Plant Circular RNA Database

Detail information of Solyc04g049380.2_circ_ag.2

			
						 General Information
					
						CircRNA Name
						Solyc04g049380.2_circ_ag.2
					
						ID in PlantcircBase
						sly_circ_001395
					
						Alias
						4:40932222|40946692
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 41784452-41798922  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Solyc04g049380.2_circ_g.2 Solyc04g049380.2_circ_ag.1 						
					
						Support reads
						7/4
					
						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  
						
							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
						NA

General Information
CircRNA Name	Solyc04g049380.2_circ_ag.2
ID in PlantcircBase	sly_circ_001395
Alias	4:40932222\|40946692
Organism	Solanum lycopersicum
Position	chr4: 41784452-41798922 JBrowse»
Reference genome	SL2.50.38
Type	ag-circRNA
Identification method	CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Solyc04g049380.2_circ_g.2 Solyc04g049380.2_circ_ag.1
Support reads	7/4
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	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	NA

			
						 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  
						
							TTGCAGGTTTTGAGTAAAATAGTGTCTGTAGCATTCAAGTATCATTTCCGCATGCCACCATACT
TCACCCTTCTTCTTCGTTCTCTTGCCTCATTAGAAGgttaacaaaggagtacaggcatcattaa
ttcaactccttgacactgggttactacacgctgatccacaccctggaaatttaagatacacatc
atcagcaa

						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	TTGCAGGTTTTGAGTAAAATAGTGTCTGTAGCATTCAAGTATCATTTCCGCATGCCACCATACT TCACCCTTCTTCTTCGTTCTCTTGCCTCATTAGAAGgttaacaaaggagtacaggcatcattaa ttcaactccttgacactgggttactacacgctgatccacaccctggaaatttaagatacacatc atcagcaa
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
						0.446239017

Conservation Information
Conserved circRNAs	NA
PMCS	0.446239017

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to chilling stress; fruit ripening

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to chilling stress; fruit ripening

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

circRNA

Detail information of Solyc04g049380.2_circ_ag.2

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