Plant Circular RNA Database

Detail information of Solyc01g006350.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g006350.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000016
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 950146-952323  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc01g006350.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g006350.2_circ_ag.1 Solyc01g006350.2_circ_g.1 						
					
						Support reads
						NA
					
						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
						Solyc01g006350.2.1:8

General Information
CircRNA Name	Solyc01g006350.2_circ_g.2
ID in PlantcircBase	sly_circ_000016
Alias	NA
Organism	Solanum lycopersicum
Position	chr1: 950146-952323 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc01g006350.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g006350.2_circ_ag.1 Solyc01g006350.2_circ_g.1
Support reads	NA
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	Solyc01g006350.2.1:8

			
						 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  
						
							CTCACAAATTAGTAATGTAATCTTCTTCCCTCAAATTCTTGACAATTTCATTCCAGAAAGGTGC
AAATCGAGCAGCATCGGCTTTGTTTCTCTCCAAAACctgggtatattttctggaggtaaaacag
aatagaaattccatcttcatttttcttaaggagttctgacatgctgtaaagaacagtttctgaa
taatatgg

									
								

					

						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: 931
Transcript exons: 950146-950255,950331-950491,950606-950696,950769-950866,
951519-951639,951751-951923,952042-952123,952229-952323
CTGGGTATATTTTCTGGAGGTAAAACAGAATAGAAATTCCATCTTCATTTTTCTTAAGGAGTTC
TGACATGCTGTAAAGAACAGTTTCTGAATAATATGGGGTGAACACGCTGAAGGATAGCATCTCA
CGGACAGGTCGTGTTACAGGCATCTCCATGAAAAGGGAATTGGTGAAGAACTCTAACCGACGCC
TAGCTTCAAGATTCTTGGGTATGTTGGCAGCAGATTCTTTAATAGTTAGGAGAGAATAAAGTCT
TTTAATCAGTTCCATCAACTCAGCATCTCTTGGCCACTTTAACTTTGAGAACAACCGGCCTTCA
TTCCTTGCTTTTGACAAAGTGTTCCATGTTTCAATGTGGTCTCTCATGTTGAAGCGAAGGACAT
CAAGTCGCAGAACATCATACAGATCTTGAATAGCTTTAACAGCCCCAGTTTCAAGCTCTGGTGT
ATGCTCCTTTTTCAGTATTCCCATTAGTGCAGTTACTTTCTGAATCACCAGTGGCAACTTATTC
ATATCAACGTCCACATTAATGCTCCTTTTAGATATGCTCCCACGAATATCCTCATATATACGTT
CAACCCACTTCTTTCCTTCATCATTTCCTTCATCATCTAATATGGATGTAAGAACAAACTTGAT
GGCGTAATAGCACTCTTCAACCGCATATATCATGTAATCATCCCTTGAAATCCTATCCCATAAC
TCATCTTGTGAGTCTTTACTCTCCACAGCTATATCTTTTGCAAGAAATATCTTGCTAGCTAGGA
GGAAAAGAGGCCACTGAACCAAGGGCAGACTCCCAGAATTCTTAGGCATCAAAAGCTGTTCCAT
CTCCAAATTAGTAATGTAATCTTCTTCCCTCAAATTCTTGACAATTTCATTCCAGAAAGGTGCA
AATCGAGCAGCATCGGCTTTGTTTCTCTCCAAAAC
						
					

