAACAAAATTGTCAGTGTAAAGCTATCCTAAGCATACCTTGAAGCTGG
AGCAGAAACCAAAGCATTAATAATAGCGGGAGTCAACGGGGCCCCCTTCATAAATGATGACCAA
CCAGGCACTTGAGTTGGCATACTGTGCGCTAACTGGTTCAAGCGTCCATTCACGTAACCAGGCC
AAAAATAAGCAGAAGTGTCCAGCAAATTTCTGGCAATGCAAGCCTCAACTATCAAGTGATGCAG
GTTACCAG
						
					

			
		

Sequences
Splice junction sequence	TTCAAGCGTCCATTCACGTAACCAGGCCAAAAATAAGCAGAAGTGTCCAGCAAATTTCTGGCAA TGCAAGCCTCAACTATCAAGTGATGCAGGTTACCAGcatgccgtgaagggagaaaatctgaaca cagtccactggtgctattccaacgagtaagacatttaacattggagcgtagcctattaaatggc tatcttta
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: 488 Transcript exons: 79409311-79409472,79409614-79409728,79410132-79410342 CATGCCGTGAAGGGAGAAAATCTGAACACAGTCCACTGGTGCTATTCCAACGAGTAAGACATTT AACATTGGAGCGTAGCCTATTAAATGGCTATCTTTACCAGAATAGTCAGTAGGAACTGGAGGAG ACAATAATCTGGTTATGAAATTGACGGTATGTTCCTGTATATTCCAACCACGAATCAGTGAGGC TCCACAAAGAATGGTAGCAGCAGCTATCTTCTCATCATCTTCTCCTTTGACCGCCATCTCGAAA ATCTTCTCAAGCTCTGCTAAACTTGAAGCTGGAGCAGAAACCAAAGCATTAATAATAGCGGGAG TCAACGGGGCCCCCTTCATAAATGATGACCAACCAGGCACTTGAGTTGGCATACTGTGCGCTAA CTGGTTCAAGCGTCCATTCACGTAACCAGGCCAAAAATAAGCAGAAGTGTCCAGCAAATTTCTG GCAATGCAAGCCTCAACTATCAAGTGATGCAGGTTACCAG
Genomic sequence	CATGCCGTGAAGGGAGAAAATCTGAACACAGTCCACTGGTGCTATTCCAACGAGTAAGACATTT AACATTGGAGCGTAGCCTATTAAATGGCTATCTTTACCAGAATAGTCAGTAGGAACTGGAGGAG ACAATAATCTGGTTATGAAATTGACGGTATGTTCCTGCGTGATCACAACCAAAAGGAAGAACCA CATTATTTCTTCGCAAGAACAATTTAATGATACTTTTAGTAATGGGTATCAGGATCGTAATGCT CTAAACAAAAGAATTTCCTTTGCTGAAGCAAACTATTTGTTTATTACCTGTATATTCCAACCAC GAATCAGTGAGGCTCCACAAAGAATGGTAGCAGCAGCTATCTTCTCATCATCTTCTCCTTTGAC CGCCATCTCGAAAATCTTCTCAAGCTCTGCTAAACTTCCATTAAATCCATGAGCTTAAATTAAG TTGCTTTTTACCCTTGGTTAAATCAATTAAAAAGAGCATCTGATATACTTTGCTTCAGGAAAGA AAAAAGCAACTCAAGACCAGGCTACCATCATGGAATACTAGAATAGATTTTGACTATTATCTGT CTTTACTGCAATTAGGAGTCATTGCCTAGGATAGGAGGACTACTATGTATAACTCTATCATCAG CCCTTTCCACGAATATACAAACAGTCAATTGTTGTTTCAGTACTGCAAGCTCCAATTGTTACAG AGTTTTGATGCTCAGATAAGTTACAACATAAACTTGGTTTTTTTTTCTTGACTTAATCACTGAA GTGTAGACATTTTAGGGAACAAAATTGTCAGTGTAAAGCTATCCTAAGCATACCTTGAAGCTGG AGCAGAAACCAAAGCATTAATAATAGCGGGAGTCAACGGGGCCCCCTTCATAAATGATGACCAA CCAGGCACTTGAGTTGGCATACTGTGCGCTAACTGGTTCAAGCGTCCATTCACGTAACCAGGCC AAAAATAAGCAGAAGTGTCCAGCAAATTTCTGGCAATGCAAGCCTCAACTATCAAGTGATGCAG GTTACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.992451963

Conservation Information
Conserved circRNAs	NA
PMCS	0.992451963

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							79410197-79409364(+)
79410228-79410324(-)
						
						Potential amino acid sequence
						
							MMTNQALELAYCALTGSSVHSRNQAKNKQKCPANFWQCKPQLSSDAGYQHAVKGENLNTVHWCY
SNE*(+)
MPTQVPGWSSFMKGAPLTPAIINALVSAPASSLAELEKIFEMAVKGEDDEKIAAATILCGASLI
RGWNIQEHTVNFITRLLSPPVPTDYSGKDSHLIGYAPMLNVLLVGIAPVDCVQIFSLHGMLVTC
IT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to chilling stress; fruit ripening

Functional Information
Coding potential	Y
Potential coding position	79410197-79409364(+) 79410228-79410324(-)
Potential amino acid sequence	MMTNQALELAYCALTGSSVHSRNQAKNKQKCPANFWQCKPQLSSDAGYQHAVKGENLNTVHWCY SNE(+) MPTQVPGWSSFMKGAPLTPAIINALVSAPASSLAELEKIFEMAVKGEDDEKIAAATILCGASLI RGWNIQEHTVNFITRLLSPPVPTDYSGKDSHLIGYAPMLNVLLVGIAPVDCVQIFSLHGMLVTC IT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to chilling stress; fruit ripening

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

circRNA

Detail information of Solyc01g080200.2_circ_g.2

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