Plant Circular RNA Database

Detail information of Solyc06g005080.2_circ_g.11

			
						 General Information
					
						CircRNA Name
						Solyc06g005080.2_circ_g.11
					
						ID in PlantcircBase
						sly_circ_001855
					
						Alias
						6:84413|86695, Slcirc098
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr6: 84413-86695  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc06g005080.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc06g005080.2_circ_g.9 Solyc06g005080.2_circ_g.10 Solyc06g005080.2_circ_g.12 						
					
						Support reads
						43/33
					
						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
						Solyc06g005080.2.1:5

General Information
CircRNA Name	Solyc06g005080.2_circ_g.11
ID in PlantcircBase	sly_circ_001855
Alias	6:84413\|86695, Slcirc098
Organism	Solanum lycopersicum
Position	chr6: 84413-86695 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc06g005080.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc06g005080.2_circ_g.9 Solyc06g005080.2_circ_g.10 Solyc06g005080.2_circ_g.12
Support reads	43/33
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	Solyc06g005080.2.1:5

			
						 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  
						
							AGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAAAATAAAG
TTCTTCAACTATCTGTTCACTTATCCTGTTCACCACcttatcaagatataattcagtagcccat
gtcgaaatcattgttatttgacatttttcatcctttgaaagattatcaagcttccgcaggagaa
atgttctc

									
								

					

						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: 489
Transcript exons: 84413-84520,85545-85604,86120-86176,86343-86462,86552-86
695
CTTATCAAGATATAATTCAGTAGCCCATGTCGAAATCATTGTTATTTGACATTTTTCATCCTTT
GAAAGATTATCAAGCTTCCGCAGGAGAAATGTTCTCAGTGCATCCTGTTCGCCTATGCTAATGA
ACTTCAATGAGATCTCTTCAAAAGATAATACATAATTAATTTTTGCATAGAATGATGCAGCTCT
GAGGAACTCCTTGGCAACAAAAGCAGCTTCAGCCTGAACCAGATAAACTTGGTCTCTCTGCAGG
GCATCACGACAACTAGCCAAAGCTGCAGCATATTCTTTTAAGTCCAAGTACACTTTCCACATAT
CACGACCTTCATCATTTACGGACACCTGGAAGATAGAATTTTGGTCATATGCATAAAACAACCC
AGCTGAGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAAAA
TAAAGTTCTTCAACTATCTGTTCACTTATCCTGTTCACCAC
						
					

