Plant Circular RNA Database

Detail information of Solyc08g013860.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc08g013860.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002480
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr8: 3302044-3303504  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc08g013860.2						
					
						Parent gene annotation
						
							Malic enzyme
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc08g013860.2_circ_g.1 						
					
						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
						Solyc08g013860.2.1:4

General Information
CircRNA Name	Solyc08g013860.2_circ_g.2
ID in PlantcircBase	sly_circ_002480
Alias	NA
Organism	Solanum lycopersicum
Position	chr8: 3302044-3303504 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc08g013860.2
Parent gene annotation	Malic enzyme
Parent gene strand	-
Alternative splicing	Solyc08g013860.2_circ_g.1
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	Solyc08g013860.2.1:4

			
						 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  
						
							AGAGCTTAGACTAGCTATCTTAAACTTGGACATTTGGAGTCTAACCCAGGAAAAAGGAACATGT
TGTTTGCTTGGTTGCAGTGTCCAACATGACCATTTCctcatcaagtttccgtaactctcggctg
tccatttcacggtatccttcagcaagatcctcttctatagcttctttcaccacagctgcagcta
cctccttt

						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
						
							CTCATCAAGTTTCCGTAACTCTCGGCTGTCCATTTCACGGTATCCTTCAGCAAGATCCTCTTCT
ATAGCTTCTTTCACCACAGCTGCAGCTACCTCCTTTGTTATATCGCGTATCCTGTGATGAAAAT
AGATCATTCACTATGTTAGCAACAATGCAAATCTGAAGCATATAGAGCAATAACATCTTAGTGA
TGCATTTCAAAATGTAAAATGATTTCTTTGAGACACAGAGAACTAGATCTAAGACGGCTGAGGA
AGTCTGGAGCTTTGTATGACATATTTACTTATATTAAGAGGGTTTCACTGGGAATTTAGCAGAT
ACTCGAGTTGGTCCCAACTTGAGAAAAGTTTCTTATTTGGTCTCCGACTAAAGAAATTCAGGTG
CATTGTCTCTGAAATTGAATTTACTTATTTTTCTGAAATTCTATTTTTGTTTATCTTTTAGTGG
AAAGCAACTTCTCAGTCAAACTGCGAAAATTTCTATTCCTCATCTATTTTTAGACGGCAGTAAG
TATGACATATGAATTAATCTGTGAGTTCCCCGCAGTAAATGTTTGATTTTGCTGCTAGGAACTG
ATTGAGATGGAAAGAATAACAGCAGAGGCAAAACATATGAGCAGATTTTGCTCCCGTGTGTCTT
TTTTAAATGTAAATGACAATCCACAACTACGTTCCAACAGTTATATAAAGGCGAGGGCATGAGA
CGATGTTTGTCTACCACGGGCGAGATGTAAGACCCACTGATATAAGCCCCAAGGTGTGATAATA
AGTCCTGTGAATTTTGTTTTGTATTGGTTTTTAGTTGAATAAAGAAATAGGCACAGTTACTGAC
ATTAGATATATTTTTTATAGTAAAAGGTAATCCTATTTTATTATTTCCGAGTTAAACTCAACAA
TATGATTTACTAGTCTCACAGTTACAATTTGTAGATCAAAGAAGCCACCCCCAGCCCCGCAAAA
AACCTTTTTTTTTTTTTGTGGGGGGGGGGGGGGGGTATGCAAGTTGTCCCCTTGTAAACCTGTA
AAATAAAGTTACCTAATACTCCTAAAGCATATACCTGGATATCGAAGGGTATATAATACCCTTG
AGTACCTCCTCCTCTGTCATATATGCAGCCAAACTGTAAAATCCACACTGTACTTAGAAAATAG
AAGTAGAAGCTATTCATGTGCTATGGATAAAAATAGACTTGGAAACTTCACAACAGCATCAAAA
AAGGGAAGTACCACTCAGCTGCAGCCTGTAACATGCCATCTGAAACGATTCTAGATCCAGACAG
AAGAGTACCAAGTCCTATTCTGAAGCATGTACGGAAGATATTGTTAGGAGGAAAGAAAGTCAAT
AGTAAAGAGAGTATAGAAGAGCTTAGACTAGCTATCTTAAACTTGGACATTTGGAGTCTAACCC
AGGAAAAAGGAACATGTTGTTTGCTTGGTTGCAGTGTCCAACATGACCATTTC

