Plant Circular RNA Database

Detail information of Solyc03g025280.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc03g025280.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000924
					
						Alias
						Slcirc052
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr3: 2720567-2724338  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc03g025280.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc03g025280.2_circ_g.1 						
					
						Support reads
						3/19
					
						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  
						
							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
						Solyc03g025280.2.1:6

General Information
CircRNA Name	Solyc03g025280.2_circ_g.2
ID in PlantcircBase	sly_circ_000924
Alias	Slcirc052
Organism	Solanum lycopersicum
Position	chr3: 2720567-2724338 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc03g025280.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc03g025280.2_circ_g.1
Support reads	3/19
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	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	Solyc03g025280.2.1:6

			
						 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  
						
							TCAAGAGATCTATCTTCTTGCTTTTCAGGGTGCAACTGTTATCTTATCGGGTCCATCAGGTCCT
CCAGTTACAACTGTTCCAGGCCAGAATTCTGAGTTGgtatgtgccttctttcttaccacctcct
atggcaactaagggcagagatcatgagaagaaggttagtgggtgtgggtgtttgaaatctctct
ggtgcaag

									
								

					

						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
						
							GTATGTGCCTTCTTTCTTACCACCTCCTATGGCAACTAAGGGCAGAGATCATGAGAAGAAGGTT
AGTGGGTGTGGGTGTTTGAAATCTCTCTGGTGCAAGAGTTGTAAACGTATATAGTTGATTTCTA
AATATGTTGGTTTCTTCTAGCAGAAGGAGGACAAGCCGAGGGAAAAAGAGAAGGGCAAGGCTAG
GAACATTGATAATTTTATGGAGGAACTGAAACATGAGCAAGAAATGAGGGAAAGGCGTAACCAA
GACCGTGAACAGTGGCGTGATCGTCATACTGAAAATTCTGCTGTAAGTGGATTTATGATTAGCA
AAGAAAAAATGTTCAGATTATTTGTTTTAATCTTCTGTTTCTATGCTTGAATTCATGAATCAGA
TCCGAGGAGATTTGAAAAAAGACGTGATAACGTATGTTGTAATAGCTTCTATTTAGTATGAATG
CGTTAAAACTTAAGGAGTGTTGGATGCATTAAAAAAGTTGTATACAGTTTGTTACATCATGTTC
TCTCGATGATATTTGGATCTGAATCTTTTGTGGGAACTGGAGAAGTAAAATTCATTACTTAGAA
GATTACTTTACCCCTTCTAGAGTAGGTACACAAGATTTGCATTGAGTTTTACATGTACACATCT
TGTTGTAATTGCTGATGTGCTATGAGTGAGCACGATCAATTTTCTCTGAACTAGAGCAACACTT
CAACAATTATGAACTTCTATGATATTATCACATTATCACAATTTATCATACTATTTGCATCTAT
AATCCATTTCCCTTTCTTAACATCTGGCATCTAAAACATAAAACAATCCTTTCATGCATTCAGG
GATTTGGCCATCTTAAGATGAATTTTCCTTTATGTTACCCTGTGCGCATCCAAAGATGATTTTC
CTTTATGGATATGTTATATGGAGGAAGACAATTACATCTTTGATGATCCTTACTTTAACTGTAT
CATTTTCATCCACAAAAATATAAGACTCCTTGCTCTGTTACTCATTGGATCACTAAACACCCCA
AAGGCCTATCCCAGCCCTCTACTATCAGAACATGGCTCAAATGTCTAATTCTGGTCTACACATG
AAAATGTTTTAGGAAATGATCATTTGTCAATTTACTTGGAAAAGTTGTGATTTAAAATATGTTA
