Plant Circular RNA Database

Detail information of Solyc09g055760.2_circ_g.4

			
						 General Information
					
						CircRNA Name
						Solyc09g055760.2_circ_g.4
					
						ID in PlantcircBase
						sly_circ_002876
					
						Alias
						9:40023452|40026251
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 44425933-44428732  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc09g055760.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc09g055760.2_circ_g.1 Solyc09g055760.2_circ_g.2 Solyc09g055760.2_circ_g.3 Solyc09g055760.2_circ_g.5 						
					
						Support reads
						7
					
						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
						Solyc09g055760.2.1:9

General Information
CircRNA Name	Solyc09g055760.2_circ_g.4
ID in PlantcircBase	sly_circ_002876
Alias	9:40023452\|40026251
Organism	Solanum lycopersicum
Position	chr9: 44425933-44428732 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	CIRI
Parent gene	Solyc09g055760.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc09g055760.2_circ_g.1 Solyc09g055760.2_circ_g.2 Solyc09g055760.2_circ_g.3 Solyc09g055760.2_circ_g.5
Support reads	7
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	Solyc09g055760.2.1:9

			
						 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  
						
							TTGCGGATCCTAAAATTCATACCGTTCGACGACCAAGGGAGACATGACGAGACTCCATCAATTC
CAATGCGAGGAAGGACCTTCTCCGCTGCTGCTTTGCctgagacctttttggacataacagcaag
cttctcttccaaatcctgcttttgagaatttagtgcagatacatgcgctatctcctccactaac
tgctgtct

									
								

					

