Plant Circular RNA Database

Detail information of Solyc01g010930.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc01g010930.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000087
					
						Alias
						1:6462808|6464408, Slcirc015
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 6462808-6464408  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc01g010930.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g010930.2_circ_g.1 Solyc01g010930.2_circ_g.2 						
					
						Support reads
						24/50
					
						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
						Solyc01g010930.2.1:4

General Information
CircRNA Name	Solyc01g010930.2_circ_g.3
ID in PlantcircBase	sly_circ_000087
Alias	1:6462808\|6464408, Slcirc015
Organism	Solanum lycopersicum
Position	chr1: 6462808-6464408 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc01g010930.2
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	Solyc01g010930.2_circ_g.1 Solyc01g010930.2_circ_g.2
Support reads	24/50
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	Solyc01g010930.2.1:4

			
						 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  
						
							ATATAAAAAGAAAAAGCGGGAAAAAGACCAACCGCCGCACGCATTTGGTTCAAACCACCATTGC
AGGACACTTGAAGAAACCCATTACTTGTATAATTTCcttaactgtttgagctcctctgcttcct
cctctgtgcagccttcagtgcaaccagagaaagccaacatatccatctcataccgtaaatgcaa
tgctacaa

									
								

					

						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: 610
Transcript exons: 6462808-6463097,6463857-6464019,6464099-6464187,6464341-
6464408
CTTAACTGTTTGAGCTCCTCTGCTTCCTCCTCTGTGCAGCCTTCAGTGCAACCAGAGAAAGCCA
ACATATCCATCTCATACCGTAAATGCAATGCTACAAATGGTCCTCTCTGCTGAAGCATATGGAC
TAACTTTTGTCCCAATGCCTCAATCTTCTGTGTGAATTTCAGAGCGTGAAAATTGACCTGACAT
CTAAGTCTCTGAAGCTCAAGAGGGATCCCGTTATTTGCTAGCCTAGTATCTGTCCTGTTGAAGT
TTACAACCTGATGCTTGCTGAAGAGAGGCAGTATCTGTTGCAAGTAGTACTTTTCACTTGACCA
ACTAACAGGAGGCATTACTACTGGATGGTATCCATAGCTCCTTGCAACTTTCTTTGGCAGTCTC
TTTATTATGTTGACTTCATCTCTTAATGAATCAATGAAGTGTCTCACATCAAAAATATCCTCAA
AATTGCTAGGATCTGCCCAGAATGATGATTTATCAAGCTCTGGGACAACCAGCGTTAAATTTAA
AAGCCGTGCAACAGTCACCATGTCACAAATCGCCGCACGCATTTGGTTCAAACCACCATTGCAG
GACACTTGAAGAAACCCATTACTTGTATAATTTC
						
					

