Plant Circular RNA Database

Detail information of Solyc07g006120.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc07g006120.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002179
					
						Alias
						7:976732|977512, Slcirc119
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 976732-977512  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI, circseq_cup
					
						Parent gene
						
							Solyc07g006120.2						
					
						Parent gene annotation
						
							Autophagy-related protein 18b
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc07g006120.2_circ_g.1 Solyc07g006120.2_circ_g.3 						
					
						Support reads
						7/20
					
						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
						Solyc07g006120.2.1:3

General Information
CircRNA Name	Solyc07g006120.2_circ_g.2
ID in PlantcircBase	sly_circ_002179
Alias	7:976732\|977512, Slcirc119
Organism	Solanum lycopersicum
Position	chr7: 976732-977512 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI, circseq_cup
Parent gene	Solyc07g006120.2
Parent gene annotation	Autophagy-related protein 18b
Parent gene strand	+
Alternative splicing	Solyc07g006120.2_circ_g.1 Solyc07g006120.2_circ_g.3
Support reads	7/20
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	Solyc07g006120.2.1:3

			
						 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  
						
							ATTGGCAGTCTTGAGTCTTTCATCAGGTGGAACTCACATTGCAACAGCATCTGAACAAGGGACC
ATGATCAGAATTCATCTCGTTTCAGATGCAACTAAGattgattgtcatattgcaggagaagaca
tttatttatgatataaatagtcttaagatactggacacaattgatacggtgccgaatccaaaag
gtctgttt

						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: 325
Transcript exons: 976732-976823,977078-977190,977393-977512
ATTGATTGTCATATTGCAGGAGAAGACATTTATTTATGATATAAATAGTCTTAAGATACTGGAC
ACAATTGATACGGTGCCGAATCCAAAAGGACTTTGTGCATTTTCACCCAGCTTGGATGGTTCAT
TTCTGGCCCTTCCAGCAAGTACAACCAAAGGATCTTTGCTAGTCTATAATGTTTCCGATCTCCG
TTTGCACTGTGAGATAGACGCTCATCGCTCACCATTGGCAGTCTTGAGTCTTTCATCAGGTGGA
ACTCACATTGCAACAGCATCTGAACAAGGGACCATGATCAGAATTCATCTCGTTTCAGATGCAA
CTAAG
						
						Genomic sequence
						
							ATTGATTGTCATATTGCAGGAGAAGACATTTATTTATGATATAAATAGTCTTAAGATACTGGAC
ACAATTGATACGGTGCCGAATCCAAAAGGTCTGTTTGGAAGTTTCTTGTTCAAGTTTTAATGGC
TCACTGCCAATCTTGTTTACTAGATGGATTAGAACATGACTCGCATAATATTCGAGATGACATT
CCCCACCCCGCTTAAAAATATCAACAGAAAAGGAAAGAATAAAAGAACTCACTGTGTTATACCT
TTCAAGTTTTTGTTTAATGAGTGGATGCTATAACATTTCCAGTTGGCCTTGCACATTTTCTTAT
CAACGAGTTCTTGTTTCAATTTTCAGGACTTTGTGCATTTTCACCCAGCTTGGATGGTTCATTT
CTGGCCCTTCCAGCAAGTACAACCAAAGGATCTTTGCTAGTCTATAATGTTTCCGATCTCCGTT
TGCACTGTGAGGTCGTGTTTCTTACTTGTATGTATTGATATTACGCAATCATCTATAACAAGAT
CAACGGGTTTGAGTTGTTATACATCATAATTTTGAAGAGTCCAGCATTTTCCTAGCTTTAAACC
AACTATTTCACCAGCATTTTCTCTTTCTTTTCCTTTACAAGATGGAGGGGTCTTATCTTATCTC
GGTTGCTGTTATTAAATGTAGATAGACGCTCATCGCTCACCATTGGCAGTCTTGAGTCTTTCAT
CAGGTGGAACTCACATTGCAACAGCATCTGAACAAGGGACCATGATCAGAATTCATCTCGTTTC
AGATGCAACTAAG