						Genomic sequence
						
							CTGGGTATATTTTCTGGAGGTAAAACAGAATAGAAATTCCATCTTCATTTTTCTTAAGGAGTTC
TGACATGCTGTAAAGAACAGTTTCTGAATAATATGGGGTGAACACGCTGCAAGAGTAAAAATTT
ATCACACAAAGGGTCTGAAGATAGTTAAATAAACAGTGACAATGTGAAAGAACAGACCTGAAGG
ATAGCATCTCACGGACAGGTCGTGTTACAGGCATCTCCATGAAAAGGGAATTGGTGAAGAACTC
TAACCGACGCCTAGCTTCAAGATTCTTGGGTATGTTGGCAGCAGATTCTTTAATAGTTAGGAGA
GAATAAAGTCTTTTAATCAGTTCCATCTGCATATATTTAGTGCATCTTTAGGAAACTTAAGTGA
GCTCAAAGGAAAAGGAGCAGAAAGGTGACAGAAAAAAAACTAACGAAATGGAAAAGGAAACCAG
ATGCAAGCCTACCAACTCAGCATCTCTTGGCCACTTTAACTTTGAGAACAACCGGCCTTCATTC
CTTGCTTTTGACAAAGTGTTCCATGTTTCAATGTGGTCTCTGAAATGACATTATAGTAATTATG
CACCACACTCAAGGGTATAATAATCCCAGAAATATGATATGAAATACCTCATGTTGAAGCGAAG
GACATCAAGTCGCAGAACATCATACAGATCTTGAATAGCTTTAACAGCCCCAGTTTCAAGCTCT
GGTGTATGCTCCTTTTTCTACGTAAGAGTATTTTAACAGATCATAAACAAAATGGCAGGATGAT
AAATATTCATTCAGTCCTTTTAAAAACCGACAATGAAAGAGAAATCCTCTCAACTGAAATAAGA
GGTCACCGAACAATGGATGCAAAAGAACAGTAAAGAAAACAAAATGCATGTGACCAATGCAGTT
TTCTGATATGGAATTGGAAAAAGAAGTATGCATCACCTATTGAGAGGTCTCTTTGTATGACAAG
ACGTACCATGAACATGTGGATATGAGAACGTTCAAATTCATTAATTTCATCTTAAATACAATGA
AGAAAGAGGATGCAAGTGAGGGGATGAGGGGCCTGGCGTGCAGCGGTAGAAGACTTGATGAGAG
CAGCAGACACTCGGAAGTCACAGAAGATGCACAAGGGAGACCCTAGATTCCAGTCCTTTGACCA
TTCTAAGGGAACATGTTTGCTAAATTTGTCAACTGACTGCCTCTTAGATGGCGCTAAAGCAGAT
CACTGATTTTCAAACTTTGTGCCGGCATAAGTTCAATACTATCTAGTCTCCAGTGTTAATGATG
ATAAGGATACCGGGAAAGAGAAAATTTCAAAAGAACAAAGCAGACCTTATGTTCTTAAGTATAA
AAGTTATCAAACTTGAAAAGAACAAGTACCAGTATTCCCATTAGTGCAGTTACTTTCTGAATCA
CCAGTGGCAACTTATTCATATCAACGTCCACATTAATGCTCCTTTTAGATATGCTCCCACGAAT
ATCCTCATATATACGTTCAACCCTAACATAGTAGACAAAACAAAGAATATAAACTGACTATGCA
TAACTCTAAATAACAGTTAATTGTGAGTTCATAAAAGACAAAGCGACTCCGAAGGGTTAGAAAT
CTTACCACTTCTTTCCTTCATCATTTCCTTCATCATCTAATATGGATGTAAGAACAAACTTGAT
GGCGTAATAGCACTCTTCAACCGCATATATCATGTAATCATCCCTTGAAATCCTATCCCATAAC
TCATCTTGTGAGTCTTTACTCTCCACAGCTATATCTTTTGCAAGAAATATCTGCACATTCAGCA
TAAATGTAAAGATATATAGCATGACAGTTGACCGCATAGATCACATTTTGCATCAGGAAAAATG
GAAACACAAGAAATTGTCTGCACTCTAACAACTGCTCAACCTTGCTAGCTAGGAGGAAAAGAGG
CCACTGAACCAAGGGCAGACTCCCAGAATTCTTAGGCATCAAAAGCTGTTCCATCTCCCTATAG
GTTGAAAATCAATCCATCAAAATTAAGAGGTTGAAGGCCATCAATCTAGTAGAAGCAAACTGAA
ACTGGGTTAGCAAAATAACAAAAACAGTCACTCACAAATTAGTAATGTAATCTTCTTCCCTCAA
ATTCTTGACAATTTCATTCCAGAAAGGTGCAAATCGAGCAGCATCGGCTTTGTTTCTCTCCAAA
AC
						
					

			
		

