Plant Circular RNA Database

Detail information of Solyc03g005430.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g005430.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000898
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 311652-315065  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g005430.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc03g005430.2_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
						Solyc03g005430.2.1:4

General Information
CircRNA Name	Solyc03g005430.2_circ_g.2
ID in PlantcircBase	sly_circ_000898
Alias	NA
Organism	Solanum lycopersicum
Position	chr3: 311652-315065 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g005430.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc03g005430.2_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	Solyc03g005430.2.1:4

			
						 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  
						
							CCAACATCAAATGCATTACTCCGAAGTTCTCTCTTGTTGATTTGTGAAAACTTATCGATCTTCC
ACGTATATTTCCCATATAGCTCAGAAGGTTTAGGGCctgattacttgaacttgagcctttatta
tgagcgtatcagcatcgacaaaaccatctaaaactttcgacagctccataaactttttccaccc
ccaatcat

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTGATTACTTGAACTTGAGCCTTTATTATGAGCGTATCAGCATCGACAAAACCATCTAAAACTT
TCGACAGCTCCATAAACTTTTTCCACCCCCAATCATGCTCTTTCTTCCAGAAACGATGTAATGT
ATCTGCAGAAAATTTGCAGCTGTATATTAATGAGAGCACAAATGGAACCAAAAATTCAATCGCG
AAGGAACACACCCAATGAACCAACCTGAATACTTGGACTTCTTTGGGTCTTTGTTCACCACAGC
AATAGTGAATTGAGCAAAATGACTCCAACCTGTTCTTATCAAAATAGAGAATGAAACATCATAA
CCATAGCTAACACATCACTTTCTAGATAGTTAGTAATGAACTATCACAGCTTTTTTGACTATTA
GAACTATCACAACATTATTGCACCTGGAAGGAGCTTGTCATGATTAGCTACACACAGAAACAAT
GAGAGATGGTTGCAAACATCACATCCCTGAGGGTATATCAAAATGTACCTGCCGCAACAATTGG
AGGAAAATTTGTCAGTCACTCTTAATTCATGAGCTGATAGTTTCCATTAAATAAAAGAAAACGA
GCATATAATGATACAACAGATACTGCTGTTATTGCATTTCCCCAAGTAACTTCCACTATCCTGA
TGAGAGTGGCATGATAACCCAAACTCCAATTTTACAATTACCATCACCAACCTCCAGATCAATA
TAACAAGACAATAACTATTGTGCCAGCCACCCATCCGCCTGAAACTAAGCTAAGTTTATTTGGT
TCAACGATGGATAAGCAGAAGGAAACAGGAATGGGAGTTGATGTGACCTATTGATCATTCACTT
CTAGAGGAAAGTAAAAAGGGTTTACCATGTTGTTTGACATGTACTAAGAAGAATATAGTGATTT
TCATTCAATTTTCTCAAGGGTTGAAGAAAGATGACATGGAGAGCTTCATGTACCTAGTCTCTCT
TTGTCTAACCAAACCATGAAAAATAACTCATTTCTCCAATTTTACTAACTTTCATCCTACTATA
TGACATATCTTGGAAATGATTATAGCAATTAATGGGGAACTGGAAATAAGTGTCAATGCAGCAT
CACTAATAAGAAAGTTAATATACATAGAAAGTAAAAATAGTTTTTAGCTAAGATGCTCGGACTC
