Plant Circular RNA Database

Detail information of Solyc11g008700.1_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc11g008700.1_circ_g.2
					
						ID in PlantcircBase
						sly_circ_003257
					
						Alias
						11:2883263|2884418
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr11: 2883263-2884418  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc11g008700.1						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						6
					
						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
						Solyc11g008700.1.1:3

General Information
CircRNA Name	Solyc11g008700.1_circ_g.2
ID in PlantcircBase	sly_circ_003257
Alias	11:2883263\|2884418
Organism	Solanum lycopersicum
Position	chr11: 2883263-2884418 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc11g008700.1
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
Support reads	6
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	Solyc11g008700.1.1:3

			
						 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  
						
							TCAGTCAGCAATCCAGGAATCGAGCAAAGTGGTTGCCATTCACTCCTTCCTTCCGACCATGCTA
GTGTACTCTCCAGGAGGTATCCAGCAGAGTAGTGCTcttcttttcagcagctttttcaggctca
tctttttcagtcagtttcctcttgccattatgtgttgctgtggcagtttcaattgaatttatag
cattctta

									
								

					

						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: 560
Transcript exons: 2883263-2883496,2883997-2884187,2884284-2884418
CTTCTTTTCAGCAGCTTTTTCAGGCTCATCTTTTTCAGTCAGTTTCCTCTTGCCATTATGTGTT
GCTGTGGCAGTTTCAATTGAATTTATAGCATTCTTATTAGCCTCAGTATTATCCATGTTCTTGT
TCTCATTTCCAGAAGAAATGTCAGCGGGCAATGTAGGGAAAAGTTCCTCCTCTTCAGCGTAAGT
CATATCTTCTAGACGATAGTCCGTTTTATCGGTTGGATCTTCCTGAGGTACCCACACTCTAAGA
GCCTTATCCCATTTGTACCTAGTTCCGTCATCATCAATGAACTCATCTTCACCATCTGGAGGAG
TTGAAGGCCTTTGATCCTCATCAACTGCTTGCTCGTCCTCTGCCTCTTTCACTTCCTTTTGAAA
CTTTTCATACTCATCAAATGGATCACTAGAAGTCAAAGAAACTGAATTTGTATCACCAGTGCTC
TGCTCAGCTACATCAGTCAGCAATCCAGGAATCGAGCAAAGTGGTTGCCATTCACTCCTTCCTT
CCGACCATGCTAGTGTACTCTCCAGGAGGTATCCAGCAGAGTAGTGCT
						
					

						Genomic sequence
						
							CTTCTTTTCAGCAGCTTTTTCAGGCTCATCTTTTTCAGTCAGTTTCCTCTTGCCATTATGTGTT
GCTGTGGCAGTTTCAATTGAATTTATAGCATTCTTATTAGCCTCAGTATTATCCATGTTCTTGT
TCTCATTTCCAGAAGAAATGTCAGCGGGCAATGTAGGGAAAAGTTCCTCCTCTTCAGCGTAAGT
CATATCTTCTAGACGATAGTCCGTTTTATCGGTTGGATCTTCCTATAAAACATCATCTGATCAA
GACACTTTCCAACACAAATAAATAAAGGAACAGAAGTACGAGTCACAAAGATGTACTCTTTCTT
CTTTTTTTTCATTTTTTTGAAATTATTGATAAAGAACAATGCAACATCGAGCATAATTATGAGA
CTAACAAAAAAAGCGCTTTTGCTTTTTCACAACTGTGGTGTCTGGGGCAACTTTCGTGCACCTC
GACTAATTCCACGAGATATGATATCTACCACCTCCTACCAACAGTGCCAGGTAACTCTATCCAC
CAAAGCTAAGGCAAATGGAAAGAGATTGCCTAGTGTTTTTTGTCTAAGAAATGAACCTGAGACC
TTATTAGTTCTCAATTCACGTTACTGACCACTAGGCCACACCCTTGGGTGCCTTTTCTTTTCTG
TTTTAAATGACCCACATGTGTTTTACATCACAAAGTTAAACTTCTGAAAGACGAGGGAACAAAG
AAGACAGCCAGAAGTAATATATTATATTACCTGAGGTACCCACACTCTAAGAGCCTTATCCCAT
TTGTACCTAGTTCCGTCATCATCAATGAACTCATCTTCACCATCTGGAGGAGTTGAAGGCCTTT
GATCCTCATCAACTGCTTGCTCGTCCTCTGCCTCTTTCACTTCCTTTTGAAACTTTTCATACTC
ATCAAATGGATCACTAGAAGTCAAAGAAACTGCAAAAACAGGTAACAGACATCTCAGCCAAGTA
CGATATAGTGTTAAGTTATTACATTTCTGCAGGTTCACCTCTTAAGTGATGAATCCCTCACCTG
AATTTGTATCACCAGTGCTCTGCTCAGCTACATCAGTCAGCAATCCAGGAATCGAGCAAAGTGG
TTGCCATTCACTCCTTCCTTCCGACCATGCTAGTGTACTCTCCAGGAGGTATCCAGCAGAGTAG
TGCT
						
					

			
		

