Plant Circular RNA Database

Detail information of Solyc05g015210.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc05g015210.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001707
					
						Alias
						5:10063412|10066958
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 10063412-10066958  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc05g015210.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc05g015210.2_circ_g.2 Solyc05g015210.2_circ_g.4 						
					
						Support reads
						4
					
						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
						Solyc05g015210.2.1:6

General Information
CircRNA Name	Solyc05g015210.2_circ_g.3
ID in PlantcircBase	sly_circ_001707
Alias	5:10063412\|10066958
Organism	Solanum lycopersicum
Position	chr5: 10063412-10066958 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc05g015210.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc05g015210.2_circ_g.2 Solyc05g015210.2_circ_g.4
Support reads	4
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	Solyc05g015210.2.1:6

			
						 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  
						
							CACTTTGCAGAGATTGTCACCAGATATGCCCCTTCAACTTGCTTCTGAGACAATATTAAGGATG
TTGAGAGCTCGACTTCACCATCATCGTCAAGGCCAAatgaagtaatcgcagcgattgatcccag
aaaagtcgacattcttttaaggtcagtggttttgtgattttacactcctttccacttcttttaa
acctattg

									
								

					

						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
						
							ATGAAGTAATCGCAGCGATTGATCCCAGAAAAGTCGACATTCTTTTAAGGTCAGTGGTTTTGTG
ATTTTACACTCCTTTCCACTTCTTTTAAACCTATTGCTATCTGTCTCCTGAAGTGAAGATTGGT
GGCTAGTGTAACATCTGTATGCAATTTTTGATTGTACTCTGGTCCAAGTTTTTTGCCTCCATTT
TGGAGATTATTTACTTCCATAAAGAAAAGTGTAGTTCTTCCTTTTCTTCCTCCTCTTAACAAGT
CTTTTGAGCAACTGAGCGCTGTATCACTTTGCGAATGATAAGCAGCTTGTTTTGGTCCTGCCCT
GCTGCCCCCTTTTTTTGATATCAAATGCATATTGTAGACCTAAACTGAGAACAGTCTGATTGAG
AATTTGGTGATGATGGTTTGTGTTTGCGGTTGAAATGAAGGAGAAGATGAAAATTAATCTGGAA
GGAGCTGCAGAAGATTAGAAGTTGGATTTGCCACCTTAAGAGTCTAGTCAGTGCTTGACATTAT
CTTCGTTCTAGTCTGCACTTTGTTTTCAAACTGTGACCAAGTGTACTTTCTTTTAGTCTTGTAA
CTTTCTAGCTTTGTCTTACTTGGCAAATCCATTAAAAAGCAGTCTTTTAGTAGATTAATGGTCT
TACAGTTAACATTGAAGCACCAAGGCCACAAAACTATTCTAGTACTGGAAAAAGGTTTTAAGGT
AAAATATTTTTTTTTGAAAAAAAGAAGTACTTTATTTTATTTTGAAATGGAACTTACTAATACT
TGGAAATTTTCTTAGAAGGTTCTGTAGTGTGACTTAGGCAGTTATGGACTAAAATATGGCCTTA
GTAAATCATAAGGTGATACATAAACACAGTAAATTTATGGTTTTATTGTTTGACCTAGTATATC
CATTAATGAATATGTCTTGATCATCTGTTGGCTTCTTCGTCAAGTTCCTTCATAAACTATTAGA
TCGTTTTAGTACAAGCCTATTTCTTCAAAATCATTCCTTTCATCAATAATTTATGATGTCACAC
AAGATGATCTGAAAAATTGCAAGTACCAACACAAACTAGCTGTAAGAATATCCTAAAATTGCAT