						Genomic sequence
						
							CTTATCAAGATATAATTCAGTAGCCCATGTCGAAATCATTGTTATTTGACATTTTTCATCCTTT
GAAAGATTATCAAGCTTCCGCAGGAGAAATGTTCTCAGTGCATCCTGCAAGCAAAGAAGTGTTA
TATCCAGGAAAAAAATTCAACTAGTTCTTTTTTCTACTGATTCTATTATTTGTGGTTGTTTTTC
TATTCAAGGTTTCCAAATGTCACATGTCAGAAAACTAACAAAATTAACTTCCAACAGCAGACCA
AGGAATACCTCTCATTATAACATATGCAGATGCAGCAAATATCACTAGAGATCTGTTGTAAAAA
GGAATGGGATATCTACACAAACATAGGTTAATTATCTTCCTAAGGAATAATATCTTCATTTTTG
ACAATGATAGGACTACTAAGCAAGAAGATGATCACGAGAAATTAAACGTGGTTCTGAACTATTA
CAATTTTTTAAATCAATAAGCAATGAGAGAACTTCAATAATAATCGGCACTGAGATAGCACTGC
ACAGAAGTACAATGAAGTTCTAAAAACAACAACTGGATAATACTACATCAGCTAACAAAAGCAG
TAGCAGCCCTCAAGTCCTGGTGAAGACTATATACAAAAAATGGAAACAGATGCTAAAATGTAAA
GATAATTGGAATTCAAGTACATTTGCTTTGTAAATAAGAAGAGATACTAAATTATCAGAATTTG
CAGTCAGGAACTCAGGATCTACCAAATAAACATGTTCTCCAATGATGCTTAGAATTAAAAAATC
CTCAGTATGATCTATTTGGGTATCATTTAAGTAACTCGAGACTAAATAGAATAACCTATAATGA
GTCGCCGCAACGGACTCCAAATGGAAATATTTGAGTTCTAACAAGCTTCTTAGTTCTTACAGCC
TAATAAACCTTGTCTCTTAAAAACGGAACAACAGGAAAAGTAATGTTCCTTTTTAGATATGAGT
TGGTTACTACTACAGATCCTTGCCTCGAATGAGCAAGATGGATTGTTTTTTCAACAGCAAGATG
GATTGAACTTTAGTGAATCTGATTTTTTTTGTTTTTTCAACGAGTGAAAATAGAAATCTTTTCT
AGCATAACCATAAATCAGTGTTCTAGAATTAAAAAAGCTCATACCTGTTCGCCTATGCTAATGA
ACTTCAATGAGATCTCTTCAAAAGATAATACATAATTAATCTGCAGTATTCATTTCCATGGATT
AGAAAGGTCTCCAGTTCCAGGAATAAATATGAATTATTTTTGTCAAACATAAATAAAAGAAAAC
AAAAGTGACATGAGTGAAGAGTTGCAGAATTTGAATCAGAGACATAGTTTTTACAAGAAATATT
CAAGACGGTAATCAATTCGATACTACTGAAAATGTAACGGATTATATGAAGCAGACCTTTTAAG
GAAGATTATCAGGGGTTTCACTTGGGGTATGATAGATGAAAGTATTCTCATTTATCAGAAAACA
AAATTCTACTGGTCTTTGTAGAATAGAGTAGACATAGGCACTGATTGCTACAGAAGTTTGTGGA
AATTTCCCATTTGCTGGTCATAATGAAATTTGCAATTAGCACACAAGGATCAGATTTTCTTAAG
GGTATGTGGTTGGTTGACAAGGATCAAGTTTACAAAAGTACAAAGAAACAACAACTAAATGGAA
ACCACAAAATGGAAGTAAATGCATAAATAAATAGATTAAATACTTTTGCATAGAATGATGCAGC
TCTGAGGAACTCCTTGGCAACAAAAGCAGCTTCAGCCTGCATAACATACATGAGGTCTATGATG
AAAAACCAAAAGAAAATATACAGCCTCCCAAGCAATAAGAGTTTCTTCAGATTATGATTAGGGG
ACAGTTACAAATGAGGCAAATATTCAAAAAAGCATCACATATCCCAGCAGAATAGAAGTTTAAT
TAGCCAAGACCTGAACCAGATAAACTTGGTCTCTCTGCAGGGCATCACGACAACTAGCCAAAGC
TGCAGCATATTCTTTTAAGTCCAAGTACACTTTCCACATATCACGACCTTCATCATTTACGGAC
ACCTAAATTCAGATTGTCGATTCAGAAACTGAAGAAGAAATATAATGGTATTACCACATCAAAT
AAGATTTAGGAAATGCCTATACTGCACCTGGAAGATAGAATTTTGGTCATATGCATAAAACAAC
CCAGCTGAGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAA
AATAAAGTTCTTCAACTATCTGTTCACTTATCCTGTTCACCAC
						
					

			
		

