Plant Circular RNA Database

Detail information of Solyc04g015690.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc04g015690.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_001322
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 5979588-5986595  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g015690.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g015690.2_circ_g.2 Solyc04g015690.2_circ_g.3 						
					
						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  
						
							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
						Solyc04g015690.2.1:7

General Information
CircRNA Name	Solyc04g015690.2_circ_g.1
ID in PlantcircBase	sly_circ_001322
Alias	NA
Organism	Solanum lycopersicum
Position	chr4: 5979588-5986595 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g015690.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc04g015690.2_circ_g.2 Solyc04g015690.2_circ_g.3
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	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	Solyc04g015690.2.1:7

			
						 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  
						
							AACTCAGACACTGGTACAGGGCATATTCCAAGAAGTTCCAAATACCAATAGAAGTTACTCCCCT
GTTACTGATCAGCCTTGCAAATCAGAACATCTTCAGaacatatgctgttttatgcaagtgagaa
gtatcctgtggagaatagttactcaaaatacatcacccaggtatcttcttttatcctattaaca
attatgat

						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: 566
Transcript exons: 5979588-5979655,5984397-5984488,5984561-5984634,5984745-
5984788,5985371-5985422,5986276-5986398,5986483-5986595
AACATATGCTGTTTTATGCAAGTGAGAAGTATCCTGTGGAGAATAGTTACTCAAAATACATCAC
CCAGCACGGAGGTTCCACCAATGCCTTTACATCTTCTGAGCGCACCAACTTTTACTTCGATATC
AATGCAGATTGTTTTGAAGAAGCATTGGACAGATTTGCGCAGTTTTTTGTCAAACCATTGATGT
CACCTGATGCCACAACAAGGGAAATAAAAGCTGTTGACTCTGAGAACCAAAACAACCTATTATC
TGATGGTCACAGACTGTACCAGCTTCAGAAACATCTGAGCTCAAAAGATCATCCATACCACAAA
TTTGGCACAGGTAATTGGGATACCCTGGAGGTGCAGCCAAAAGCAAGAGGCTTGAATACAAGGC
AGGAGCTTCTCAAATTTTATAAAGAAAATTATTCAGCCAACTTAATGCATTTGGTTGTTTATGC
AAAAGATTGCCTTGATAAAACTCAGACACTGGTACAGGGCATATTCCAAGAAGTTCCAAATACC
AATAGAAGTTACTCCCCTGTTACTGATCAGCCTTGCAAATCAGAACATCTTCAG
						
						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	AACTCAGACACTGGTACAGGGCATATTCCAAGAAGTTCCAAATACCAATAGAAGTTACTCCCCT GTTACTGATCAGCCTTGCAAATCAGAACATCTTCAGaacatatgctgttttatgcaagtgagaa gtatcctgtggagaatagttactcaaaatacatcacccaggtatcttcttttatcctattaaca attatgat
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: 566 Transcript exons: 5979588-5979655,5984397-5984488,5984561-5984634,5984745- 5984788,5985371-5985422,5986276-5986398,5986483-5986595 AACATATGCTGTTTTATGCAAGTGAGAAGTATCCTGTGGAGAATAGTTACTCAAAATACATCAC CCAGCACGGAGGTTCCACCAATGCCTTTACATCTTCTGAGCGCACCAACTTTTACTTCGATATC AATGCAGATTGTTTTGAAGAAGCATTGGACAGATTTGCGCAGTTTTTTGTCAAACCATTGATGT CACCTGATGCCACAACAAGGGAAATAAAAGCTGTTGACTCTGAGAACCAAAACAACCTATTATC TGATGGTCACAGACTGTACCAGCTTCAGAAACATCTGAGCTCAAAAGATCATCCATACCACAAA TTTGGCACAGGTAATTGGGATACCCTGGAGGTGCAGCCAAAAGCAAGAGGCTTGAATACAAGGC AGGAGCTTCTCAAATTTTATAAAGAAAATTATTCAGCCAACTTAATGCATTTGGTTGTTTATGC AAAAGATTGCCTTGATAAAACTCAGACACTGGTACAGGGCATATTCCAAGAAGTTCCAAATACC AATAGAAGTTACTCCCCTGTTACTGATCAGCCTTGCAAATCAGAACATCTTCAG
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
						0.299525817

Conservation Information
Conserved circRNAs	NA
PMCS	0.299525817

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5986391-5979609(+)
5979594-5984586(+)
						
						Potential amino acid sequence
						
							MQKIALIKLRHWYRAYSKKFQIPIEVTPLLLISLANQNIFRTYAVLCK*(+)
MLFYASEKYPVENSYSKYITQHGGSTNAFTSSERTNFYFDINADCFEEALDRFAQFFVKPLMSP
DATTREIKAVDSENQNNLLSDGHRLYQLQKHLSSKDHPYHKFGTGNWDTLEVQPKARGLNTRQE
LLKFYKENYSANLMHLVVYAKDCLDKTQTLVQGIFQEVPNTNRSYSPVTDQPCKSEHLQNICCF
MQVRSILWRIVTQNTSPSTEVPPMPLHLLSAPTFTSISMQIVLKKHWTDLRSFLSNH*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5986391-5979609(+) 5979594-5984586(+)
Potential amino acid sequence	MQKIALIKLRHWYRAYSKKFQIPIEVTPLLLISLANQNIFRTYAVLCK(+) MLFYASEKYPVENSYSKYITQHGGSTNAFTSSERTNFYFDINADCFEEALDRFAQFFVKPLMSP DATTREIKAVDSENQNNLLSDGHRLYQLQKHLSSKDHPYHKFGTGNWDTLEVQPKARGLNTRQE LLKFYKENYSANLMHLVVYAKDCLDKTQTLVQGIFQEVPNTNRSYSPVTDQPCKSEHLQNICCF MQVRSILWRIVTQNTSPSTEVPPMPLHLLSAPTFTSISMQIVLKKHWTDLRSFLSNH(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc04g015690.2_circ_g.1

Address

Any questions?

Supported by