Plant Circular RNA Database

Detail information of Solyc06g011380.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc06g011380.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001904
					
						Alias
						6:6771445|6773313
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 6771445-6773313  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc06g011380.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc06g011380.2_circ_ag.1 Solyc06g011400.2_circ_g.1 						
					
						Support reads
						15
					
						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
						Solyc06g011380.2.1:3

General Information
CircRNA Name	Solyc06g011380.2_circ_g.1
ID in PlantcircBase	sly_circ_001904
Alias	6:6771445\|6773313
Organism	Solanum lycopersicum
Position	chr6: 6771445-6773313 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc06g011380.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc06g011380.2_circ_ag.1 Solyc06g011400.2_circ_g.1
Support reads	15
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	Solyc06g011380.2.1:3

			
						 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  
						
							TATGAGCTGCATCATGGCGTTAAAATATCAGACAGTGCTCTTGTGTCAGCTGCAGTTCTTGCAG
ATCGATATATTACTGAGCGATTTTTGCCGGATAAAGgttagctcaaaggatagtacgtggagat
gttcctgaacctttgatgaatcggaaggttataacttctttctcattgcttaatttaattgaat
ttatatta

									
								

					

						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: 515
Transcript exons: 6771445-6771499,6772192-6772342,6773005-6773313
GTTAGCTCAAAGGATAGTACGTGGAGATGTTCCTGAACCTTTGATGAATCGGAAGTTGATATCT
CTCGATATGGGTGCCTTGCTTGCTGGTGCAAAGTACCGTGGAGATTTTGAGGAGAGGTTGAAAG
CTGTTTTAAAGGAAGTCTCTGCATCCAATGGGCAGATTATATTGTTTATTGATGAGATACACAC
TGTAGTTGGTGCAGGAGCTACTAGCGGGGCCATGGATGCAGGGAATTTGTTGAAACCCATGCTT
GGTCGGGGTGAACTTAGATGTATTGGAGCAACCACTTTGAATGAATATAGGAAGTACATTGAGA
AGGACCCTGCTCTAGAGCGTAGATTTCAACAAGTATATTGTGGCCAACCTTCTGTGGAAGATAC
AATTTCTATCCTCCGTGGATTGCGTGAACGATATGAGCTGCATCATGGCGTTAAAATATCAGAC
AGTGCTCTTGTGTCAGCTGCAGTTCTTGCAGATCGATATATTACTGAGCGATTTTTGCCGGATA
AAG
						
					

						Genomic sequence
						
							GTTAGCTCAAAGGATAGTACGTGGAGATGTTCCTGAACCTTTGATGAATCGGAAGGTTATAACT
TCTTTCTCATTGCTTAATTTAATTGAATTTATATTATTGTGTGAAGGACAGCAAGAATATCTCT
TTGCATGAGTTTAATCAAGTGATTGTGTATGTGAAAAGCTTGGAATATGGCATTTGCAGTGTTA
GTCAGATTGCTTTTTCTTCTATTTTTTTTGTTTGGAAATATCTTGATTTGAAGAATAAATGATT
AGTTGAAAATTGCTGCTCTTCTATTGAAAAGTATGGGCCTGCCTTAAGCTGTTGTTTACTGAAA
AAAGGTGATGTCTCTCTTGTTGCAGTGATATTTTTATGACAAAAATATCTTGGTTTCTTTTAGC
TCTCCCAGTATTGGTACATAATTTTCTGTTGAAGATGCAAGTCGGTTTAAGACAGTTGATGCAG
TTCTTACTCAACTGAACCAGCATGGCAAAGTTACATATTGTCTTAATAATTTCTGGGAGTGATT
TCCAATCGAGTTTGATACTGAGAAAATATGCATCACACCTGCACTTAAAAGTAGACTAAATTTT
AATCAACTAAGCTAGTCCGCTTCATAAGCTGGTCTTTCACCCAACCCCTCACTCTCTGAGGGAT
AGGAGGAAAAGGATACGAATAACCTCATTCTCTAATTGTCTATAAGGATTATAGTCTTTCAAGT
GCTAATACTGTACTCTTATTCGTGTTCTTTTCATTTTATTTAGTTGATATCTCTCGATATGGGT
GCCTTGCTTGCTGGTGCAAAGTACCGTGGAGATTTTGAGGAGAGGTTGAAAGCTGTTTTAAAGG
AAGTCTCTGCATCCAATGGGCAGATTATATTGTTTATTGATGAGATACACACTGTAGTTGGTGC
AGGTTTAGTATATTATTTTTACTTTCTATCTACCCGTGAATGAAGTTGTTTATTTCTACTGAAT
GTTTATTAACTTCTTCAACTGTAATCTTTCTCTGAACGATCATTTCTCTATTGTCTATTTATAA
ATTTCTATGTTGAAAAGTGCTGGCTCAAGCTACTTCTCTGTTTTCAAATATCAAGATTATGGAC
AACAAGTGGTGGCTTTCTCTTTCTGTTGGATGATTTTTCTCCTTGCTTAATTATTCTTAAGCAA
TATAAATTTCGTAGTAGTTCATGTGATGTCATTAGGGAATACTAGGTCTGGACTCTAGTGAAGT
CAAAAGCCCTGTTGCTTCACCAATTATGTTTTAGGTGATTAACTTTTGGATTGAGCTTGGACCG
TAGAAATCCTTCAATTATCATCCTGTTAATTTGGTCCTGGACTTTGGAAATGATTGAACCAGGT
TTGTTTTTTTTGTTATCATATCATAAAGCTGATAAAAAATGATTGATAATGTTCTTTATGTAAG
CGGCCGGGTAGAGAAGAAGGCATCTTGATACCCAAGATATAGCTTCTGATTGTAGCTGGGCTTA
TATATCAACTAATTTAGTGAATATTACTTGGTTAAAACTTGATGATATGTTTTATTCTAAAAAT
TGTGCTTGTTTCCGTTGGTTTTAGGAGCTACTAGCGGGGCCATGGATGCAGGGAATTTGTTGAA
ACCCATGCTTGGTCGGGGTGAACTTAGATGTATTGGAGCAACCACTTTGAATGAATATAGGAAG
TACATTGAGAAGGACCCTGCTCTAGAGCGTAGATTTCAACAAGTATATTGTGGCCAACCTTCTG
TGGAAGATACAATTTCTATCCTCCGTGGATTGCGTGAACGATATGAGCTGCATCATGGCGTTAA
AATATCAGACAGTGCTCTTGTGTCAGCTGCAGTTCTTGCAGATCGATATATTACTGAGCGATTT
TTGCCGGATAAAG
						