Sequences
Splice junction sequence	CTCACAAATTAGTAATGTAATCTTCTTCCCTCAAATTCTTGACAATTTCATTCCAGAAAGGTGC AAATCGAGCAGCATCGGCTTTGTTTCTCTCCAAAACctgggtatattttctggaggtaaaacag aatagaaattccatcttcatttttcttaaggagttctgacatgctgtaaagaacagtttctgaa taatatgg
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: 931 Transcript exons: 950146-950255,950331-950491,950606-950696,950769-950866, 951519-951639,951751-951923,952042-952123,952229-952323 CTGGGTATATTTTCTGGAGGTAAAACAGAATAGAAATTCCATCTTCATTTTTCTTAAGGAGTTC TGACATGCTGTAAAGAACAGTTTCTGAATAATATGGGGTGAACACGCTGAAGGATAGCATCTCA CGGACAGGTCGTGTTACAGGCATCTCCATGAAAAGGGAATTGGTGAAGAACTCTAACCGACGCC TAGCTTCAAGATTCTTGGGTATGTTGGCAGCAGATTCTTTAATAGTTAGGAGAGAATAAAGTCT TTTAATCAGTTCCATCAACTCAGCATCTCTTGGCCACTTTAACTTTGAGAACAACCGGCCTTCA TTCCTTGCTTTTGACAAAGTGTTCCATGTTTCAATGTGGTCTCTCATGTTGAAGCGAAGGACAT CAAGTCGCAGAACATCATACAGATCTTGAATAGCTTTAACAGCCCCAGTTTCAAGCTCTGGTGT ATGCTCCTTTTTCAGTATTCCCATTAGTGCAGTTACTTTCTGAATCACCAGTGGCAACTTATTC ATATCAACGTCCACATTAATGCTCCTTTTAGATATGCTCCCACGAATATCCTCATATATACGTT CAACCCACTTCTTTCCTTCATCATTTCCTTCATCATCTAATATGGATGTAAGAACAAACTTGAT GGCGTAATAGCACTCTTCAACCGCATATATCATGTAATCATCCCTTGAAATCCTATCCCATAAC TCATCTTGTGAGTCTTTACTCTCCACAGCTATATCTTTTGCAAGAAATATCTTGCTAGCTAGGA GGAAAAGAGGCCACTGAACCAAGGGCAGACTCCCAGAATTCTTAGGCATCAAAAGCTGTTCCAT CTCCAAATTAGTAATGTAATCTTCTTCCCTCAAATTCTTGACAATTTCATTCCAGAAAGGTGCA AATCGAGCAGCATCGGCTTTGTTTCTCTCCAAAAC
Genomic sequence	CTGGGTATATTTTCTGGAGGTAAAACAGAATAGAAATTCCATCTTCATTTTTCTTAAGGAGTTC TGACATGCTGTAAAGAACAGTTTCTGAATAATATGGGGTGAACACGCTGCAAGAGTAAAAATTT ATCACACAAAGGGTCTGAAGATAGTTAAATAAACAGTGACAATGTGAAAGAACAGACCTGAAGG ATAGCATCTCACGGACAGGTCGTGTTACAGGCATCTCCATGAAAAGGGAATTGGTGAAGAACTC TAACCGACGCCTAGCTTCAAGATTCTTGGGTATGTTGGCAGCAGATTCTTTAATAGTTAGGAGA GAATAAAGTCTTTTAATCAGTTCCATCTGCATATATTTAGTGCATCTTTAGGAAACTTAAGTGA GCTCAAAGGAAAAGGAGCAGAAAGGTGACAGAAAAAAAACTAACGAAATGGAAAAGGAAACCAG ATGCAAGCCTACCAACTCAGCATCTCTTGGCCACTTTAACTTTGAGAACAACCGGCCTTCATTC CTTGCTTTTGACAAAGTGTTCCATGTTTCAATGTGGTCTCTGAAATGACATTATAGTAATTATG CACCACACTCAAGGGTATAATAATCCCAGAAATATGATATGAAATACCTCATGTTGAAGCGAAG GACATCAAGTCGCAGAACATCATACAGATCTTGAATAGCTTTAACAGCCCCAGTTTCAAGCTCT GGTGTATGCTCCTTTTTCTACGTAAGAGTATTTTAACAGATCATAAACAAAATGGCAGGATGAT AAATATTCATTCAGTCCTTTTAAAAACCGACAATGAAAGAGAAATCCTCTCAACTGAAATAAGA GGTCACCGAACAATGGATGCAAAAGAACAGTAAAGAAAACAAAATGCATGTGACCAATGCAGTT TTCTGATATGGAATTGGAAAAAGAAGTATGCATCACCTATTGAGAGGTCTCTTTGTATGACAAG ACGTACCATGAACATGTGGATATGAGAACGTTCAAATTCATTAATTTCATCTTAAATACAATGA AGAAAGAGGATGCAAGTGAGGGGATGAGGGGCCTGGCGTGCAGCGGTAGAAGACTTGATGAGAG CAGCAGACACTCGGAAGTCACAGAAGATGCACAAGGGAGACCCTAGATTCCAGTCCTTTGACCA TTCTAAGGGAACATGTTTGCTAAATTTGTCAACTGACTGCCTCTTAGATGGCGCTAAAGCAGAT CACTGATTTTCAAACTTTGTGCCGGCATAAGTTCAATACTATCTAGTCTCCAGTGTTAATGATG ATAAGGATACCGGGAAAGAGAAAATTTCAAAAGAACAAAGCAGACCTTATGTTCTTAAGTATAA AAGTTATCAAACTTGAAAAGAACAAGTACCAGTATTCCCATTAGTGCAGTTACTTTCTGAATCA CCAGTGGCAACTTATTCATATCAACGTCCACATTAATGCTCCTTTTAGATATGCTCCCACGAAT ATCCTCATATATACGTTCAACCCTAACATAGTAGACAAAACAAAGAATATAAACTGACTATGCA TAACTCTAAATAACAGTTAATTGTGAGTTCATAAAAGACAAAGCGACTCCGAAGGGTTAGAAAT CTTACCACTTCTTTCCTTCATCATTTCCTTCATCATCTAATATGGATGTAAGAACAAACTTGAT GGCGTAATAGCACTCTTCAACCGCATATATCATGTAATCATCCCTTGAAATCCTATCCCATAAC TCATCTTGTGAGTCTTTACTCTCCACAGCTATATCTTTTGCAAGAAATATCTGCACATTCAGCA TAAATGTAAAGATATATAGCATGACAGTTGACCGCATAGATCACATTTTGCATCAGGAAAAATG GAAACACAAGAAATTGTCTGCACTCTAACAACTGCTCAACCTTGCTAGCTAGGAGGAAAAGAGG CCACTGAACCAAGGGCAGACTCCCAGAATTCTTAGGCATCAAAAGCTGTTCCATCTCCCTATAG GTTGAAAATCAATCCATCAAAATTAAGAGGTTGAAGGCCATCAATCTAGTAGAAGCAAACTGAA ACTGGGTTAGCAAAATAACAAAAACAGTCACTCACAAATTAGTAATGTAATCTTCTTCCCTCAA ATTCTTGACAATTTCATTCCAGAAAGGTGCAAATCGAGCAGCATCGGCTTTGTTTCTCTCCAAA AC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.369208229

