Plant Circular RNA Database

Detail information of Solyc10g006890.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc10g006890.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_003044
					
						Alias
						10:1328362|1329697, Slcirc148
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr10: 1328362-1329697  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, circseq_cup
					
						Parent gene
						
							Solyc10g006890.2						
					
						Parent gene annotation
						
							nontranslating_CDS
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc10g006890.2_circ_g.1 Solyc10g006890.2_circ_g.2 Solyc10g006890.2_circ_g.4 Solyc10g006890.2_circ_g.5 Solyc10g006890.2_circ_g.6 Solyc10g006890.2_circ_g.7 Solyc10g006890.2_circ_g.8 						
					
						Support reads
						932/521
					
						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
						Solyc10g006890.2.1:4

General Information
CircRNA Name	Solyc10g006890.2_circ_g.3
ID in PlantcircBase	sly_circ_003044
Alias	10:1328362\|1329697, Slcirc148
Organism	Solanum lycopersicum
Position	chr10: 1328362-1329697 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI, circseq_cup
Parent gene	Solyc10g006890.2
Parent gene annotation	nontranslating_CDS
Parent gene strand	+
Alternative splicing	Solyc10g006890.2_circ_g.1 Solyc10g006890.2_circ_g.2 Solyc10g006890.2_circ_g.4 Solyc10g006890.2_circ_g.5 Solyc10g006890.2_circ_g.6 Solyc10g006890.2_circ_g.7 Solyc10g006890.2_circ_g.8
Support reads	932/521
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	Solyc10g006890.2.1:4

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: CATCAACAGGGTTAAACTGG
 R: GCATATGGAGCATTCCTGAGC
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	Yes 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	F: CATCAACAGGGTTAAACTGG R: GCATATGGAGCATTCCTGAGC 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  
						
							GAACAGTTTGTGCCAGGAAGTATGTCACAAGTGCTTATAACATCTGCAGACTCAAGAATTCGGG
TTGTGGATGATGCTGATCTTTTTCACAAGTTCAAAGtaacctgcatccagtttaaccctgttga
tgatagatacttcatcagtggctccctagatgctaaggttcgcatatggagcattcctgagcgg
caagttgt

									
								

					

						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: 387
Transcript exons: 1328362-1328519,1328650-1328701,1328802-1328884,1329604-
1329697
TAACCTGCATCCAGTTTAACCCTGTTGATGATAGATACTTCATCAGTGGCTCCCTAGATGCTAA
GGTTCGCATATGGAGCATTCCTGAGCGGCAAGTTGTTGATTGGAATGATCTGCATGAGATGGTC
ACTGCTGCTTGCTACACACCAGATGGTCAGGGGGCACTTGTTGGGTCATACAAGGGGAGCTGTC
ATTTGTACAACATATTAGATAATAAATTGCAGCAAAAAGCTCAAATCAATCTGCAGAATAAGAA
GAAGAGGACTCACCAAAGGAAAATTACTGGTTTCCAGTTTGTGCCAGGAAGTATGTCACAAGTG
CTTATAACATCTGCAGACTCAAGAATTCGGGTTGTGGATGATGCTGATCTTTTTCACAAGTTCA
AAG
						
					