					

			
		

Sequences
Splice junction sequence	TATGAGCTGCATCATGGCGTTAAAATATCAGACAGTGCTCTTGTGTCAGCTGCAGTTCTTGCAG ATCGATATATTACTGAGCGATTTTTGCCGGATAAAGgttagctcaaaggatagtacgtggagat gttcctgaacctttgatgaatcggaaggttataacttctttctcattgcttaatttaattgaat ttatatta
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: 515 Transcript exons: 6771445-6771499,6772192-6772342,6773005-6773313 GTTAGCTCAAAGGATAGTACGTGGAGATGTTCCTGAACCTTTGATGAATCGGAAGTTGATATCT CTCGATATGGGTGCCTTGCTTGCTGGTGCAAAGTACCGTGGAGATTTTGAGGAGAGGTTGAAAG CTGTTTTAAAGGAAGTCTCTGCATCCAATGGGCAGATTATATTGTTTATTGATGAGATACACAC TGTAGTTGGTGCAGGAGCTACTAGCGGGGCCATGGATGCAGGGAATTTGTTGAAACCCATGCTT GGTCGGGGTGAACTTAGATGTATTGGAGCAACCACTTTGAATGAATATAGGAAGTACATTGAGA AGGACCCTGCTCTAGAGCGTAGATTTCAACAAGTATATTGTGGCCAACCTTCTGTGGAAGATAC AATTTCTATCCTCCGTGGATTGCGTGAACGATATGAGCTGCATCATGGCGTTAAAATATCAGAC AGTGCTCTTGTGTCAGCTGCAGTTCTTGCAGATCGATATATTACTGAGCGATTTTTGCCGGATA AAG
Genomic sequence	GTTAGCTCAAAGGATAGTACGTGGAGATGTTCCTGAACCTTTGATGAATCGGAAGGTTATAACT TCTTTCTCATTGCTTAATTTAATTGAATTTATATTATTGTGTGAAGGACAGCAAGAATATCTCT TTGCATGAGTTTAATCAAGTGATTGTGTATGTGAAAAGCTTGGAATATGGCATTTGCAGTGTTA GTCAGATTGCTTTTTCTTCTATTTTTTTTGTTTGGAAATATCTTGATTTGAAGAATAAATGATT AGTTGAAAATTGCTGCTCTTCTATTGAAAAGTATGGGCCTGCCTTAAGCTGTTGTTTACTGAAA AAAGGTGATGTCTCTCTTGTTGCAGTGATATTTTTATGACAAAAATATCTTGGTTTCTTTTAGC TCTCCCAGTATTGGTACATAATTTTCTGTTGAAGATGCAAGTCGGTTTAAGACAGTTGATGCAG TTCTTACTCAACTGAACCAGCATGGCAAAGTTACATATTGTCTTAATAATTTCTGGGAGTGATT TCCAATCGAGTTTGATACTGAGAAAATATGCATCACACCTGCACTTAAAAGTAGACTAAATTTT AATCAACTAAGCTAGTCCGCTTCATAAGCTGGTCTTTCACCCAACCCCTCACTCTCTGAGGGAT AGGAGGAAAAGGATACGAATAACCTCATTCTCTAATTGTCTATAAGGATTATAGTCTTTCAAGT GCTAATACTGTACTCTTATTCGTGTTCTTTTCATTTTATTTAGTTGATATCTCTCGATATGGGT GCCTTGCTTGCTGGTGCAAAGTACCGTGGAGATTTTGAGGAGAGGTTGAAAGCTGTTTTAAAGG AAGTCTCTGCATCCAATGGGCAGATTATATTGTTTATTGATGAGATACACACTGTAGTTGGTGC AGGTTTAGTATATTATTTTTACTTTCTATCTACCCGTGAATGAAGTTGTTTATTTCTACTGAAT GTTTATTAACTTCTTCAACTGTAATCTTTCTCTGAACGATCATTTCTCTATTGTCTATTTATAA