						Genomic sequence
						
							CTTAACTGTTTGAGCTCCTCTGCTTCCTCCTCTGTGCAGCCTTCAGTGCAACCAGAGAAAGCCA
ACATATCCATCTCATACCGTAAATGCAATGCTACAAATGGTCCTCTCTGCTGAAGCATATGGAC
TAACTTTTGTCCCAATGCCTCAATCTTCTGTGTGAATTTCAGAGCGTGAAAATTGACCTGACAT
CTAAGTCTCTGAAGCTCAAGAGGGATCCCGTTATTTGCTAGCCTAGTATCTGTCCTGTTGAAGT
TTACAACCTGATGCTTGCTGAAGAGAGGCAGTATCTGTTAATACATATAAAACGCATTATAGTA
GGATCTTTTACCGTTAAATAACATGTAAATGTTCAGTGTGTGACAGAAGGAATATCAGTAATCA
AGGCTACTGATATTTAATGACTACGAATTCATCGTTCGACTACATACTGATTAATGTCAAAGTA
GTATACACACATAGCAACAACATCACTTAGTCAAAACTTGTGAAGTGAAAGTACTTGTACAGAA
GCCAGCTTGGCTTAACTGATAAGTTTTAGGTGAATTTTGATAAGTAAGCAGTTATGAATTACGT
GCTAGAAGTGATGAAACAGAACATAAGTAGTCAATATACTTGGAAAAAAACTGCTGATAAGCTA
GTCTTTTGTTAAAATGCCCTTAAAATTTTTACCAATAATTAAAAATTTAAATGTATCGTTGCAA
AGAAGAGAAACGATAGATATGGGGTGAAGAAGAAGTCCTGGGTTGGTCAAACTAAGAGTGCTTA
TAAGTTGAAAAGCCATAAGTTGGAGATGACCATCTTAGAGCTTATGATTAATTTTGGCTTATAC
GCACTTAGTATTTACCAAAAGCGTAGACAAGCCAAAAATTCGTTATAAATCAGTTTAACCAGCT
TGTCAGCTTAGCCAAACGCCCTTGGTCTTCTAAATGATGACAAATAATATTGTTGCACAACCAT
GAAGAACAACTAGTTCGGTAAGGTCAATCATGCATCTACCAGTTAACAAATTATATGATAATAA
CGTACTCCAGAACAAATAGACCAACCTGTTGCAAGTAGTACTTTTCACTTGACCAACTAACAGG
AGGCATTACTACTGGATGGTATCCATAGCTCCTTGCAACTTTCTTTGGCAGTCTCTTTATTATG
TTGACTTCATCTCTTAATGAATCAATGAAGTGTCTCACATCAAAAATATCCTCAAAATTGCTGC
CAAGATATGCTGCAGTTATTATAAATCACTAAGCAACAGGACAAAGGAAACAGCAGTACATAAC
ACCAGAATTACCTAGGATCTGCCCAGAATGATGATTTATCAAGCTCTGGGACAACCAGCGTTAA
ATTTAAAAGCCGTGCAACAGTCACCATGTCACAAATCTACATTCAAATTGGCTGAATTTATCAG
GTTAGGAGTTTGTATCAAAATTTTGTGGGTCTAATTCAATTTGAATGCACTTGTACAATTTCCA
ACTTCCTCAACGCCAAAAAGAGAAAATTGATATAAAAAGAAAAAGCGGGAAAAAGACCAACCGC
CGCACGCATTTGGTTCAAACCACCATTGCAGGACACTTGAAGAAACCCATTACTTGTATAATTT
C
						
					

			
		