						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
						
							CTGAGACCTTTTTGGACATAACAGCAAGCTTCTCTTCCAAATCCTGCTTTTGAGAATTTAGTGC
AGATACATGCGCTATCTCCTCCACTAACTGCTGTCTTTCTTGTTGCCTCAACAGGGTCACTTGC
TGTAATTACAAAAATGGTATAGCAAATAAATAAAGCTTAAAGAGGTATTCATGACAACTTAAAC
AAACAATGTGACCTCTAATTGAGATTTTAAATTTGCTAGCTCCTTCTCCATAGCTTGCATACAA
TCTGGCGGAAAATTCATTGAAGTTAAACCACTTATAGGACCAGTCAATGCTTGCTGCTGTAATG
AGTTTAGTTCTGCTCTTAGAGATCCCGCATCCTCTTCAGCCTAATCCCAAAAGGATTCAAACGT
ATTAAGGCATACTATTCCACTTCAACTCATTAAGTGAAAGAAAATTCTAGCATACCCGATACTG
TTCCTCTTCTACTTCCTTCAAACGTTTCTTAATTGTACGAAGCAGAGCTGAAAGATCCTCCTAT
ATTTAAACAACACGGCTCATATGAAAAAGACAGATGGATCACATATAAGGTTAATAACAATAGA
ATGGTAGTAGAAATGATATGTACTCGTGCAACAACTGCTGCATCCTTTTCCATGGCAACATCCT
TGAGCGCTTTTCTTAATGAAGGTATAGTGATTTGCTCCTGCACTTCCAAAGAAAAGAAAGTGAA
GCCACCTATCTACTGAAAAGAGGTCTCAATATCTTGCTTAGATTCCTTCTTATTCCTCCTTTCA
GCAAAGTGAAGACAAATTCAGAAAGGTTTATCATCTAAGGAAAAGGATCCAAGTGTGCAAAATA
ACGTATTGTACTGGGAAACCGCAACTTAATATATTGCAGTACTATTATCTTTAATTAAGGTAAT
TGCAGTGTCATGATCTCATCCATGAATGAACAATAGTGCTAGGATATGAGCAGATAAAGCCCAT
ATTAATAAGGCTATGATATTTGTTTCATATATTACAATGTCTATAAATAATACTCCCTCCATCC
CATAAATTTGAAGGTGTTAGACTGGGCACGGAGTAGAATGAAGGATATACTTTTGAAACCTGTA
ATCTAAAACAAGTCATTAAGAATTGTGTGGCAGTAAATTGTCTCATTAAGGGTAAATAGGAGTG
TCACATAAATTGAGACAAAAGGTAGTAGGAACAACGTCCACTACCTAAGTCATACTTTATCAGA
GTCCTTGTATTTTATTTTATTTTTGAGAATGAACTTTATCAAAGTCTTTATATTGACTCCTAAT
ACTTGCTGATTGTTAAAAGTTACAATCATTTAAGGGACATTTTCTAGCTGTTACTGTGGCGCAA
CTGAGATATGGAAATGAGTGGTGTTTGAGCCTTATAAGGGGTTCTTCGATTGGGAAATTGAAGG
ATGACTACCTTGCTGCAAAAATTGAGTCTGGTATCAGTAGATGCTGAAATGAGGATTCATTGCT
ATGGACTGGACAGAGCAACGGTGTTTTTTATGTGCAATCCTGCTATATAATTTTGGTAACAGCA
GAATTTTTTTCTCTATGGCCTTGGAAAATTTGGGAAGCCAAAATTACTATATGAAGTGGCATGT
TTCAGCTGCATATTGGCTCATGATGGATACTTGACAGAGACAAATTAACAGAAAAGAGGTCTGC
AGTCATGAAGCAGATGATTCCGAATTGAAGGTAGTAGGAATTCCAGCACTGTGAGGTCGTTGGT
TACCTTTGATATCTCTTTTGCAGTATCTTTGGGCTGGAAGATGTTTTTAATAGACGGAACTTCA
TTTGGAGCCAAACACAACCTTAGAAACTCAAGGATGACGAGTCTAATCTTCTACCCTTCTCCAC
TAAAAAAGTTAAGACTTAGTTTGATTGGCACAAAGGCTTGTTACTTAGTGCTGGAAGTTTATAT
GAATGAAGCATATACCATATAAAAAAAAGGGACACTATGGATTTGAATCCCATAAATTGATGAC
TTTCAAATAACTGATCATATAAATTTTTTCCAGTAAGAACTTATTCTATATGGACCATTTACAT
GACTGGTTTCCATTGAAGAAACTATAACTAAAATACATCATCTTTTTCCCCAGATAAATAAGTG
TAAATATAACATTTGAAAGATGCATTACCAGATCGTTAAGACGTTTTTGCAACATGTTGTTCTC
AACTTCTTTTGTCTGAAGCTGAAGAAGAAAATTTTAGAACAAGAGATATTCGTTAGTACATTGA
CAAAAACGTATTCAAAATGAGGGAGGGAGGAAAGAATTAAATACCTTTGAGGCGAATGCTCTGT
TTTCTTCATCTAGCTGTGTGTTTTGTTTTTGCACAACTTTTAATTGAGAAACTAAGGCAGTGAT
ATCATTCTGCAGATGGATGTTTAACTCAAAATAAAACCTAATGGGGGTATACTGCACATTGTGA
AAAGGAAATTGAGTTTACCTCTGATAGGCGAGTTGCACTCCGAGATTTTGTAATCCCCAAAACC
TCTGGCAAAAAAATAAAATATTTTTGAAGATGAGAAGAATGGAGAAAAAGAAGGATTGTTGATT
AAAGTTTTGTTACCAGGTTTGGCAAGATCTGGTCCAGAAGACATCTTGCTTAATCTCTCCGCTG
CTCTCCTTTGACGAATTTCTTCCAACTGCATACAAACAAACAAGGTATGGAAAATGTTGTAAAT
GAGAAACCAAAATTGCGGATCCTAAAATTCATACCGTTCGACGACCAAGGGAGACATGACGAGA
CTCCATCAATTCCAATGCGAGGAAGGACCTTCTCCGCTGCTGCTTTGC
						
					

			
		