Sequences
Splice junction sequence	AGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAAAATAAAG TTCTTCAACTATCTGTTCACTTATCCTGTTCACCACcttatcaagatataattcagtagcccat gtcgaaatcattgttatttgacatttttcatcctttgaaagattatcaagcttccgcaggagaa atgttctc
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: 489 Transcript exons: 84413-84520,85545-85604,86120-86176,86343-86462,86552-86 695 CTTATCAAGATATAATTCAGTAGCCCATGTCGAAATCATTGTTATTTGACATTTTTCATCCTTT GAAAGATTATCAAGCTTCCGCAGGAGAAATGTTCTCAGTGCATCCTGTTCGCCTATGCTAATGA ACTTCAATGAGATCTCTTCAAAAGATAATACATAATTAATTTTTGCATAGAATGATGCAGCTCT GAGGAACTCCTTGGCAACAAAAGCAGCTTCAGCCTGAACCAGATAAACTTGGTCTCTCTGCAGG GCATCACGACAACTAGCCAAAGCTGCAGCATATTCTTTTAAGTCCAAGTACACTTTCCACATAT CACGACCTTCATCATTTACGGACACCTGGAAGATAGAATTTTGGTCATATGCATAAAACAACCC AGCTGAGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAAAA TAAAGTTCTTCAACTATCTGTTCACTTATCCTGTTCACCAC
Genomic sequence	CTTATCAAGATATAATTCAGTAGCCCATGTCGAAATCATTGTTATTTGACATTTTTCATCCTTT GAAAGATTATCAAGCTTCCGCAGGAGAAATGTTCTCAGTGCATCCTGCAAGCAAAGAAGTGTTA TATCCAGGAAAAAAATTCAACTAGTTCTTTTTTCTACTGATTCTATTATTTGTGGTTGTTTTTC TATTCAAGGTTTCCAAATGTCACATGTCAGAAAACTAACAAAATTAACTTCCAACAGCAGACCA AGGAATACCTCTCATTATAACATATGCAGATGCAGCAAATATCACTAGAGATCTGTTGTAAAAA GGAATGGGATATCTACACAAACATAGGTTAATTATCTTCCTAAGGAATAATATCTTCATTTTTG ACAATGATAGGACTACTAAGCAAGAAGATGATCACGAGAAATTAAACGTGGTTCTGAACTATTA CAATTTTTTAAATCAATAAGCAATGAGAGAACTTCAATAATAATCGGCACTGAGATAGCACTGC ACAGAAGTACAATGAAGTTCTAAAAACAACAACTGGATAATACTACATCAGCTAACAAAAGCAG TAGCAGCCCTCAAGTCCTGGTGAAGACTATATACAAAAAATGGAAACAGATGCTAAAATGTAAA GATAATTGGAATTCAAGTACATTTGCTTTGTAAATAAGAAGAGATACTAAATTATCAGAATTTG CAGTCAGGAACTCAGGATCTACCAAATAAACATGTTCTCCAATGATGCTTAGAATTAAAAAATC CTCAGTATGATCTATTTGGGTATCATTTAAGTAACTCGAGACTAAATAGAATAACCTATAATGA GTCGCCGCAACGGACTCCAAATGGAAATATTTGAGTTCTAACAAGCTTCTTAGTTCTTACAGCC TAATAAACCTTGTCTCTTAAAAACGGAACAACAGGAAAAGTAATGTTCCTTTTTAGATATGAGT TGGTTACTACTACAGATCCTTGCCTCGAATGAGCAAGATGGATTGTTTTTTCAACAGCAAGATG GATTGAACTTTAGTGAATCTGATTTTTTTTGTTTTTTCAACGAGTGAAAATAGAAATCTTTTCT AGCATAACCATAAATCAGTGTTCTAGAATTAAAAAAGCTCATACCTGTTCGCCTATGCTAATGA ACTTCAATGAGATCTCTTCAAAAGATAATACATAATTAATCTGCAGTATTCATTTCCATGGATT AGAAAGGTCTCCAGTTCCAGGAATAAATATGAATTATTTTTGTCAAACATAAATAAAAGAAAAC AAAAGTGACATGAGTGAAGAGTTGCAGAATTTGAATCAGAGACATAGTTTTTACAAGAAATATT CAAGACGGTAATCAATTCGATACTACTGAAAATGTAACGGATTATATGAAGCAGACCTTTTAAG GAAGATTATCAGGGGTTTCACTTGGGGTATGATAGATGAAAGTATTCTCATTTATCAGAAAACA AAATTCTACTGGTCTTTGTAGAATAGAGTAGACATAGGCACTGATTGCTACAGAAGTTTGTGGA AATTTCCCATTTGCTGGTCATAATGAAATTTGCAATTAGCACACAAGGATCAGATTTTCTTAAG GGTATGTGGTTGGTTGACAAGGATCAAGTTTACAAAAGTACAAAGAAACAACAACTAAATGGAA ACCACAAAATGGAAGTAAATGCATAAATAAATAGATTAAATACTTTTGCATAGAATGATGCAGC TCTGAGGAACTCCTTGGCAACAAAAGCAGCTTCAGCCTGCATAACATACATGAGGTCTATGATG AAAAACCAAAAGAAAATATACAGCCTCCCAAGCAATAAGAGTTTCTTCAGATTATGATTAGGGG ACAGTTACAAATGAGGCAAATATTCAAAAAAGCATCACATATCCCAGCAGAATAGAAGTTTAAT TAGCCAAGACCTGAACCAGATAAACTTGGTCTCTCTGCAGGGCATCACGACAACTAGCCAAAGC TGCAGCATATTCTTTTAAGTCCAAGTACACTTTCCACATATCACGACCTTCATCATTTACGGAC ACCTAAATTCAGATTGTCGATTCAGAAACTGAAGAAGAAATATAATGGTATTACCACATCAAAT AAGATTTAGGAAATGCCTATACTGCACCTGGAAGATAGAATTTTGGTCATATGCATAAAACAAC CCAGCTGAGGCATCACTACATAAGCCAATAATACCTCTTGAAACTGCATCAGATGTCTGATCAA AATAAAGTTCTTCAACTATCTGTTCACTTATCCTGTTCACCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.775757235