ATTTCTATGTTGAAAAGTGCTGGCTCAAGCTACTTCTCTGTTTTCAAATATCAAGATTATGGAC AACAAGTGGTGGCTTTCTCTTTCTGTTGGATGATTTTTCTCCTTGCTTAATTATTCTTAAGCAA TATAAATTTCGTAGTAGTTCATGTGATGTCATTAGGGAATACTAGGTCTGGACTCTAGTGAAGT CAAAAGCCCTGTTGCTTCACCAATTATGTTTTAGGTGATTAACTTTTGGATTGAGCTTGGACCG TAGAAATCCTTCAATTATCATCCTGTTAATTTGGTCCTGGACTTTGGAAATGATTGAACCAGGT TTGTTTTTTTTGTTATCATATCATAAAGCTGATAAAAAATGATTGATAATGTTCTTTATGTAAG CGGCCGGGTAGAGAAGAAGGCATCTTGATACCCAAGATATAGCTTCTGATTGTAGCTGGGCTTA TATATCAACTAATTTAGTGAATATTACTTGGTTAAAACTTGATGATATGTTTTATTCTAAAAAT TGTGCTTGTTTCCGTTGGTTTTAGGAGCTACTAGCGGGGCCATGGATGCAGGGAATTTGTTGAA ACCCATGCTTGGTCGGGGTGAACTTAGATGTATTGGAGCAACCACTTTGAATGAATATAGGAAG TACATTGAGAAGGACCCTGCTCTAGAGCGTAGATTTCAACAAGTATATTGTGGCCAACCTTCTG TGGAAGATACAATTTCTATCCTCCGTGGATTGCGTGAACGATATGAGCTGCATCATGGCGTTAA AATATCAGACAGTGCTCTTGTGTCAGCTGCAGTTCTTGCAGATCGATATATTACTGAGCGATTT TTGCCGGATAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.402308455

Conservation Information
Conserved circRNAs	NA
PMCS	0.402308455

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6771489-6771446(+)
6773216-6771477(+)
6772290-6773261(-)
						
						Potential amino acid sequence
						
							MNRKLISLDMGALLAGAKYRGDFEERLKAVLKEVSASNGQIILFIDEIHTVVGAGATSGAMDAG
NLLKPMLGRGELRCIGATTLNEYRKYIEKDPALERRFQQVYCGQPSVEDTISILRGLRERYELH
HGVKISDSALVSAAVLADRYITERFLPDKG*(+)
MSCIMALKYQTVLLCQLQFLQIDILLSDFCRIKVSSKDSTWRCS*(+)
MQRLPLKQLSTSPQNLHGTLHQQARHPYREISTSDSSKVQEHLHVLSFELTFIRQKSLSNISIC
KNCS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	6771489-6771446(+) 6773216-6771477(+) 6772290-6773261(-)
Potential amino acid sequence	MNRKLISLDMGALLAGAKYRGDFEERLKAVLKEVSASNGQIILFIDEIHTVVGAGATSGAMDAG NLLKPMLGRGELRCIGATTLNEYRKYIEKDPALERRFQQVYCGQPSVEDTISILRGLRERYELH HGVKISDSALVSAAVLADRYITERFLPDKG(+) MSCIMALKYQTVLLCQLQFLQIDILLSDFCRIKVSSKDSTWRCS(+) MQRLPLKQLSTSPQNLHGTLHQQARHPYREISTSDSSKVQEHLHVLSFELTFIRQKSLSNISIC KNCS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc06g011380.2_circ_g.1

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