GGCAATTTTTTAGTGCGGCACACGTGTCGACACAACACTGACACGGGTAAGGGTGTGGGATCTG
TGTAGGATTGGATCAAACGAGATTGGGTGTGTTGACCAACAATTTGGAGAAAGAAGTGAAATTT
TGGTATCTCAAAGTAAAGATTTGAGTATAAACAGAATACCATCAATTTTGCTGCTATATAGTAA
TTTATACTAGTCCTTTTGTCTCCTTTGAAGCTTTTTCTTGATAAATCTTCTTAATCATGTTGGC
TGTTGCAGGTTTCTAAAATTTAAGAGCTCTACGATTTCTATCTTGGAATAGAGAAGCCAAGAAT
TGGTGATGCCTTGGTGGACTAAAAGACTCCTGTGTGTTGTGAGTTTTATTGTACTGGGAAAACA
AAGACATGGAAAACTTGTTGGGGAAGCCGAGAATTGGTGATGCCTTGGTGGACTACAAGACTTC
TGTGTGTTGTGAGTTTTATTGTATTGGGGAAAAAAAAAGACATGGAAAACTCGTTGGGGAAGAA
GATGGATGAGAGAAAACAAAGCATAGGAACAAAGCTGAAGAAGACAACTAAGACCCTGAGAGTA
ACTTATTATCTATTTTAATTGACCTTTAGTCCTTTATTAGCTGCCACGTTTATTGTTTATTATA
TTCAGGACAAACGTATTATATATATTTTGGGTAAAATGAGATAAACATAACATATTAATTAGAG
TTCATAAATGAGAAACATTATAATTATGTAATTATAATAAAAATTGCCAAGTCCACTGAACCCT
ATCCGTATCTAGGTTCAAAACCCAGTATCTTAAAAATTAGATCATGAAGAACCCAACATGCGTA
CCTGCACCCATGTCGGACACCCGAGTCCGAGCAACTTAAATTTTTAGCATAGCATTTAGAATAA
GACAATTTTCGTCGTTGAAAATATAAGATGTAGTTATCGTATCCAATAGTGTGGCCTAGAGGTC
ACTAAACCAGTGAATGGAACCTAGGGTTCAAGTCCCTATAGAGACAAAAAGAAGGTTAGGTGAT
TTCTCCCTCTTTTTGTAGCCTTGGTGGGAGGTAGCAAGTACCCAGTGTAATAGTTGATACCCGA
AGTCTGGAAGCTGTCCAGAAAAATGCACGTGTCATTTATGTAACAACTATGAGAAACTGAAAAG
TCACTTTCTTATTCCATTCTCAATTTTTCAAGTTATTCTAATAGTTTATTCTCAAGTCAGTCAC
ATCCCATTTCCTCTAACTATCGATGGTCTACCATCTCAAGAAAAATTGTCACTCAATATTTAGC
TCATACAAACAACCGGCAAGACAATTTTATGGAACGTCCTAGAAGATCTCAAAAGTCAGTATAT
TTTATTACAACCTTGGTTCATTTAGAGCACATGCCCCAGCACGAGAAGAAGTGGTGGAAATGGT
ATCGGTAGCTAATGTAGCATTGGATAAATGATGGTACCTTTTTTCAATTTATGTGAACATATTT
GACTGGACACAAGTTTAAGAAATAAAGGAACGAATTTTGGTTGTTGCAGTCTTTAAACATGCCA
AAACATTTGTGTCGCTATAGAATTTTTGGAACTTGTGGGTTCTAAACATGTTATAACATTTGTG
TGGCTATAAAAGCTGCTCACTAAGGGTAAATTGGGAAGTTCAAATTAAATTAATTCCAACATCA
GAAAGGTGTCTTTCTTTTTAAATGGACTAAAAAGGATATAGGTTCACGTAGATTGAAATGGAAA
TAGAGTAACAAACCCTAATATAGGGTTGGAAATAAGAAATACTTCATGTAAAGAAGGAAAAGAT
AATAGGAGTTGAGAGTCATGGCAAAGAATAAGATTCTAGTGATTCTAGTAAATATAAGATGTAA
TATCAACTGCCATGTGTCAAATCACTCGGGCAATCCACAAATCATTGTTTTCGTCAATTCTCGT
TCTCAAAAGTCTTCTTAATCTATTCAAGTACTTAACTAAATAAAATAGAGTGCACATGGAAGAC
TTCTTTTACATAAGATTCTAAATGCAGTTACAAAAATGAGCTTACAGAAGAGGTTACAGAGGCT
ATCCAAATAAGTATGTTCACAAAAAAATAATTCTTCACCAATTGTTACCTTTGTCAAAAATAAT
GATAATAATAATAATAATTCTTCACCAAAACATCATACCATTTGTAGCCGCCAACATCAAATGC
ATTACTCCGAAGTTCTCTCTTGTTGATTTGTGAAAACTTATCGATCTTCCACGTATATTTCCCA
TATAGCTCAGAAGGTTTAGGGC
						