TCCGTCACTCTTAGCCTGATGAGAGCTGAAAAAAGCAAGTAGCATGTAGCATGCTAAATTTCTT
TCCTTTTATTTTAATTTGTTCAATATAATTTTTATCCATAACATTGGTTTCCTTGGGTGCCTAA
TTGGTTTGGGTAATATTATCTTATAAAGATGTATCTGTATATTAATGAGGCATTTAACTGTCTA
TATGTTTCTTTGAATTATAAACTGAAGCTTTACCGTGCAGATATCTCCAGTGGTTAATTGAAGA
TCAAGACTCCGGTGACACACGGTTTCATACAACTTATGCCCTCTTGCTTTCTAAATCAGCACTT
GATGCTAGTGAAAAGGAGCATGTTACGCACAATCTTGAAGGTGTAAACCATAAGGAGATAAACA
TCTCAGACCGTTGGAACAACTCAATATTTCATACTCATGTCAGAGAGAGATTGCAATTTTTTTT
ACAGTCGTCTGACTTGTATGATCCAGAGGAGGTTCTTGACTTGGTTGAAGGATCCGAGTTATGG
CTCGAGAAGGTCAGTAAAAAATTTAGGCCCTTCATAGAAATAATGGCATATGCATCTCTGCTGG
ATAACAGCTTGAACTGTTTTATTCTCCTTGTGATTTGCAGTCCTTGTGTTATTGATGGTTTCAT
TACAGGCTATTCTTTACAGGAAGCTCGGTCAAGAAACATTAGTGCTTCAAATTCTTGCCTTGTA
AGTTCATAAATGTTTGGTTATTGCTTGGGTACATCACAACAAGCTTTATCATAACAAATGAACA
ACTTAAAAGATGTTCTGTTTTCCAAATGTGAGCAATGCATGGTTGACATGCTCTTCTGCTGCTT
TACATGTGAAGTCCCTCACTTAAACAGGCGAAAATATTTGAAATCTTAGTATTCACATTGTTGC
TAAATATGTATTTCATAATTGAATCGGCAATTACTCTGAATAAGATGACTATCTGTGGGATTGT
AATTTAAAGTTGCGTTCATCTGGCAGAAAGTTGGAAGACTGTGAAGCTGCAGAACAATATTGTG
CTGAGATCGGTAGGCCAGATGCTTACATGCAGTTAGTACAGTATTCTCTCATTTGTTTCTTTAG
ATTATTGGTCTAGTAGAAGTTCTCTTAGCCTTTCCCTTACCTTGTCTCTTCTTAGGCTGCTTGA
AATGTATTTGGAGCCAATGAATGGTAAAGAGCCTATGTTCAAAGCTGCTGTGCGCCTGTTGCAC
AATCATGGAGAAATGCTAGACCCTTTGCAAGTTTTGGAGGTACTAAAACTTATCCTTCTTCTGC
TCTATTACTCATGTAATGGTCAATGAGGAGACAAAAGGCTTGTTCTACCCCCAGGGCTTTGGTT
TAGTGGCAACACTACGTGTGTGTGCTGGTTAGATACATATTACAAGTTCAAACAACAGAGCAAA
CAAAAGTCTGGTATTTAAGTGGAAAGGGTTGAGGGGGCCCATAATTTACCAAATTTATGCCAAG
TCAAATGGTGCTACATAAATTTGGACGGAGTGAGTATTTGTTTATCCACCATATCATGTCAGTA
ACATGGTTGATTGGGCTGGAAGATCAAAAATCTGATTAATTTTCGCACTGGATTTATAGTATGA
GAACCTATCTCCAAAGTTATAAAATAAAATATGGTAGAAGAGAAAAGTCATCCTAGAAATTTAT
TTGAAGGAAAAACATCTCATCGTACCTTAAAAGTAGAAATTTTGATTTTTACCAATAGACAAAT
GTTGGATCTTTGTTATTAGCAGTGTACGAAATATTTGGTTGTCACTTGTCAAAACAGGGAACCT
CTTCTTTAAATCTTGAAGATTGGAGCATATTCTTTTTTCTTTGGGAAATTAAGTTTTCTTGTCC
TAATTTTAGCTATTGGTGCATATTCAGTCACATAGTGCGTTACAGATTAGAAGTAGTCCTCTTA
CTTCGTTCCAAACATCTAATTATGCAACTTGTAACACAGTGATACCATTTTTGGATATCAACTT
TTAGAATTGCCTTTCTATAGTGAAAGATGAAGTCTGAGTTTTGTTTATGGTGATTTTAAATTTT
CAAAGGCCGGAAAAAAGAATTGTCTGATGACTTGATAGGTCTAATGATATTTAGGTTACCTTTT
CTAAATTACTGGGTGGATGGGGGTGGGGTTTCAATGGTTGTATCTTCATAGTTTCATTTGCTAA
GTATTCAGGTTACTCGATAAAATCATTTTAGATAACTAGACAATGTATATTTGTTTTGGATTAT
TTTTTCATGCTGTTTTAAGGGAACCAGATGATGAGAAGGCAAATAACATCTATTTGACTTAATT
TTCTTTGCAAAAAGTTACTAACAATGTCAACGTTACTCATTCTGAGTTGAGGTTTCACTTTGCA
GAGATTGTCACCAGATATGCCCCTTCAACTTGCTTCTGAGACAATATTAAGGATGTTGAGAGCT
CGACTTCACCATCATCGTCAAGGCCAA
						
					

			
		