TGTCTAACCAAATGGAGGTTTGATATGGCATCTTGTTGTGTCATAATGATGATATTTGTATATC
CTTAAACCTTACTCTTTCCTCAGCCATCTAGTCGGTTTGATGAACTGCCCGATGACTTTGATCC
TAGTGGAAGGCCTGGATCATTTGATGATGGAGACCCACAAACGACAAATCTCTACGTAGGAAAT
CTATCACCTCAGGTAAGGTTCTTGTTTTTTATTTTGAGATCATTGTTTTTTTGCTTTAGCTGTT
TCTTTTGTTTGATACCTATTTATTTTATTTATTTGCAGGTTGATGAGAATTTTCTTTTGCGCAC
ATTTGGGAGATTTGGCCCCATTGCAAGTGTAAAAATAATGTGGCCAAGGACTGAAGAGGAAAGA
AGGCGACAGAGGAATTGCGGTTTTGTAGCTTTCATGAATAGAGCTGATGCTCAGGCTGCAAAAG
ATGAGATGGAAGGTTAGCTTCAGCTTCTTGATTTGAATGTAATTTATTTCTTGATCTGTTCTTT
TTTATCTGATGAGTGTGATTGTCTTGCTCTTTGTAGAGCACTTCTATTGAGGTCCCCTCCTTTT
CTTTTTTCTTTCCCTCCAGCCGCTTAGGAATTGTTCATTAGGTTCTTAGTGATTGACCAAGTTG
ACATTATGTATGGTTTTTTTTTTAAAGTACAGAGTTATAGGATCCTCAATGTCAAGTGGTCAGT
AGGATCAGGATGACAGTAAGTAGTTAAATAGGATATATGTTTGTTAAAAAACATACACGCGGAG
TTGCTCCCAAGGCTTTGTTCTAGTGGTAAGACCGTTACATGTGATGTGTACAGTAGGCTCATGT
CGCGGTTCAAACCCTGCCGCAAAAGAAAGATTTCGAACTGTAAAGAAAAAGAAAAACATACATG
TGGAGTCTACTATGCGTAAATGTATGAAGCGGAAAAGGAAGAAAATTCTGTAGCCAAAGGCTGT
TATATTCTGTATCAAAACATGCAAACAAATGTTGCTGATCTTATTTGTTCTAGTTGACTGTCTC
CATCCCTGTCCTTTTCTTGGGTTTCCTCTCCTTTTTCTGTGTCTATTCTGATTCCTTATTTGTT
TGAGATATACATTTTTAATAGAAGGATATTCACAAGGAACAAGGTTTTGATCAGTGATTCTACA
TTCTTTGTTTTGTCGATTGTCTTCTTCACGAAGTAGTCAAAAGAGAACTGCAGAAGTTGAGGTG
CGCGCAAGCTGACCCAGACACCACTATATGTATATTAAAAAAGCTAAGCACTAAAGTTTGTTGC
AATTATAGGTGCAAAGCACAAGCTAAGTATCAACTTTAATGAAGAAGCGCTTGTGAAGAGAGAA
CTAGAAATATGTATGTAATATAAGGAAAAAGATCTACAAACACGAACAATGATTATTTGGACTA
AATAATTGAAAAAGCTATAATTAAGCAAAACATATGAAGTAAAAATCATGTCCAAAGTTTAAAA
ACCATTTTATTCTGATTTAGAAGGAAAAAAATGTAGTTTAACTTGTATGGTTAGCTTTCTTGTA
CGAAATTTATAATAACTAATTGCTGATCACTAAATATTTGTTCAGAACCTTTTTGAACAGTTAA
TAAATTAGTTTACCAGCTATAAACTAAAGTGCTGTCCTGTTTTAGGCAAAGTCATAGTGTGAGG
TGTATGTCTTAGCATGTGAGGATTGAGACTAAAACACCACCCAAGTGTGGCAAAGCACGTAACT
TGCCTTTCACTGAGCTTCAGGCATTAGCGCCTCAACTGAGCCCTTAATAACTTTGCTTCTTAGG
TGGTGCCTCCTCTAGTTTCAGCTATGTACTCATTGCAGAAGTGTCTTTTCCATGGCCTATGTAC
ATTTTGGTATGAAGTTGGAAATTAATTAGTCGTGAGCATGTGGATGCTAGCATGTGTACTCATT
CCATGTGTACTCGCTCTATTGCTTAACATTTTGTATCTTTTGCAAGAATGTATTTTTGTTATCT
AAACCATGTTATTCTTATCCAGGAGTTATTGTTTATGAATATGAGTTGAAGATTGGGTGGGGTA
AATCTGTCTCTCTGCCTTCTCAAGCACTCCCTGCTCCTCCTCCAGGACATATGGCTATCAGGAG
TAAGGAGGTTTGTCTATTATTTTAAGTACAATGCTCTGTTATATACATGTTAAGAATTTGATAA
ATGGTCGAGTCGAGGAGTTTTTGTATTAATAATCAGTAAGTGATAGAGTGAATGGTTTGATGAG
TTATGTATGTTAAAATATTGTATGATCAGTTGAATAAATGTTATAAACAAAGACAATAGTTTGA
AGCATGTGTTCATGTTGGAGTAAGTTGTGTCTTGCATCTTTATTTGTTGGTTTGATATGTATAG
ACATCCTGTAGTGGTGTATCTCACCCTTTTCCTTGGAAATGTTTCCCATGTAATAGTCTTCTGT
TATAGCTGTAGTTCAGCAAGCTAGAGATGCTTTTTATTGTCACCTCCCGGTTTCTCTTTATGAT
ATCAGCTTATGCTCATGTACTTATTCAAGAGATCTATCTTCTTGCTTTTCAGGGTGCAACTGTT
ATCTTATCGGGTCCATCAGGTCCTCCAGTTACAACTGTTCCAGGCCAGAATTCTGAGTTG
						