Sequences
Splice junction sequence	TCAGTCAGCAATCCAGGAATCGAGCAAAGTGGTTGCCATTCACTCCTTCCTTCCGACCATGCTA GTGTACTCTCCAGGAGGTATCCAGCAGAGTAGTGCTcttcttttcagcagctttttcaggctca tctttttcagtcagtttcctcttgccattatgtgttgctgtggcagtttcaattgaatttatag cattctta
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: 560 Transcript exons: 2883263-2883496,2883997-2884187,2884284-2884418 CTTCTTTTCAGCAGCTTTTTCAGGCTCATCTTTTTCAGTCAGTTTCCTCTTGCCATTATGTGTT GCTGTGGCAGTTTCAATTGAATTTATAGCATTCTTATTAGCCTCAGTATTATCCATGTTCTTGT TCTCATTTCCAGAAGAAATGTCAGCGGGCAATGTAGGGAAAAGTTCCTCCTCTTCAGCGTAAGT CATATCTTCTAGACGATAGTCCGTTTTATCGGTTGGATCTTCCTGAGGTACCCACACTCTAAGA GCCTTATCCCATTTGTACCTAGTTCCGTCATCATCAATGAACTCATCTTCACCATCTGGAGGAG TTGAAGGCCTTTGATCCTCATCAACTGCTTGCTCGTCCTCTGCCTCTTTCACTTCCTTTTGAAA CTTTTCATACTCATCAAATGGATCACTAGAAGTCAAAGAAACTGAATTTGTATCACCAGTGCTC TGCTCAGCTACATCAGTCAGCAATCCAGGAATCGAGCAAAGTGGTTGCCATTCACTCCTTCCTT CCGACCATGCTAGTGTACTCTCCAGGAGGTATCCAGCAGAGTAGTGCT
Genomic sequence	CTTCTTTTCAGCAGCTTTTTCAGGCTCATCTTTTTCAGTCAGTTTCCTCTTGCCATTATGTGTT GCTGTGGCAGTTTCAATTGAATTTATAGCATTCTTATTAGCCTCAGTATTATCCATGTTCTTGT TCTCATTTCCAGAAGAAATGTCAGCGGGCAATGTAGGGAAAAGTTCCTCCTCTTCAGCGTAAGT CATATCTTCTAGACGATAGTCCGTTTTATCGGTTGGATCTTCCTATAAAACATCATCTGATCAA GACACTTTCCAACACAAATAAATAAAGGAACAGAAGTACGAGTCACAAAGATGTACTCTTTCTT CTTTTTTTTCATTTTTTTGAAATTATTGATAAAGAACAATGCAACATCGAGCATAATTATGAGA CTAACAAAAAAAGCGCTTTTGCTTTTTCACAACTGTGGTGTCTGGGGCAACTTTCGTGCACCTC GACTAATTCCACGAGATATGATATCTACCACCTCCTACCAACAGTGCCAGGTAACTCTATCCAC CAAAGCTAAGGCAAATGGAAAGAGATTGCCTAGTGTTTTTTGTCTAAGAAATGAACCTGAGACC TTATTAGTTCTCAATTCACGTTACTGACCACTAGGCCACACCCTTGGGTGCCTTTTCTTTTCTG TTTTAAATGACCCACATGTGTTTTACATCACAAAGTTAAACTTCTGAAAGACGAGGGAACAAAG AAGACAGCCAGAAGTAATATATTATATTACCTGAGGTACCCACACTCTAAGAGCCTTATCCCAT TTGTACCTAGTTCCGTCATCATCAATGAACTCATCTTCACCATCTGGAGGAGTTGAAGGCCTTT GATCCTCATCAACTGCTTGCTCGTCCTCTGCCTCTTTCACTTCCTTTTGAAACTTTTCATACTC ATCAAATGGATCACTAGAAGTCAAAGAAACTGCAAAAACAGGTAACAGACATCTCAGCCAAGTA CGATATAGTGTTAAGTTATTACATTTCTGCAGGTTCACCTCTTAAGTGATGAATCCCTCACCTG AATTTGTATCACCAGTGCTCTGCTCAGCTACATCAGTCAGCAATCCAGGAATCGAGCAAAGTGG TTGCCATTCACTCCTTCCTTCCGACCATGCTAGTGTACTCTCCAGGAGGTATCCAGCAGAGTAG TGCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.361315525

Conservation Information
Conserved circRNAs	NA
PMCS	0.361315525

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2884378-2883343(+)
2883293-2884360(-)
2883459-2884382(-)
						
						Potential amino acid sequence
						
							MLVYSPGGIQQSSALLFSSFFRLIFFSQFPLAIMCCCGSFN*(+)
MSLKKLLKRRALLCWIPPGEYTSMVGRKE*(-)
MTYAEEEELFPTLPADISSGNENKNMDNTEANKNAINSIETATATHNGKRKLTEKDEPEKAAEK
KSTTLLDTSWRVH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	2884378-2883343(+) 2883293-2884360(-) 2883459-2884382(-)
Potential amino acid sequence	MLVYSPGGIQQSSALLFSSFFRLIFFSQFPLAIMCCCGSFN(+) MSLKKLLKRRALLCWIPPGEYTSMVGRKE(-) MTYAEEEELFPTLPADISSGNENKNMDNTEANKNAINSIETATATHNGKRKLTEKDEPEKAAEK KSTTLLDTSWRVH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc11g008700.1_circ_g.2

Address

Any questions?

Supported by