Sequences
Splice junction sequence	CACTTTGCAGAGATTGTCACCAGATATGCCCCTTCAACTTGCTTCTGAGACAATATTAAGGATG TTGAGAGCTCGACTTCACCATCATCGTCAAGGCCAAatgaagtaatcgcagcgattgatcccag aaaagtcgacattcttttaaggtcagtggttttgtgattttacactcctttccacttcttttaa acctattg
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	ATGAAGTAATCGCAGCGATTGATCCCAGAAAAGTCGACATTCTTTTAAGGTCAGTGGTTTTGTG ATTTTACACTCCTTTCCACTTCTTTTAAACCTATTGCTATCTGTCTCCTGAAGTGAAGATTGGT GGCTAGTGTAACATCTGTATGCAATTTTTGATTGTACTCTGGTCCAAGTTTTTTGCCTCCATTT TGGAGATTATTTACTTCCATAAAGAAAAGTGTAGTTCTTCCTTTTCTTCCTCCTCTTAACAAGT CTTTTGAGCAACTGAGCGCTGTATCACTTTGCGAATGATAAGCAGCTTGTTTTGGTCCTGCCCT GCTGCCCCCTTTTTTTGATATCAAATGCATATTGTAGACCTAAACTGAGAACAGTCTGATTGAG AATTTGGTGATGATGGTTTGTGTTTGCGGTTGAAATGAAGGAGAAGATGAAAATTAATCTGGAA GGAGCTGCAGAAGATTAGAAGTTGGATTTGCCACCTTAAGAGTCTAGTCAGTGCTTGACATTAT CTTCGTTCTAGTCTGCACTTTGTTTTCAAACTGTGACCAAGTGTACTTTCTTTTAGTCTTGTAA CTTTCTAGCTTTGTCTTACTTGGCAAATCCATTAAAAAGCAGTCTTTTAGTAGATTAATGGTCT TACAGTTAACATTGAAGCACCAAGGCCACAAAACTATTCTAGTACTGGAAAAAGGTTTTAAGGT AAAATATTTTTTTTTGAAAAAAAGAAGTACTTTATTTTATTTTGAAATGGAACTTACTAATACT TGGAAATTTTCTTAGAAGGTTCTGTAGTGTGACTTAGGCAGTTATGGACTAAAATATGGCCTTA GTAAATCATAAGGTGATACATAAACACAGTAAATTTATGGTTTTATTGTTTGACCTAGTATATC CATTAATGAATATGTCTTGATCATCTGTTGGCTTCTTCGTCAAGTTCCTTCATAAACTATTAGA TCGTTTTAGTACAAGCCTATTTCTTCAAAATCATTCCTTTCATCAATAATTTATGATGTCACAC AAGATGATCTGAAAAATTGCAAGTACCAACACAAACTAGCTGTAAGAATATCCTAAAATTGCAT TCCGTCACTCTTAGCCTGATGAGAGCTGAAAAAAGCAAGTAGCATGTAGCATGCTAAATTTCTT TCCTTTTATTTTAATTTGTTCAATATAATTTTTATCCATAACATTGGTTTCCTTGGGTGCCTAA TTGGTTTGGGTAATATTATCTTATAAAGATGTATCTGTATATTAATGAGGCATTTAACTGTCTA TATGTTTCTTTGAATTATAAACTGAAGCTTTACCGTGCAGATATCTCCAGTGGTTAATTGAAGA TCAAGACTCCGGTGACACACGGTTTCATACAACTTATGCCCTCTTGCTTTCTAAATCAGCACTT GATGCTAGTGAAAAGGAGCATGTTACGCACAATCTTGAAGGTGTAAACCATAAGGAGATAAACA TCTCAGACCGTTGGAACAACTCAATATTTCATACTCATGTCAGAGAGAGATTGCAATTTTTTTT ACAGTCGTCTGACTTGTATGATCCAGAGGAGGTTCTTGACTTGGTTGAAGGATCCGAGTTATGG CTCGAGAAGGTCAGTAAAAAATTTAGGCCCTTCATAGAAATAATGGCATATGCATCTCTGCTGG ATAACAGCTTGAACTGTTTTATTCTCCTTGTGATTTGCAGTCCTTGTGTTATTGATGGTTTCAT TACAGGCTATTCTTTACAGGAAGCTCGGTCAAGAAACATTAGTGCTTCAAATTCTTGCCTTGTA AGTTCATAAATGTTTGGTTATTGCTTGGGTACATCACAACAAGCTTTATCATAACAAATGAACA ACTTAAAAGATGTTCTGTTTTCCAAATGTGAGCAATGCATGGTTGACATGCTCTTCTGCTGCTT TACATGTGAAGTCCCTCACTTAAACAGGCGAAAATATTTGAAATCTTAGTATTCACATTGTTGC TAAATATGTATTTCATAATTGAATCGGCAATTACTCTGAATAAGATGACTATCTGTGGGATTGT