Plant Circular RNA Database

Detail information of Solyc01g112240.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc01g112240.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_000556
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr1: 98285985-98294960  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc01g112240.2						
					
						Parent gene annotation
						
							Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltrans
ferase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc01g112240.2_circ_g.1 Solyc01g112240.2_circ_g.3 Solyc01g112240.2_circ_g.4 Solyc01g112240.2_circ_g.5 						
					
						Support reads
						2
					
						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
						Solyc01g112240.2.1:11

General Information
CircRNA Name	Solyc01g112240.2_circ_g.2
ID in PlantcircBase	sly_circ_000556
Alias	NA
Organism	Solanum lycopersicum
Position	chr1: 98285985-98294960 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc01g112240.2
Parent gene annotation	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltrans ferase
Parent gene strand	-
Alternative splicing	Solyc01g112240.2_circ_g.1 Solyc01g112240.2_circ_g.3 Solyc01g112240.2_circ_g.4 Solyc01g112240.2_circ_g.5
Support reads	2
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	Solyc01g112240.2.1:11

			
						 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  
						
							AAAAGCTGAAAGAAGAAAGAGGAGTTTATCGACTTACTTTCAAGATCCTGAACAAGAGCCCTTA
ATTGTCGGCACTCCTGGTCCTGGCGCTTCATTTGTTatgctcaccaaaattgtacgttctgcaa
acttctgggcgaataaattgtcgacctctgtgattttctttgagcctcagccagtcatcccagt
aagtaaaa

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAAAGCTGAAAGAAGAAAGAGGAGTTTATCGACTTACTTTCAAGATCCTGAACAAGAGCCCTTA ATTGTCGGCACTCCTGGTCCTGGCGCTTCATTTGTTatgctcaccaaaattgtacgttctgcaa acttctgggcgaataaattgtcgacctctgtgattttctttgagcctcagccagtcatcccagt aagtaaaa
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.111823638

Conservation Information
Conserved circRNAs	NA
PMCS	0.111823638

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							98294957-98294954(-)
						
						Potential amino acid sequence
						
							MKRQDQECRQLRALVQDLESKGIKKLIGNVQMPVAAVVVMACSRSDYLEKTIKSILKYQTSVAS
KYPLFISQDGSNPDVRKLALSYDQLTYMQHLDFEPVHTERPGELVAYYKIARHYKWALDQLFHK
HNFSRVIILEDDMEIAADFFDYFEAGATLLDRDKSIMAISSWNDNGQRQFVQDPYALYRSDFFP
GLGWMLSKSTWSELSPKWPKAYWDDWLRLKENHRGRQFIRPEVCRTYNFGEHNK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	98294957-98294954(-)
Potential amino acid sequence	MKRQDQECRQLRALVQDLESKGIKKLIGNVQMPVAAVVVMACSRSDYLEKTIKSILKYQTSVAS KYPLFISQDGSNPDVRKLALSYDQLTYMQHLDFEPVHTERPGELVAYYKIARHYKWALDQLFHK HNFSRVIILEDDMEIAADFFDYFEAGATLLDRDKSIMAISSWNDNGQRQFVQDPYALYRSDFFP GLGWMLSKSTWSELSPKWPKAYWDDWLRLKENHRGRQFIRPEVCRTYNFGEHNK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc01g112240.2_circ_g.2

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