					

			
		

Sequences
Splice junction sequence	CCAACATCAAATGCATTACTCCGAAGTTCTCTCTTGTTGATTTGTGAAAACTTATCGATCTTCC ACGTATATTTCCCATATAGCTCAGAAGGTTTAGGGCctgattacttgaacttgagcctttatta tgagcgtatcagcatcgacaaaaccatctaaaactttcgacagctccataaactttttccaccc ccaatcat
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTGATTACTTGAACTTGAGCCTTTATTATGAGCGTATCAGCATCGACAAAACCATCTAAAACTT TCGACAGCTCCATAAACTTTTTCCACCCCCAATCATGCTCTTTCTTCCAGAAACGATGTAATGT ATCTGCAGAAAATTTGCAGCTGTATATTAATGAGAGCACAAATGGAACCAAAAATTCAATCGCG AAGGAACACACCCAATGAACCAACCTGAATACTTGGACTTCTTTGGGTCTTTGTTCACCACAGC AATAGTGAATTGAGCAAAATGACTCCAACCTGTTCTTATCAAAATAGAGAATGAAACATCATAA CCATAGCTAACACATCACTTTCTAGATAGTTAGTAATGAACTATCACAGCTTTTTTGACTATTA GAACTATCACAACATTATTGCACCTGGAAGGAGCTTGTCATGATTAGCTACACACAGAAACAAT GAGAGATGGTTGCAAACATCACATCCCTGAGGGTATATCAAAATGTACCTGCCGCAACAATTGG AGGAAAATTTGTCAGTCACTCTTAATTCATGAGCTGATAGTTTCCATTAAATAAAAGAAAACGA GCATATAATGATACAACAGATACTGCTGTTATTGCATTTCCCCAAGTAACTTCCACTATCCTGA TGAGAGTGGCATGATAACCCAAACTCCAATTTTACAATTACCATCACCAACCTCCAGATCAATA TAACAAGACAATAACTATTGTGCCAGCCACCCATCCGCCTGAAACTAAGCTAAGTTTATTTGGT TCAACGATGGATAAGCAGAAGGAAACAGGAATGGGAGTTGATGTGACCTATTGATCATTCACTT CTAGAGGAAAGTAAAAAGGGTTTACCATGTTGTTTGACATGTACTAAGAAGAATATAGTGATTT TCATTCAATTTTCTCAAGGGTTGAAGAAAGATGACATGGAGAGCTTCATGTACCTAGTCTCTCT TTGTCTAACCAAACCATGAAAAATAACTCATTTCTCCAATTTTACTAACTTTCATCCTACTATA TGACATATCTTGGAAATGATTATAGCAATTAATGGGGAACTGGAAATAAGTGTCAATGCAGCAT CACTAATAAGAAAGTTAATATACATAGAAAGTAAAAATAGTTTTTAGCTAAGATGCTCGGACTC GGCAATTTTTTAGTGCGGCACACGTGTCGACACAACACTGACACGGGTAAGGGTGTGGGATCTG TGTAGGATTGGATCAAACGAGATTGGGTGTGTTGACCAACAATTTGGAGAAAGAAGTGAAATTT TGGTATCTCAAAGTAAAGATTTGAGTATAAACAGAATACCATCAATTTTGCTGCTATATAGTAA TTTATACTAGTCCTTTTGTCTCCTTTGAAGCTTTTTCTTGATAAATCTTCTTAATCATGTTGGC TGTTGCAGGTTTCTAAAATTTAAGAGCTCTACGATTTCTATCTTGGAATAGAGAAGCCAAGAAT TGGTGATGCCTTGGTGGACTAAAAGACTCCTGTGTGTTGTGAGTTTTATTGTACTGGGAAAACA AAGACATGGAAAACTTGTTGGGGAAGCCGAGAATTGGTGATGCCTTGGTGGACTACAAGACTTC TGTGTGTTGTGAGTTTTATTGTATTGGGGAAAAAAAAAGACATGGAAAACTCGTTGGGGAAGAA GATGGATGAGAGAAAACAAAGCATAGGAACAAAGCTGAAGAAGACAACTAAGACCCTGAGAGTA ACTTATTATCTATTTTAATTGACCTTTAGTCCTTTATTAGCTGCCACGTTTATTGTTTATTATA TTCAGGACAAACGTATTATATATATTTTGGGTAAAATGAGATAAACATAACATATTAATTAGAG