						Genomic sequence
						
							TAACCTGCATCCAGTTTAACCCTGTTGATGATAGATACTTCATCAGTGGCTCCCTAGATGCTAA
GGTTCGCATATGGAGCATTCCTGAGCGGCAAGTTGTTGATTGGAATGATCTGCATGAGATGGTC
ACTGCTGCTTGCTACACACCAGATGGTCAGGTGAGACTCTGCTAAACATAGAGCTCGCTTTGAT
GTTGTGCCAAACCTAATAAAGGTGAAAACTAGGTGTTTTTTATCTGCATATTTCACAGTTAAGT
TTCTAAAGTGTTTTTGTTTCTTATTTTTCAAGGGGGCACTTGTTGGGTCATACAAGGGGAGCTG
TCATTTGTACAACATATTAGGTTTGATTTATTGTGCCTTTCCTGTCTCTCTTATTCCCTTCTTC
TGTAGAGGAAAGTTATGTACTTGCACGTGTTGATAATTTATGCTTCTCTCTTTCAGATAATAAA
TTGCAGCAAAAAGCTCAAATCAATCTGCAGAATAAGAAGAAGAGGACTCACCAAAGGAAAATTA
CTGGTTTCCAGGTACAGTAACTTTGATTGATTGCTGATGCTGGAGCTTATCTGTGCTAGCTCAG
ATATGCCGCCTCTATTATCCCAGATGCAGTTATTCGAAGACGCGAAGTACTTCTCTTGTATTAA
CAAGATACTGTGCATGTGTTATGTATGTGCATATTTTAAACCAACTTTTAACTGTTTACTGCTG
TTATATTCTAAAAGGCAAAGTAAATAATTTGTGAAGGTTTTTTTCAAGCTAAAGAAAATAACAA
AAATACTGAATAATGAGTAAAAAATAGGAAGTAGGGTACACATACAAATAGGTGTTTGCACTTT
CTAGTGGTATAGATTAGGAGCTAAATTCTCTCCCCAGAGAGCAGGAAAAGTGAGATGGCAAAAA
GTGATGAATCATCGCTAAAACCCTTTATCATGCTATTTAATTCATAATCCAATTTTACTTGGCT
CAGTTATTGATGTAAAGTTGAATTATATCATACGTAAATATAATTTGGTCAATATATTTGAGAT
AAGATTACATGTTTGAAGAATTGGGACTTCTCTAGAGTATAGAATTGAGTCTCACATACATATT
GCACATAAAGATATTGAAAAGTAAAGGAAAAAGTTAACTTTGGGACAATCCAAAATAGGAAGTA
GGGCAAAATTTGTAATGGATGAAGCAATCCAAGTAAATTTTTGTCCTTACCTTGTGTGCTAATT
AGTAACTTATATTTCTTAATGAACAGTTTGTGCCAGGAAGTATGTCACAAGTGCTTATAACATC
TGCAGACTCAAGAATTCGGGTTGTGGATGATGCTGATCTTTTTCACAAGTTCAAAG
						
					

			
		