Sequences
Splice junction sequence	TTGCGGATCCTAAAATTCATACCGTTCGACGACCAAGGGAGACATGACGAGACTCCATCAATTC CAATGCGAGGAAGGACCTTCTCCGCTGCTGCTTTGCctgagacctttttggacataacagcaag cttctcttccaaatcctgcttttgagaatttagtgcagatacatgcgctatctcctccactaac tgctgtct
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	CTGAGACCTTTTTGGACATAACAGCAAGCTTCTCTTCCAAATCCTGCTTTTGAGAATTTAGTGC AGATACATGCGCTATCTCCTCCACTAACTGCTGTCTTTCTTGTTGCCTCAACAGGGTCACTTGC TGTAATTACAAAAATGGTATAGCAAATAAATAAAGCTTAAAGAGGTATTCATGACAACTTAAAC AAACAATGTGACCTCTAATTGAGATTTTAAATTTGCTAGCTCCTTCTCCATAGCTTGCATACAA TCTGGCGGAAAATTCATTGAAGTTAAACCACTTATAGGACCAGTCAATGCTTGCTGCTGTAATG AGTTTAGTTCTGCTCTTAGAGATCCCGCATCCTCTTCAGCCTAATCCCAAAAGGATTCAAACGT ATTAAGGCATACTATTCCACTTCAACTCATTAAGTGAAAGAAAATTCTAGCATACCCGATACTG TTCCTCTTCTACTTCCTTCAAACGTTTCTTAATTGTACGAAGCAGAGCTGAAAGATCCTCCTAT ATTTAAACAACACGGCTCATATGAAAAAGACAGATGGATCACATATAAGGTTAATAACAATAGA ATGGTAGTAGAAATGATATGTACTCGTGCAACAACTGCTGCATCCTTTTCCATGGCAACATCCT TGAGCGCTTTTCTTAATGAAGGTATAGTGATTTGCTCCTGCACTTCCAAAGAAAAGAAAGTGAA GCCACCTATCTACTGAAAAGAGGTCTCAATATCTTGCTTAGATTCCTTCTTATTCCTCCTTTCA GCAAAGTGAAGACAAATTCAGAAAGGTTTATCATCTAAGGAAAAGGATCCAAGTGTGCAAAATA ACGTATTGTACTGGGAAACCGCAACTTAATATATTGCAGTACTATTATCTTTAATTAAGGTAAT TGCAGTGTCATGATCTCATCCATGAATGAACAATAGTGCTAGGATATGAGCAGATAAAGCCCAT ATTAATAAGGCTATGATATTTGTTTCATATATTACAATGTCTATAAATAATACTCCCTCCATCC CATAAATTTGAAGGTGTTAGACTGGGCACGGAGTAGAATGAAGGATATACTTTTGAAACCTGTA ATCTAAAACAAGTCATTAAGAATTGTGTGGCAGTAAATTGTCTCATTAAGGGTAAATAGGAGTG TCACATAAATTGAGACAAAAGGTAGTAGGAACAACGTCCACTACCTAAGTCATACTTTATCAGA GTCCTTGTATTTTATTTTATTTTTGAGAATGAACTTTATCAAAGTCTTTATATTGACTCCTAAT ACTTGCTGATTGTTAAAAGTTACAATCATTTAAGGGACATTTTCTAGCTGTTACTGTGGCGCAA CTGAGATATGGAAATGAGTGGTGTTTGAGCCTTATAAGGGGTTCTTCGATTGGGAAATTGAAGG ATGACTACCTTGCTGCAAAAATTGAGTCTGGTATCAGTAGATGCTGAAATGAGGATTCATTGCT ATGGACTGGACAGAGCAACGGTGTTTTTTATGTGCAATCCTGCTATATAATTTTGGTAACAGCA GAATTTTTTTCTCTATGGCCTTGGAAAATTTGGGAAGCCAAAATTACTATATGAAGTGGCATGT TTCAGCTGCATATTGGCTCATGATGGATACTTGACAGAGACAAATTAACAGAAAAGAGGTCTGC AGTCATGAAGCAGATGATTCCGAATTGAAGGTAGTAGGAATTCCAGCACTGTGAGGTCGTTGGT TACCTTTGATATCTCTTTTGCAGTATCTTTGGGCTGGAAGATGTTTTTAATAGACGGAACTTCA TTTGGAGCCAAACACAACCTTAGAAACTCAAGGATGACGAGTCTAATCTTCTACCCTTCTCCAC TAAAAAAGTTAAGACTTAGTTTGATTGGCACAAAGGCTTGTTACTTAGTGCTGGAAGTTTATAT GAATGAAGCATATACCATATAAAAAAAAGGGACACTATGGATTTGAATCCCATAAATTGATGAC TTTCAAATAACTGATCATATAAATTTTTTCCAGTAAGAACTTATTCTATATGGACCATTTACAT GACTGGTTTCCATTGAAGAAACTATAACTAAAATACATCATCTTTTTCCCCAGATAAATAAGTG TAAATATAACATTTGAAAGATGCATTACCAGATCGTTAAGACGTTTTTGCAACATGTTGTTCTC AACTTCTTTTGTCTGAAGCTGAAGAAGAAAATTTTAGAACAAGAGATATTCGTTAGTACATTGA CAAAAACGTATTCAAAATGAGGGAGGGAGGAAAGAATTAAATACCTTTGAGGCGAATGCTCTGT TTTCTTCATCTAGCTGTGTGTTTTGTTTTTGCACAACTTTTAATTGAGAAACTAAGGCAGTGAT ATCATTCTGCAGATGGATGTTTAACTCAAAATAAAACCTAATGGGGGTATACTGCACATTGTGA AAAGGAAATTGAGTTTACCTCTGATAGGCGAGTTGCACTCCGAGATTTTGTAATCCCCAAAACC TCTGGCAAAAAAATAAAATATTTTTGAAGATGAGAAGAATGGAGAAAAAGAAGGATTGTTGATT AAAGTTTTGTTACCAGGTTTGGCAAGATCTGGTCCAGAAGACATCTTGCTTAATCTCTCCGCTG CTCTCCTTTGACGAATTTCTTCCAACTGCATACAAACAAACAAGGTATGGAAAATGTTGTAAAT GAGAAACCAAAATTGCGGATCCTAAAATTCATACCGTTCGACGACCAAGGGAGACATGACGAGA CTCCATCAATTCCAATGCGAGGAAGGACCTTCTCCGCTGCTGCTTTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.350495871