					

			
		

Sequences
Splice junction sequence	TCAAGAGATCTATCTTCTTGCTTTTCAGGGTGCAACTGTTATCTTATCGGGTCCATCAGGTCCT CCAGTTACAACTGTTCCAGGCCAGAATTCTGAGTTGgtatgtgccttctttcttaccacctcct atggcaactaagggcagagatcatgagaagaaggttagtgggtgtgggtgtttgaaatctctct ggtgcaag
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	GTATGTGCCTTCTTTCTTACCACCTCCTATGGCAACTAAGGGCAGAGATCATGAGAAGAAGGTT AGTGGGTGTGGGTGTTTGAAATCTCTCTGGTGCAAGAGTTGTAAACGTATATAGTTGATTTCTA AATATGTTGGTTTCTTCTAGCAGAAGGAGGACAAGCCGAGGGAAAAAGAGAAGGGCAAGGCTAG GAACATTGATAATTTTATGGAGGAACTGAAACATGAGCAAGAAATGAGGGAAAGGCGTAACCAA GACCGTGAACAGTGGCGTGATCGTCATACTGAAAATTCTGCTGTAAGTGGATTTATGATTAGCA AAGAAAAAATGTTCAGATTATTTGTTTTAATCTTCTGTTTCTATGCTTGAATTCATGAATCAGA TCCGAGGAGATTTGAAAAAAGACGTGATAACGTATGTTGTAATAGCTTCTATTTAGTATGAATG CGTTAAAACTTAAGGAGTGTTGGATGCATTAAAAAAGTTGTATACAGTTTGTTACATCATGTTC TCTCGATGATATTTGGATCTGAATCTTTTGTGGGAACTGGAGAAGTAAAATTCATTACTTAGAA GATTACTTTACCCCTTCTAGAGTAGGTACACAAGATTTGCATTGAGTTTTACATGTACACATCT TGTTGTAATTGCTGATGTGCTATGAGTGAGCACGATCAATTTTCTCTGAACTAGAGCAACACTT CAACAATTATGAACTTCTATGATATTATCACATTATCACAATTTATCATACTATTTGCATCTAT AATCCATTTCCCTTTCTTAACATCTGGCATCTAAAACATAAAACAATCCTTTCATGCATTCAGG GATTTGGCCATCTTAAGATGAATTTTCCTTTATGTTACCCTGTGCGCATCCAAAGATGATTTTC CTTTATGGATATGTTATATGGAGGAAGACAATTACATCTTTGATGATCCTTACTTTAACTGTAT CATTTTCATCCACAAAAATATAAGACTCCTTGCTCTGTTACTCATTGGATCACTAAACACCCCA AAGGCCTATCCCAGCCCTCTACTATCAGAACATGGCTCAAATGTCTAATTCTGGTCTACACATG AAAATGTTTTAGGAAATGATCATTTGTCAATTTACTTGGAAAAGTTGTGATTTAAAATATGTTA TGTCTAACCAAATGGAGGTTTGATATGGCATCTTGTTGTGTCATAATGATGATATTTGTATATC CTTAAACCTTACTCTTTCCTCAGCCATCTAGTCGGTTTGATGAACTGCCCGATGACTTTGATCC TAGTGGAAGGCCTGGATCATTTGATGATGGAGACCCACAAACGACAAATCTCTACGTAGGAAAT CTATCACCTCAGGTAAGGTTCTTGTTTTTTATTTTGAGATCATTGTTTTTTTGCTTTAGCTGTT