Sequences
Splice junction sequence	GAACAGTTTGTGCCAGGAAGTATGTCACAAGTGCTTATAACATCTGCAGACTCAAGAATTCGGG TTGTGGATGATGCTGATCTTTTTCACAAGTTCAAAGtaacctgcatccagtttaaccctgttga tgatagatacttcatcagtggctccctagatgctaaggttcgcatatggagcattcctgagcgg caagttgt
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: 387 Transcript exons: 1328362-1328519,1328650-1328701,1328802-1328884,1329604- 1329697 TAACCTGCATCCAGTTTAACCCTGTTGATGATAGATACTTCATCAGTGGCTCCCTAGATGCTAA GGTTCGCATATGGAGCATTCCTGAGCGGCAAGTTGTTGATTGGAATGATCTGCATGAGATGGTC ACTGCTGCTTGCTACACACCAGATGGTCAGGGGGCACTTGTTGGGTCATACAAGGGGAGCTGTC ATTTGTACAACATATTAGATAATAAATTGCAGCAAAAAGCTCAAATCAATCTGCAGAATAAGAA GAAGAGGACTCACCAAAGGAAAATTACTGGTTTCCAGTTTGTGCCAGGAAGTATGTCACAAGTG CTTATAACATCTGCAGACTCAAGAATTCGGGTTGTGGATGATGCTGATCTTTTTCACAAGTTCA AAG
Genomic sequence	TAACCTGCATCCAGTTTAACCCTGTTGATGATAGATACTTCATCAGTGGCTCCCTAGATGCTAA GGTTCGCATATGGAGCATTCCTGAGCGGCAAGTTGTTGATTGGAATGATCTGCATGAGATGGTC ACTGCTGCTTGCTACACACCAGATGGTCAGGTGAGACTCTGCTAAACATAGAGCTCGCTTTGAT GTTGTGCCAAACCTAATAAAGGTGAAAACTAGGTGTTTTTTATCTGCATATTTCACAGTTAAGT TTCTAAAGTGTTTTTGTTTCTTATTTTTCAAGGGGGCACTTGTTGGGTCATACAAGGGGAGCTG TCATTTGTACAACATATTAGGTTTGATTTATTGTGCCTTTCCTGTCTCTCTTATTCCCTTCTTC TGTAGAGGAAAGTTATGTACTTGCACGTGTTGATAATTTATGCTTCTCTCTTTCAGATAATAAA TTGCAGCAAAAAGCTCAAATCAATCTGCAGAATAAGAAGAAGAGGACTCACCAAAGGAAAATTA CTGGTTTCCAGGTACAGTAACTTTGATTGATTGCTGATGCTGGAGCTTATCTGTGCTAGCTCAG ATATGCCGCCTCTATTATCCCAGATGCAGTTATTCGAAGACGCGAAGTACTTCTCTTGTATTAA CAAGATACTGTGCATGTGTTATGTATGTGCATATTTTAAACCAACTTTTAACTGTTTACTGCTG TTATATTCTAAAAGGCAAAGTAAATAATTTGTGAAGGTTTTTTTCAAGCTAAAGAAAATAACAA AAATACTGAATAATGAGTAAAAAATAGGAAGTAGGGTACACATACAAATAGGTGTTTGCACTTT CTAGTGGTATAGATTAGGAGCTAAATTCTCTCCCCAGAGAGCAGGAAAAGTGAGATGGCAAAAA GTGATGAATCATCGCTAAAACCCTTTATCATGCTATTTAATTCATAATCCAATTTTACTTGGCT CAGTTATTGATGTAAAGTTGAATTATATCATACGTAAATATAATTTGGTCAATATATTTGAGAT AAGATTACATGTTTGAAGAATTGGGACTTCTCTAGAGTATAGAATTGAGTCTCACATACATATT GCACATAAAGATATTGAAAAGTAAAGGAAAAAGTTAACTTTGGGACAATCCAAAATAGGAAGTA GGGCAAAATTTGTAATGGATGAAGCAATCCAAGTAAATTTTTGTCCTTACCTTGTGTGCTAATT AGTAACTTATATTTCTTAATGAACAGTTTGTGCCAGGAAGTATGTCACAAGTGCTTATAACATC TGCAGACTCAAGAATTCGGGTTGTGGATGATGCTGATCTTTTTCACAAGTTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.190156239

Conservation Information
Conserved circRNAs	NA
PMCS	1.190156239

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1328485-1329694(+)
1328445-1329686(-)
						
						Potential amino acid sequence
						
							MVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGSMS
QVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWNDLH
EMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGSM
SQVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWNDL
HEMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGS
MSQVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWND
LHEMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPG
SMSQVLITSADSRIRVVDDADLFHKFK(+)
MLHMRTLASREPLMKYLSSTGLNWMQVTLNL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1328485-1329694(+) 1328445-1329686(-)
Potential amino acid sequence	MVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGSMS QVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWNDLH EMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGSM SQVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWNDL HEMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPGS MSQVLITSADSRIRVVDDADLFHKFKVTCIQFNPVDDRYFISGSLDAKVRIWSIPERQVVDWND LHEMVTAACYTPDGQGALVGSYKGSCHLYNILDNKLQQKAQINLQNKKKRTHQRKITGFQFVPG SMSQVLITSADSRIRVVDDADLFHKFK(+) MLHMRTLASREPLMKYLSSTGLNWMQVTLNL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Solyc10g006890.2_circ_g.3

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