Sequences
Splice junction sequence	AGAGCTTAGACTAGCTATCTTAAACTTGGACATTTGGAGTCTAACCCAGGAAAAAGGAACATGT TGTTTGCTTGGTTGCAGTGTCCAACATGACCATTTCctcatcaagtttccgtaactctcggctg tccatttcacggtatccttcagcaagatcctcttctatagcttctttcaccacagctgcagcta cctccttt
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	CTCATCAAGTTTCCGTAACTCTCGGCTGTCCATTTCACGGTATCCTTCAGCAAGATCCTCTTCT ATAGCTTCTTTCACCACAGCTGCAGCTACCTCCTTTGTTATATCGCGTATCCTGTGATGAAAAT AGATCATTCACTATGTTAGCAACAATGCAAATCTGAAGCATATAGAGCAATAACATCTTAGTGA TGCATTTCAAAATGTAAAATGATTTCTTTGAGACACAGAGAACTAGATCTAAGACGGCTGAGGA AGTCTGGAGCTTTGTATGACATATTTACTTATATTAAGAGGGTTTCACTGGGAATTTAGCAGAT ACTCGAGTTGGTCCCAACTTGAGAAAAGTTTCTTATTTGGTCTCCGACTAAAGAAATTCAGGTG CATTGTCTCTGAAATTGAATTTACTTATTTTTCTGAAATTCTATTTTTGTTTATCTTTTAGTGG AAAGCAACTTCTCAGTCAAACTGCGAAAATTTCTATTCCTCATCTATTTTTAGACGGCAGTAAG TATGACATATGAATTAATCTGTGAGTTCCCCGCAGTAAATGTTTGATTTTGCTGCTAGGAACTG ATTGAGATGGAAAGAATAACAGCAGAGGCAAAACATATGAGCAGATTTTGCTCCCGTGTGTCTT TTTTAAATGTAAATGACAATCCACAACTACGTTCCAACAGTTATATAAAGGCGAGGGCATGAGA CGATGTTTGTCTACCACGGGCGAGATGTAAGACCCACTGATATAAGCCCCAAGGTGTGATAATA AGTCCTGTGAATTTTGTTTTGTATTGGTTTTTAGTTGAATAAAGAAATAGGCACAGTTACTGAC ATTAGATATATTTTTTATAGTAAAAGGTAATCCTATTTTATTATTTCCGAGTTAAACTCAACAA TATGATTTACTAGTCTCACAGTTACAATTTGTAGATCAAAGAAGCCACCCCCAGCCCCGCAAAA AACCTTTTTTTTTTTTTGTGGGGGGGGGGGGGGGGTATGCAAGTTGTCCCCTTGTAAACCTGTA AAATAAAGTTACCTAATACTCCTAAAGCATATACCTGGATATCGAAGGGTATATAATACCCTTG AGTACCTCCTCCTCTGTCATATATGCAGCCAAACTGTAAAATCCACACTGTACTTAGAAAATAG AAGTAGAAGCTATTCATGTGCTATGGATAAAAATAGACTTGGAAACTTCACAACAGCATCAAAA AAGGGAAGTACCACTCAGCTGCAGCCTGTAACATGCCATCTGAAACGATTCTAGATCCAGACAG AAGAGTACCAAGTCCTATTCTGAAGCATGTACGGAAGATATTGTTAGGAGGAAAGAAAGTCAAT AGTAAAGAGAGTATAGAAGAGCTTAGACTAGCTATCTTAAACTTGGACATTTGGAGTCTAACCC AGGAAAAAGGAACATGTTGTTTGCTTGGTTGCAGTGTCCAACATGACCATTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.174507141

Conservation Information
Conserved circRNAs	NA
PMCS	0.174507141

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3303495-3303494(+)
3302050-3303312(-)
3303468-3303340(-)
						
						Potential amino acid sequence
						
							MTISSSSFRNSRLSISRYPSARSSSIASFTTAAATSFVISRILDIEGYIIPLSTSSSVIYAAKH
SAAACNMPSETILDPDRRVPSPIPGKRNMLFAWLQCPT*(+)
MRKWSCWTLQPSKQHVPFSWNRTWYSSVWI*(-)
MFLFPGIGLGTLLSGSRIVSDGMLQAAAECLAAYMTEEEVLKGIIYPSISRIRDITKEVAAAVV
KEAIEEDLAEGYREMDSRELRKLDEEMVMLDTATKQTTCSFFLE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3303495-3303494(+) 3302050-3303312(-) 3303468-3303340(-)
Potential amino acid sequence	MTISSSSFRNSRLSISRYPSARSSSIASFTTAAATSFVISRILDIEGYIIPLSTSSSVIYAAKH SAAACNMPSETILDPDRRVPSPIPGKRNMLFAWLQCPT(+) MRKWSCWTLQPSKQHVPFSWNRTWYSSVWI(-) MFLFPGIGLGTLLSGSRIVSDGMLQAAAECLAAYMTEEEVLKGIIYPSISRIRDITKEVAAAVV KEAIEEDLAEGYREMDSRELRKLDEEMVMLDTATKQTTCSFFLE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc08g013860.2_circ_g.2

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