TCTTTTGTTTGATACCTATTTATTTTATTTATTTGCAGGTTGATGAGAATTTTCTTTTGCGCAC ATTTGGGAGATTTGGCCCCATTGCAAGTGTAAAAATAATGTGGCCAAGGACTGAAGAGGAAAGA AGGCGACAGAGGAATTGCGGTTTTGTAGCTTTCATGAATAGAGCTGATGCTCAGGCTGCAAAAG ATGAGATGGAAGGTTAGCTTCAGCTTCTTGATTTGAATGTAATTTATTTCTTGATCTGTTCTTT TTTATCTGATGAGTGTGATTGTCTTGCTCTTTGTAGAGCACTTCTATTGAGGTCCCCTCCTTTT CTTTTTTCTTTCCCTCCAGCCGCTTAGGAATTGTTCATTAGGTTCTTAGTGATTGACCAAGTTG ACATTATGTATGGTTTTTTTTTTAAAGTACAGAGTTATAGGATCCTCAATGTCAAGTGGTCAGT AGGATCAGGATGACAGTAAGTAGTTAAATAGGATATATGTTTGTTAAAAAACATACACGCGGAG TTGCTCCCAAGGCTTTGTTCTAGTGGTAAGACCGTTACATGTGATGTGTACAGTAGGCTCATGT CGCGGTTCAAACCCTGCCGCAAAAGAAAGATTTCGAACTGTAAAGAAAAAGAAAAACATACATG TGGAGTCTACTATGCGTAAATGTATGAAGCGGAAAAGGAAGAAAATTCTGTAGCCAAAGGCTGT TATATTCTGTATCAAAACATGCAAACAAATGTTGCTGATCTTATTTGTTCTAGTTGACTGTCTC CATCCCTGTCCTTTTCTTGGGTTTCCTCTCCTTTTTCTGTGTCTATTCTGATTCCTTATTTGTT TGAGATATACATTTTTAATAGAAGGATATTCACAAGGAACAAGGTTTTGATCAGTGATTCTACA TTCTTTGTTTTGTCGATTGTCTTCTTCACGAAGTAGTCAAAAGAGAACTGCAGAAGTTGAGGTG CGCGCAAGCTGACCCAGACACCACTATATGTATATTAAAAAAGCTAAGCACTAAAGTTTGTTGC AATTATAGGTGCAAAGCACAAGCTAAGTATCAACTTTAATGAAGAAGCGCTTGTGAAGAGAGAA CTAGAAATATGTATGTAATATAAGGAAAAAGATCTACAAACACGAACAATGATTATTTGGACTA AATAATTGAAAAAGCTATAATTAAGCAAAACATATGAAGTAAAAATCATGTCCAAAGTTTAAAA ACCATTTTATTCTGATTTAGAAGGAAAAAAATGTAGTTTAACTTGTATGGTTAGCTTTCTTGTA CGAAATTTATAATAACTAATTGCTGATCACTAAATATTTGTTCAGAACCTTTTTGAACAGTTAA TAAATTAGTTTACCAGCTATAAACTAAAGTGCTGTCCTGTTTTAGGCAAAGTCATAGTGTGAGG TGTATGTCTTAGCATGTGAGGATTGAGACTAAAACACCACCCAAGTGTGGCAAAGCACGTAACT TGCCTTTCACTGAGCTTCAGGCATTAGCGCCTCAACTGAGCCCTTAATAACTTTGCTTCTTAGG TGGTGCCTCCTCTAGTTTCAGCTATGTACTCATTGCAGAAGTGTCTTTTCCATGGCCTATGTAC ATTTTGGTATGAAGTTGGAAATTAATTAGTCGTGAGCATGTGGATGCTAGCATGTGTACTCATT