Sequences
Splice junction sequence	ATTGGCAGTCTTGAGTCTTTCATCAGGTGGAACTCACATTGCAACAGCATCTGAACAAGGGACC ATGATCAGAATTCATCTCGTTTCAGATGCAACTAAGattgattgtcatattgcaggagaagaca tttatttatgatataaatagtcttaagatactggacacaattgatacggtgccgaatccaaaag gtctgttt
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: 325 Transcript exons: 976732-976823,977078-977190,977393-977512 ATTGATTGTCATATTGCAGGAGAAGACATTTATTTATGATATAAATAGTCTTAAGATACTGGAC ACAATTGATACGGTGCCGAATCCAAAAGGACTTTGTGCATTTTCACCCAGCTTGGATGGTTCAT TTCTGGCCCTTCCAGCAAGTACAACCAAAGGATCTTTGCTAGTCTATAATGTTTCCGATCTCCG TTTGCACTGTGAGATAGACGCTCATCGCTCACCATTGGCAGTCTTGAGTCTTTCATCAGGTGGA ACTCACATTGCAACAGCATCTGAACAAGGGACCATGATCAGAATTCATCTCGTTTCAGATGCAA CTAAG
Genomic sequence	ATTGATTGTCATATTGCAGGAGAAGACATTTATTTATGATATAAATAGTCTTAAGATACTGGAC ACAATTGATACGGTGCCGAATCCAAAAGGTCTGTTTGGAAGTTTCTTGTTCAAGTTTTAATGGC TCACTGCCAATCTTGTTTACTAGATGGATTAGAACATGACTCGCATAATATTCGAGATGACATT CCCCACCCCGCTTAAAAATATCAACAGAAAAGGAAAGAATAAAAGAACTCACTGTGTTATACCT TTCAAGTTTTTGTTTAATGAGTGGATGCTATAACATTTCCAGTTGGCCTTGCACATTTTCTTAT CAACGAGTTCTTGTTTCAATTTTCAGGACTTTGTGCATTTTCACCCAGCTTGGATGGTTCATTT CTGGCCCTTCCAGCAAGTACAACCAAAGGATCTTTGCTAGTCTATAATGTTTCCGATCTCCGTT TGCACTGTGAGGTCGTGTTTCTTACTTGTATGTATTGATATTACGCAATCATCTATAACAAGAT CAACGGGTTTGAGTTGTTATACATCATAATTTTGAAGAGTCCAGCATTTTCCTAGCTTTAAACC AACTATTTCACCAGCATTTTCTCTTTCTTTTCCTTTACAAGATGGAGGGGTCTTATCTTATCTC GGTTGCTGTTATTAAATGTAGATAGACGCTCATCGCTCACCATTGGCAGTCTTGAGTCTTTCAT CAGGTGGAACTCACATTGCAACAGCATCTGAACAAGGGACCATGATCAGAATTCATCTCGTTTC AGATGCAACTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.621848134

Conservation Information
Conserved circRNAs	NA
PMCS	0.621848134

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							977478-976767(+)
977503-976767(+)
						
						Potential amino acid sequence
						
							MIRIHLVSDATKIDCHIAGEDIYL*(+)
MQLRLIVILQEKTFIYDINSLKILDTIDTVPNPKGLCAFSPSLDGSFLALPASTTKGSLLVYNV
SDLRLHCEIDAHRSPLAVLSLSSGGTHIATASEQGTMIRIHLVSDATKIDCHIAGEDIYL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to chilling stress

Functional Information
Coding potential	Y
Potential coding position	977478-976767(+) 977503-976767(+)
Potential amino acid sequence	MIRIHLVSDATKIDCHIAGEDIYL(+) MQLRLIVILQEKTFIYDINSLKILDTIDTVPNPKGLCAFSPSLDGSFLALPASTTKGSLLVYNV SDLRLHCEIDAHRSPLAVLSLSSGGTHIATASEQGTMIRIHLVSDATKIDCHIAGEDIYL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to chilling stress

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

circRNA

Detail information of Solyc07g006120.2_circ_g.2

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