TTCATAAATGAGAAACATTATAATTATGTAATTATAATAAAAATTGCCAAGTCCACTGAACCCT ATCCGTATCTAGGTTCAAAACCCAGTATCTTAAAAATTAGATCATGAAGAACCCAACATGCGTA CCTGCACCCATGTCGGACACCCGAGTCCGAGCAACTTAAATTTTTAGCATAGCATTTAGAATAA GACAATTTTCGTCGTTGAAAATATAAGATGTAGTTATCGTATCCAATAGTGTGGCCTAGAGGTC ACTAAACCAGTGAATGGAACCTAGGGTTCAAGTCCCTATAGAGACAAAAAGAAGGTTAGGTGAT TTCTCCCTCTTTTTGTAGCCTTGGTGGGAGGTAGCAAGTACCCAGTGTAATAGTTGATACCCGA AGTCTGGAAGCTGTCCAGAAAAATGCACGTGTCATTTATGTAACAACTATGAGAAACTGAAAAG TCACTTTCTTATTCCATTCTCAATTTTTCAAGTTATTCTAATAGTTTATTCTCAAGTCAGTCAC ATCCCATTTCCTCTAACTATCGATGGTCTACCATCTCAAGAAAAATTGTCACTCAATATTTAGC TCATACAAACAACCGGCAAGACAATTTTATGGAACGTCCTAGAAGATCTCAAAAGTCAGTATAT TTTATTACAACCTTGGTTCATTTAGAGCACATGCCCCAGCACGAGAAGAAGTGGTGGAAATGGT ATCGGTAGCTAATGTAGCATTGGATAAATGATGGTACCTTTTTTCAATTTATGTGAACATATTT GACTGGACACAAGTTTAAGAAATAAAGGAACGAATTTTGGTTGTTGCAGTCTTTAAACATGCCA AAACATTTGTGTCGCTATAGAATTTTTGGAACTTGTGGGTTCTAAACATGTTATAACATTTGTG TGGCTATAAAAGCTGCTCACTAAGGGTAAATTGGGAAGTTCAAATTAAATTAATTCCAACATCA GAAAGGTGTCTTTCTTTTTAAATGGACTAAAAAGGATATAGGTTCACGTAGATTGAAATGGAAA TAGAGTAACAAACCCTAATATAGGGTTGGAAATAAGAAATACTTCATGTAAAGAAGGAAAAGAT AATAGGAGTTGAGAGTCATGGCAAAGAATAAGATTCTAGTGATTCTAGTAAATATAAGATGTAA TATCAACTGCCATGTGTCAAATCACTCGGGCAATCCACAAATCATTGTTTTCGTCAATTCTCGT TCTCAAAAGTCTTCTTAATCTATTCAAGTACTTAACTAAATAAAATAGAGTGCACATGGAAGAC TTCTTTTACATAAGATTCTAAATGCAGTTACAAAAATGAGCTTACAGAAGAGGTTACAGAGGCT ATCCAAATAAGTATGTTCACAAAAAAATAATTCTTCACCAATTGTTACCTTTGTCAAAAATAAT GATAATAATAATAATAATTCTTCACCAAAACATCATACCATTTGTAGCCGCCAACATCAAATGC ATTACTCCGAAGTTCTCTCTTGTTGATTTGTGAAAACTTATCGATCTTCCACGTATATTTCCCA TATAGCTCAGAAGGTTTAGGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.316827465

Conservation Information
Conserved circRNAs	NA
PMCS	0.316827465

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							311730-315061(-)
						
						Potential amino acid sequence
						
							MELSKVLDGFVDADTLIIKAQVQVIRP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	311730-315061(-)
Potential amino acid sequence	MELSKVLDGFVDADTLIIKAQVQVIRP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc03g005430.2_circ_g.2

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