CCATGTGTACTCGCTCTATTGCTTAACATTTTGTATCTTTTGCAAGAATGTATTTTTGTTATCT AAACCATGTTATTCTTATCCAGGAGTTATTGTTTATGAATATGAGTTGAAGATTGGGTGGGGTA AATCTGTCTCTCTGCCTTCTCAAGCACTCCCTGCTCCTCCTCCAGGACATATGGCTATCAGGAG TAAGGAGGTTTGTCTATTATTTTAAGTACAATGCTCTGTTATATACATGTTAAGAATTTGATAA ATGGTCGAGTCGAGGAGTTTTTGTATTAATAATCAGTAAGTGATAGAGTGAATGGTTTGATGAG TTATGTATGTTAAAATATTGTATGATCAGTTGAATAAATGTTATAAACAAAGACAATAGTTTGA AGCATGTGTTCATGTTGGAGTAAGTTGTGTCTTGCATCTTTATTTGTTGGTTTGATATGTATAG ACATCCTGTAGTGGTGTATCTCACCCTTTTCCTTGGAAATGTTTCCCATGTAATAGTCTTCTGT TATAGCTGTAGTTCAGCAAGCTAGAGATGCTTTTTATTGTCACCTCCCGGTTTCTCTTTATGAT ATCAGCTTATGCTCATGTACTTATTCAAGAGATCTATCTTCTTGCTTTTCAGGGTGCAACTGTT ATCTTATCGGGTCCATCAGGTCCTCCAGTTACAACTGTTCCAGGCCAGAATTCTGAGTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.148057852

Conservation Information
Conserved circRNAs	NA
PMCS	0.148057852

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2720596-2720602(+)
						
						Potential amino acid sequence
						
							MATKGRDHEKKKEDKPREKEKGKARNIDNFMEELKHEQEMRERRNQDREQWRDRHTENSAPSSR
FDELPDDFDPSGRPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEE
RRRQRNCGFVAFMNRADAQAAKDEMEGVIVYEYELKIGWGKSVSLPSQALPAPPPGHMAIRSKE
GATVILSGPSGPPVTTVPGQNSELVCAFFLTTSYGN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2720596-2720602(+)
Potential amino acid sequence	MATKGRDHEKKKEDKPREKEKGKARNIDNFMEELKHEQEMRERRNQDREQWRDRHTENSAPSSR FDELPDDFDPSGRPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEE RRRQRNCGFVAFMNRADAQAAKDEMEGVIVYEYELKIGWGKSVSLPSQALPAPPPGHMAIRSKE GATVILSGPSGPPVTTVPGQNSELVCAFFLTTSYGN*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Wang et al., 2018b

circRNA

Detail information of Solyc03g025280.2_circ_g.2

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