Conservation Information
Conserved circRNAs	NA
PMCS	0.775757235

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							86642-84432(+)
86437-84415(-)
						
						Potential amino acid sequence
						
							MSDQNKVLQLSVHLSCSPPYQDIIQ*(+)
MWKVYLDLKEYAAALASCRDALQRDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKF
ISIGEQDALRTFLLRKLDNLSKDEKCQITMISTWATELYLDKVVNRISEQIVEELYFDQTSDAV
SRGIIGLCSDASAGLFYAYDQNSIFQVSVNDEGRDMWKVYLDLKEYAAALASCRDALQRDQVYL
VQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKFISIGEQDALRTFLLRKLDNLSKDEKCQIT
MISTWATELYLDKVVNRISEQIVEELYFDQTSDAVSRGIIGLCSDASAGLFYAYDQNSIFQVSV
NDEGRDMWKVYLDLKEYAAALASCRDALQRDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFE
EISLKFISIGEQDALRTFLLRKLDNLSKDEKCQITMISTWATELYLDKVVNRISEQIVEELYFD
QTSDAVSRGIIGLCSDASAGLFYAYDQNSIFQVSVNDEGRDMWKVYLDLKEYAAALASCRDALQ
RDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKFISIGEQDALRTFLLRKLDNLSKD
EKCQITMISTWATELYLDK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	86642-84432(+) 86437-84415(-)
Potential amino acid sequence	MSDQNKVLQLSVHLSCSPPYQDIIQ*(+) MWKVYLDLKEYAAALASCRDALQRDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKF ISIGEQDALRTFLLRKLDNLSKDEKCQITMISTWATELYLDKVVNRISEQIVEELYFDQTSDAV SRGIIGLCSDASAGLFYAYDQNSIFQVSVNDEGRDMWKVYLDLKEYAAALASCRDALQRDQVYL VQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKFISIGEQDALRTFLLRKLDNLSKDEKCQIT MISTWATELYLDKVVNRISEQIVEELYFDQTSDAVSRGIIGLCSDASAGLFYAYDQNSIFQVSV NDEGRDMWKVYLDLKEYAAALASCRDALQRDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFE EISLKFISIGEQDALRTFLLRKLDNLSKDEKCQITMISTWATELYLDKVVNRISEQIVEELYFD QTSDAVSRGIIGLCSDASAGLFYAYDQNSIFQVSVNDEGRDMWKVYLDLKEYAAALASCRDALQ RDQVYLVQAEAAFVAKEFLRAASFYAKINYVLSFEEISLKFISIGEQDALRTFLLRKLDNLSKD EKCQITMISTWATELYLDK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc06g005080.2_circ_g.11

Address

Any questions?

Supported by