Conservation Information
Conserved circRNAs	NA
PMCS	0.369208229

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							952121-952273(-)
950195-952273(-)
						
						Potential amino acid sequence
						
							MEQLLMPKNSGSLPLVQWPLFLLASKIFLAKDIAVESKDSQDELWDRISRDDYMIYAVEECYYA
IKFVLTSILDDEGNDEGKKWVERIYEDIRGSISKRSINVDVDMNKLPLVIQKVTALMGILKKEH
TPELETGAVKAIQDLYDVLRLDVLRFNMRDHIETWNTLSKARNEGRLFSKLKWPRDAELMELIK
RLYSLLTIKESAANIPKNLEARRRLEFFTNSLFMEMPVTRPVREMLSFSVFTPYYSETVLYSMS
ELLKKNEDGISILFYLQKIYPGFGEKQSRCCSICTFLE*(-)
MKMEFLFCFTSRKYTQVLERNKADAARFAPFWNEIVKNLREEDYITNLEMEQLLMPKNSGSLPL
VQWPLFLLASKIFLAKDIAVESKDSQDELWDRISRDDYMIYAVEECYYAIKFVLTSILDDEGND
EGKKWVERIYEDIRGSISKRSINVDVDMNKLPLVIQKVTALMGILKKEHTPELETGAVKAIQDL
YDVLRLDVLRFNMRDHIETWNTLSKARNEGRLFSKLKWPRDAELMELIKRLYSLLTIKESAANI
PKNLEARRRLEFFTNSLFMEMPVTRPVREMLSFSVFTPYYSETVLYSMSELLKKNEDGISILFY
LQKIYPGFGEKQSRCCSICTFLE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	952121-952273(-) 950195-952273(-)
Potential amino acid sequence	MEQLLMPKNSGSLPLVQWPLFLLASKIFLAKDIAVESKDSQDELWDRISRDDYMIYAVEECYYA IKFVLTSILDDEGNDEGKKWVERIYEDIRGSISKRSINVDVDMNKLPLVIQKVTALMGILKKEH TPELETGAVKAIQDLYDVLRLDVLRFNMRDHIETWNTLSKARNEGRLFSKLKWPRDAELMELIK RLYSLLTIKESAANIPKNLEARRRLEFFTNSLFMEMPVTRPVREMLSFSVFTPYYSETVLYSMS ELLKKNEDGISILFYLQKIYPGFGEKQSRCCSICTFLE(-) MKMEFLFCFTSRKYTQVLERNKADAARFAPFWNEIVKNLREEDYITNLEMEQLLMPKNSGSLPL VQWPLFLLASKIFLAKDIAVESKDSQDELWDRISRDDYMIYAVEECYYAIKFVLTSILDDEGND EGKKWVERIYEDIRGSISKRSINVDVDMNKLPLVIQKVTALMGILKKEHTPELETGAVKAIQDL YDVLRLDVLRFNMRDHIETWNTLSKARNEGRLFSKLKWPRDAELMELIKRLYSLLTIKESAANI PKNLEARRRLEFFTNSLFMEMPVTRPVREMLSFSVFTPYYSETVLYSMSELLKKNEDGISILFY LQKIYPGFGEKQSRCCSICTFLE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc01g006350.2_circ_g.2

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