Sequences
Splice junction sequence	ATATAAAAAGAAAAAGCGGGAAAAAGACCAACCGCCGCACGCATTTGGTTCAAACCACCATTGC AGGACACTTGAAGAAACCCATTACTTGTATAATTTCcttaactgtttgagctcctctgcttcct cctctgtgcagccttcagtgcaaccagagaaagccaacatatccatctcataccgtaaatgcaa tgctacaa
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: 610 Transcript exons: 6462808-6463097,6463857-6464019,6464099-6464187,6464341- 6464408 CTTAACTGTTTGAGCTCCTCTGCTTCCTCCTCTGTGCAGCCTTCAGTGCAACCAGAGAAAGCCA ACATATCCATCTCATACCGTAAATGCAATGCTACAAATGGTCCTCTCTGCTGAAGCATATGGAC TAACTTTTGTCCCAATGCCTCAATCTTCTGTGTGAATTTCAGAGCGTGAAAATTGACCTGACAT CTAAGTCTCTGAAGCTCAAGAGGGATCCCGTTATTTGCTAGCCTAGTATCTGTCCTGTTGAAGT TTACAACCTGATGCTTGCTGAAGAGAGGCAGTATCTGTTGCAAGTAGTACTTTTCACTTGACCA ACTAACAGGAGGCATTACTACTGGATGGTATCCATAGCTCCTTGCAACTTTCTTTGGCAGTCTC TTTATTATGTTGACTTCATCTCTTAATGAATCAATGAAGTGTCTCACATCAAAAATATCCTCAA AATTGCTAGGATCTGCCCAGAATGATGATTTATCAAGCTCTGGGACAACCAGCGTTAAATTTAA AAGCCGTGCAACAGTCACCATGTCACAAATCGCCGCACGCATTTGGTTCAAACCACCATTGCAG GACACTTGAAGAAACCCATTACTTGTATAATTTC
Genomic sequence	CTTAACTGTTTGAGCTCCTCTGCTTCCTCCTCTGTGCAGCCTTCAGTGCAACCAGAGAAAGCCA ACATATCCATCTCATACCGTAAATGCAATGCTACAAATGGTCCTCTCTGCTGAAGCATATGGAC TAACTTTTGTCCCAATGCCTCAATCTTCTGTGTGAATTTCAGAGCGTGAAAATTGACCTGACAT CTAAGTCTCTGAAGCTCAAGAGGGATCCCGTTATTTGCTAGCCTAGTATCTGTCCTGTTGAAGT TTACAACCTGATGCTTGCTGAAGAGAGGCAGTATCTGTTAATACATATAAAACGCATTATAGTA GGATCTTTTACCGTTAAATAACATGTAAATGTTCAGTGTGTGACAGAAGGAATATCAGTAATCA AGGCTACTGATATTTAATGACTACGAATTCATCGTTCGACTACATACTGATTAATGTCAAAGTA GTATACACACATAGCAACAACATCACTTAGTCAAAACTTGTGAAGTGAAAGTACTTGTACAGAA GCCAGCTTGGCTTAACTGATAAGTTTTAGGTGAATTTTGATAAGTAAGCAGTTATGAATTACGT GCTAGAAGTGATGAAACAGAACATAAGTAGTCAATATACTTGGAAAAAAACTGCTGATAAGCTA GTCTTTTGTTAAAATGCCCTTAAAATTTTTACCAATAATTAAAAATTTAAATGTATCGTTGCAA AGAAGAGAAACGATAGATATGGGGTGAAGAAGAAGTCCTGGGTTGGTCAAACTAAGAGTGCTTA TAAGTTGAAAAGCCATAAGTTGGAGATGACCATCTTAGAGCTTATGATTAATTTTGGCTTATAC GCACTTAGTATTTACCAAAAGCGTAGACAAGCCAAAAATTCGTTATAAATCAGTTTAACCAGCT TGTCAGCTTAGCCAAACGCCCTTGGTCTTCTAAATGATGACAAATAATATTGTTGCACAACCAT GAAGAACAACTAGTTCGGTAAGGTCAATCATGCATCTACCAGTTAACAAATTATATGATAATAA CGTACTCCAGAACAAATAGACCAACCTGTTGCAAGTAGTACTTTTCACTTGACCAACTAACAGG AGGCATTACTACTGGATGGTATCCATAGCTCCTTGCAACTTTCTTTGGCAGTCTCTTTATTATG TTGACTTCATCTCTTAATGAATCAATGAAGTGTCTCACATCAAAAATATCCTCAAAATTGCTGC CAAGATATGCTGCAGTTATTATAAATCACTAAGCAACAGGACAAAGGAAACAGCAGTACATAAC ACCAGAATTACCTAGGATCTGCCCAGAATGATGATTTATCAAGCTCTGGGACAACCAGCGTTAA ATTTAAAAGCCGTGCAACAGTCACCATGTCACAAATCTACATTCAAATTGGCTGAATTTATCAG GTTAGGAGTTTGTATCAAAATTTTGTGGGTCTAATTCAATTTGAATGCACTTGTACAATTTCCA ACTTCCTCAACGCCAAAAAGAGAAAATTGATATAAAAAGAAAAAGCGGGAAAAAGACCAACCGC CGCACGCATTTGGTTCAAACCACCATTGCAGGACACTTGAAGAAACCCATTACTTGTATAATTT C

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.854985814

Conservation Information
Conserved circRNAs	NA
PMCS	0.854985814

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6464116-6462921(+)
6464354-6464395(-)
						
						Potential amino acid sequence
						
							MMIYQALGQPALNLKAVQQSPCHKSPHAFGSNHHCRTLEETHYLYNFLNCLSSSASSSVQPSVQ
PEKANISISYRKCNATNGPLC*(+)
MRAAICDMVTVARLLNLTLVVPELDKSSFWADPSNFEDIFDVRHFIDSLRDEVNIIKRLPKKVA
RSYGYHPVVMPPVSWSSEKYYLQQILPLFSKHQVVNFNRTDTRLANNGIPLELQRLRCQVNFHA
LKFTQKIEALGQKLVHMLQQRGPFVALHLRYEMDMLAFSGCTEGCTEEEAEELKQLRKLYK*(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6464116-6462921(+) 6464354-6464395(-)
Potential amino acid sequence	MMIYQALGQPALNLKAVQQSPCHKSPHAFGSNHHCRTLEETHYLYNFLNCLSSSASSSVQPSVQ PEKANISISYRKCNATNGPLC(+) MRAAICDMVTVARLLNLTLVVPELDKSSFWADPSNFEDIFDVRHFIDSLRDEVNIIKRLPKKVA RSYGYHPVVMPPVSWSSEKYYLQQILPLFSKHQVVNFNRTDTRLANNGIPLELQRLRCQVNFHA LKFTQKIEALGQKLVHMLQQRGPFVALHLRYEMDMLAFSGCTEGCTEEEAEELKQLRKLYK(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016; Tan et al., 2017; Yin et al., 2018; Wang et al., 2018b

circRNA

Detail information of Solyc01g010930.2_circ_g.3

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