Plant Circular RNA Database

Detail information of Solyc10g079880.1_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc10g079880.1_circ_g.1
					
						ID in PlantcircBase
						sly_circ_003178
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr10: 61350488-61351294  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc10g079880.1						
					
						Parent gene annotation
						
							Eukaryotic translation initiation factor 3 subunit E
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Solyc10g079880.1.1:3

General Information
CircRNA Name	Solyc10g079880.1_circ_g.1
ID in PlantcircBase	sly_circ_003178
Alias	NA
Organism	Solanum lycopersicum
Position	chr10: 61350488-61351294 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc10g079880.1
Parent gene annotation	Eukaryotic translation initiation factor 3 subunit E
Parent gene strand	-
Alternative splicing	NA
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	Solyc10g079880.1.1:3

			
						 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  
						
							TGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTGCAGCTTCCTCAAGTGCTTTCA
ACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTTttgtcctggttaaacaggtcaatgatca
gtgtcctgccattgtcatggttgaagaagatgaatagactccaatgcattagccatattctatt
ctgaactt

						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: 505
Transcript exons: 61350488-61350609,61350741-61350968,61351140-61351294
TTGTCCTGGTTAAACAGGTCAATGATCAGTGTCCTGCCATTGTCATGGTTGAAGAAGATGAATA
GACTCCAATGCATTAGCCATATTCTATTCTGAACTTGATTCAACGGAGTAGAGAAACTCTTTGA
GTCGATAATTTCTTTCAAGCGGTTGAGTTCCTCGAGTGCAATATCCCAATTCTGCATTAGTATC
TCCGCTGCAAGCTTTCCCCACAATGCACTGACGCTCCTGTCACTGTTTGTGCACAATGCTCGGT
ACTGGTAAAGATAATCAGCAGCACCAGAATAGTTTCCACATTCAAACTGAAATTTGGCATATTG
ATACAATGCCTCTATCTGGTCCGGACCAATCTGGTACCGCTCCTGGAGCAACTGAAGATTGTGC
TGTTTGTCAGCTCTCAACTCCTGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTG
CAGCTTCCTCAAGTGCTTTCAACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTT
						
						Genomic sequence
						
							TTGTCCTGGTTAAACAGGTCAATGATCAGTGTCCTGCCATTGTCATGGTTGAAGAAGATGAATA
GACTCCAATGCATTAGCCATATTCTATTCTGAACTTGATTCAACGGAGTAGAGAAACTCTGCAA
GACAAGCGACACTTTTAGTACACTTGGTAAACTGAGGATCATTCAGTTTTTTCCTACAGGATAC
TCAACTTGGTAAGACTAACTCAAACAGACAGATTGTTGACTCAATATATGCAAAATATTACCTT
TGAGTCGATAATTTCTTTCAAGCGGTTGAGTTCCTCGAGTGCAATATCCCAATTCTGCATTAGT
ATCTCCGCTGCAAGCTTTCCCCACAATGCACTGACGCTCCTGTCACTGTTTGTGCACAATGCTC
GGTACTGGTAAAGATAATCAGCAGCACCAGAATAGTTTCCACATTCAAACTGAAATTTGGCATA
TTGATACAATGCCTCTATCTGGTCCGGACCAATCTGGACAGGTTTGTAAGAGCATTACTAAAAT
AAAAAATGTATATTCACAAAATTAGCTAGAGACCAACTTCTGTTTGTGATCCCTTTAACAAGTA
TATTATTAATTATACAACATTAAGTACTAAAGAAGAAGGAACTCTATATCATGTAAATCAAACT
AGATCTATGCACCTGGTACCGCTCCTGGAGCAACTGAAGATTGTGCTGTTTGTCAGCTCTCAAC
TCCTGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTGCAGCTTCCTCAAGTGCTT
TCAACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTT

Sequences
Splice junction sequence	TGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTGCAGCTTCCTCAAGTGCTTTCA ACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTTttgtcctggttaaacaggtcaatgatca gtgtcctgccattgtcatggttgaagaagatgaatagactccaatgcattagccatattctatt ctgaactt
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: 505 Transcript exons: 61350488-61350609,61350741-61350968,61351140-61351294 TTGTCCTGGTTAAACAGGTCAATGATCAGTGTCCTGCCATTGTCATGGTTGAAGAAGATGAATA GACTCCAATGCATTAGCCATATTCTATTCTGAACTTGATTCAACGGAGTAGAGAAACTCTTTGA GTCGATAATTTCTTTCAAGCGGTTGAGTTCCTCGAGTGCAATATCCCAATTCTGCATTAGTATC TCCGCTGCAAGCTTTCCCCACAATGCACTGACGCTCCTGTCACTGTTTGTGCACAATGCTCGGT ACTGGTAAAGATAATCAGCAGCACCAGAATAGTTTCCACATTCAAACTGAAATTTGGCATATTG ATACAATGCCTCTATCTGGTCCGGACCAATCTGGTACCGCTCCTGGAGCAACTGAAGATTGTGC TGTTTGTCAGCTCTCAACTCCTGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTG CAGCTTCCTCAAGTGCTTTCAACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTT
Genomic sequence	TTGTCCTGGTTAAACAGGTCAATGATCAGTGTCCTGCCATTGTCATGGTTGAAGAAGATGAATA GACTCCAATGCATTAGCCATATTCTATTCTGAACTTGATTCAACGGAGTAGAGAAACTCTGCAA GACAAGCGACACTTTTAGTACACTTGGTAAACTGAGGATCATTCAGTTTTTTCCTACAGGATAC TCAACTTGGTAAGACTAACTCAAACAGACAGATTGTTGACTCAATATATGCAAAATATTACCTT TGAGTCGATAATTTCTTTCAAGCGGTTGAGTTCCTCGAGTGCAATATCCCAATTCTGCATTAGT ATCTCCGCTGCAAGCTTTCCCCACAATGCACTGACGCTCCTGTCACTGTTTGTGCACAATGCTC GGTACTGGTAAAGATAATCAGCAGCACCAGAATAGTTTCCACATTCAAACTGAAATTTGGCATA TTGATACAATGCCTCTATCTGGTCCGGACCAATCTGGACAGGTTTGTAAGAGCATTACTAAAAT AAAAAATGTATATTCACAAAATTAGCTAGAGACCAACTTCTGTTTGTGATCCCTTTAACAAGTA TATTATTAATTATACAACATTAAGTACTAAAGAAGAAGGAACTCTATATCATGTAAATCAAACT AGATCTATGCACCTGGTACCGCTCCTGGAGCAACTGAAGATTGTGCTGTTTGTCAGCTCTCAAC TCCTGCACAGCACTGGAATTCTGCAAAAAAGTGATCAATGGGGCTGCAGCTTCCTCAAGTGCTT TCAACCTTGCCACAACCTCGGCTCTCCTCTCCATCATTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.481700452

Conservation Information
Conserved circRNAs	NA
PMCS	0.481700452

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							61351230-61350580(+)
61351294-61351248(-)
						
						Potential amino acid sequence
						
							MGLQLPQVLSTLPQPRLSSPSFLSWLNRSMISVLPLSWLKKMNRLQCISHILF*(+)
MMERRAEVVARLKALEEAAAPLITFLQNSSAVQELRADKQHNLQLLQERYQIGPDQIEALYQYA
KFQFECGNYSGAADYLYQYRALCTNSDRSVSALWGKLAAEILMQNWDIALEELNRLKEIIDSKS
FSTPLNQVQNRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKNDGEESRGCGKVEST*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	61351230-61350580(+) 61351294-61351248(-)
Potential amino acid sequence	MGLQLPQVLSTLPQPRLSSPSFLSWLNRSMISVLPLSWLKKMNRLQCISHILF(+) MMERRAEVVARLKALEEAAAPLITFLQNSSAVQELRADKQHNLQLLQERYQIGPDQIEALYQYA KFQFECGNYSGAADYLYQYRALCTNSDRSVSALWGKLAAEILMQNWDIALEELNRLKEIIDSKS FSTPLNQVQNRIWLMHWSLFIFFNHDNGRTLIIDLFNQDKNDGEESRGCGKVEST(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc10g079880.1_circ_g.1

Address

Any questions?

Supported by