Conservation Information
Conserved circRNAs	NA
PMCS	0.350495871

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							44428700-44425982(+)
44428677-44425950(+)
44428692-44428507(-)
						
						Potential amino acid sequence
						
							MRGRTFSAAALPETFLDITASFSSKSCF*(+)
MTRLHQFQCEEGPSPLLLCLRPFWT*(+)
MESRHVSLGRRTLEEIRQRRAAERLSKMSSGPDLAKPEVLGITKSRSATRLSENDITALVSQLK
VVQKQNTQLDEENRAFASKLQTKEVENNMLQKRLNDLEQITIPSLRKALKDVAMEKDAAVVARE
DLSALLRTIKKRLKEVEEEQYRAEEDAGSLRAELNSLQQQALTGPISGLTSMNFPPDCMQAMEK
ELANLKSQLEQVTLLRQQERQQLVEEIAHVSALNSQKQDLEEKLAVMSKKVSGKAAAEKVLPRI
GIDGVSSCLPWSSNVGRNSSKESSGEIKQDVFWTRSCQT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	44428700-44425982(+) 44428677-44425950(+) 44428692-44428507(-)
Potential amino acid sequence	MRGRTFSAAALPETFLDITASFSSKSCF(+) MTRLHQFQCEEGPSPLLLCLRPFWT(+) MESRHVSLGRRTLEEIRQRRAAERLSKMSSGPDLAKPEVLGITKSRSATRLSENDITALVSQLK VVQKQNTQLDEENRAFASKLQTKEVENNMLQKRLNDLEQITIPSLRKALKDVAMEKDAAVVARE DLSALLRTIKKRLKEVEEEQYRAEEDAGSLRAELNSLQQQALTGPISGLTSMNFPPDCMQAMEK ELANLKSQLEQVTLLRQQERQQLVEEIAHVSALNSQKQDLEEKLAVMSKKVSGKAAAEKVLPRI GIDGVSSCLPWSSNVGRNSSKESSGEIKQDVFWTRSCQT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc09g055760.2_circ_g.4

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