AATTTAAAGTTGCGTTCATCTGGCAGAAAGTTGGAAGACTGTGAAGCTGCAGAACAATATTGTG CTGAGATCGGTAGGCCAGATGCTTACATGCAGTTAGTACAGTATTCTCTCATTTGTTTCTTTAG ATTATTGGTCTAGTAGAAGTTCTCTTAGCCTTTCCCTTACCTTGTCTCTTCTTAGGCTGCTTGA AATGTATTTGGAGCCAATGAATGGTAAAGAGCCTATGTTCAAAGCTGCTGTGCGCCTGTTGCAC AATCATGGAGAAATGCTAGACCCTTTGCAAGTTTTGGAGGTACTAAAACTTATCCTTCTTCTGC TCTATTACTCATGTAATGGTCAATGAGGAGACAAAAGGCTTGTTCTACCCCCAGGGCTTTGGTT TAGTGGCAACACTACGTGTGTGTGCTGGTTAGATACATATTACAAGTTCAAACAACAGAGCAAA CAAAAGTCTGGTATTTAAGTGGAAAGGGTTGAGGGGGCCCATAATTTACCAAATTTATGCCAAG TCAAATGGTGCTACATAAATTTGGACGGAGTGAGTATTTGTTTATCCACCATATCATGTCAGTA ACATGGTTGATTGGGCTGGAAGATCAAAAATCTGATTAATTTTCGCACTGGATTTATAGTATGA GAACCTATCTCCAAAGTTATAAAATAAAATATGGTAGAAGAGAAAAGTCATCCTAGAAATTTAT TTGAAGGAAAAACATCTCATCGTACCTTAAAAGTAGAAATTTTGATTTTTACCAATAGACAAAT GTTGGATCTTTGTTATTAGCAGTGTACGAAATATTTGGTTGTCACTTGTCAAAACAGGGAACCT CTTCTTTAAATCTTGAAGATTGGAGCATATTCTTTTTTCTTTGGGAAATTAAGTTTTCTTGTCC TAATTTTAGCTATTGGTGCATATTCAGTCACATAGTGCGTTACAGATTAGAAGTAGTCCTCTTA CTTCGTTCCAAACATCTAATTATGCAACTTGTAACACAGTGATACCATTTTTGGATATCAACTT TTAGAATTGCCTTTCTATAGTGAAAGATGAAGTCTGAGTTTTGTTTATGGTGATTTTAAATTTT CAAAGGCCGGAAAAAAGAATTGTCTGATGACTTGATAGGTCTAATGATATTTAGGTTACCTTTT CTAAATTACTGGGTGGATGGGGGTGGGGTTTCAATGGTTGTATCTTCATAGTTTCATTTGCTAA GTATTCAGGTTACTCGATAAAATCATTTTAGATAACTAGACAATGTATATTTGTTTTGGATTAT TTTTTCATGCTGTTTTAAGGGAACCAGATGATGAGAAGGCAAATAACATCTATTTGACTTAATT TTCTTTGCAAAAAGTTACTAACAATGTCAACGTTACTCATTCTGAGTTGAGGTTTCACTTTGCA GAGATTGTCACCAGATATGCCCCTTCAACTTGCTTCTGAGACAATATTAAGGATGTTGAGAGCT CGACTTCACCATCATCGTCAAGGCCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.172846126

Conservation Information
Conserved circRNAs	NA
PMCS	0.172846126

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10065551-10063417(+)
10063453-10065692(-)
						
						Potential amino acid sequence
						
							MQLLEMYLEPMNGKEPMFKAAVRLLHNHGEMLDPLQVLERLSPDMPLQLASETILRMLRARLHH
HRQGQMK*(+)
MSTFLGSIAAITSFGLDDDGEVELSTSLILSQKQVEGAYLVTISPKLAKGLAFLHDCATGAQQL
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10065551-10063417(+) 10063453-10065692(-)
Potential amino acid sequence	MQLLEMYLEPMNGKEPMFKAAVRLLHNHGEMLDPLQVLERLSPDMPLQLASETILRMLRARLHH HRQGQMK(+) MSTFLGSIAAITSFGLDDDGEVELSTSLILSQKQVEGAYLVTISPKLAKGLAFLHDCATGAQQL (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018

circRNA

Detail information of Solyc05g015210.2_circ_g.3

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