Plant Circular RNA Database

Detail information of Solyc05g015070.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc05g015070.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_001704
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 9778479-9779633  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc05g015070.2						
					
						Parent gene annotation
						
							RING-type E3 ubiquitin transferase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc05g015070.2_circ_g.1 Solyc05g015070.2_circ_g.2 						
					
						Support reads
						NA
					
						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
						Solyc05g015070.2.1:3

General Information
CircRNA Name	Solyc05g015070.2_circ_g.3
ID in PlantcircBase	sly_circ_001704
Alias	NA
Organism	Solanum lycopersicum
Position	chr5: 9778479-9779633 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc05g015070.2
Parent gene annotation	RING-type E3 ubiquitin transferase
Parent gene strand	-
Alternative splicing	Solyc05g015070.2_circ_g.1 Solyc05g015070.2_circ_g.2
Support reads	NA
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	Solyc05g015070.2.1:3

			
						 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  
						
							CATACCTTAGGCTCACCGATAGATAACAAGTTCTCCTCAACCTCACTATTCTCCATCATCAACA
TCGAATAGAATATTCAACTTCCTCAATCAGCAGTATctgacagccaatactttgtggtactata
tcttcaacacgctttagactatcttcaagagcacatcttgctctctcaaatttcagaactatag
agtcacct

									
								

					

						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: 389
Transcript exons: 9778479-9778586,9779043-9779228,9779539-9779633
CTGACAGCCAATACTTTGTGGTACTATATCTTCAACACGCTTTAGACTATCTTCAAGAGCACAT
CTTGCTCTCTCAAATTTCAGAACTATAGAGTCACCTGTTATGGCCAGGTAAAGTTTACTGCATT
CAGCACAATGTTGAAGAACAGTCTTTGTTTTCTCAAGGGCTATATGCAAAGCACACAATGCTTG
AATACCAGATGTGCTTCTTGGTCTTGCAGCTTCTAGTTCAGGAAATATTCCCAGCACTTTTGCA
TATACAGCCGATAAGCTCTTGCACATTCCTCCATGTAACTTAGGCTCACCGATAGATAACAAGT
TCTCCTCAACCTCACTATTCTCCATCATCAACATCGAATAGAATATTCAACTTCCTCAATCAGC
AGTAT
						
					

						Genomic sequence
						
							CTGACAGCCAATACTTTGTGGTACTATATCTTCAACACGCTTTAGACTATCTTCAAGAGCACAT
CTTGCTCTCTCAAATTTCAGAACTATAGAGTCACCTGTTATGGCCTGAAAACAAAGACATTTCA
ATAAATATAAATTGTCAGAAAAAGAAAGTTTAGTGGACAGACATTGTAACCATTAAGAAAAATT
CGGTAGCGTCTCTTCTTACTACTTCTGTTTGGTAATAAACATACTGCATGAGCAAATAAATTAT
AGTTATATCTTTACGAAATAGCACTTTACATTTAAAAACTTTCAAGTTGATCAAGTATTCCATT
TGGAAACTGTTGTTAGATATTAACAACTACAAGACGTCAACCCCAAGCAACTTGGGAAGTGGTT
AGGAAACATAATAAATAGGAAATCTTGTTATGTAGGATCCGGACCCAAGGTAACTCACCAGAGG
AATAAGAAGGCACATTCATATCCCTCTTAAGAAATTAATAATACAGTACAGTCGAAGATTGCCA
AAAAACATTCTCTCAATATTGACAATCAAAACTAAAAAGGTACCATCATTACCAGGTAAAGTTT
ACTGCATTCAGCACAATGTTGAAGAACAGTCTTTGTTTTCTCAAGGGCTATATGCAAAGCACAC
AATGCTTGAATACCAGATGTGCTTCTTGGTCTTGCAGCTTCTAGTTCAGGAAATATTCCCAGCA
CTTTTGCATATACAGCCGATAAGCTCTTGCACATTCCTCCATGTAACTATGTAACACAAAACTT
TATTACTTATAGAAATATGATAAATGAACATCAAGAAACCCATATAAGTATCAAACAAGTATAA
ACTTAGATGATATAAAAGAACTACTTAAACCATCATATCCACCGACAGGTTGTAAAAAGTCAAC
TAGATAAGAAAAGGTTATTGAAAAAGCTAATCAGCGTCGAGTATACAAGGTGTTTTCATTTCAA
AACCCAACTTTAAAAATTTTCCTAGTTGTAAGTCTACATAGATCCAATAAAATGGAAAATGAAA
GCAACCATTTGTACATTAAGTGTTTCATAAGCATACCTTAGGCTCACCGATAGATAACAAGTTC
TCCTCAACCTCACTATTCTCCATCATCAACATCGAATAGAATATTCAACTTCCTCAATCAGCAG
TAT
						
					

			
		

Sequences
Splice junction sequence	CATACCTTAGGCTCACCGATAGATAACAAGTTCTCCTCAACCTCACTATTCTCCATCATCAACA TCGAATAGAATATTCAACTTCCTCAATCAGCAGTATctgacagccaatactttgtggtactata tcttcaacacgctttagactatcttcaagagcacatcttgctctctcaaatttcagaactatag agtcacct
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: 389 Transcript exons: 9778479-9778586,9779043-9779228,9779539-9779633 CTGACAGCCAATACTTTGTGGTACTATATCTTCAACACGCTTTAGACTATCTTCAAGAGCACAT CTTGCTCTCTCAAATTTCAGAACTATAGAGTCACCTGTTATGGCCAGGTAAAGTTTACTGCATT CAGCACAATGTTGAAGAACAGTCTTTGTTTTCTCAAGGGCTATATGCAAAGCACACAATGCTTG AATACCAGATGTGCTTCTTGGTCTTGCAGCTTCTAGTTCAGGAAATATTCCCAGCACTTTTGCA TATACAGCCGATAAGCTCTTGCACATTCCTCCATGTAACTTAGGCTCACCGATAGATAACAAGT TCTCCTCAACCTCACTATTCTCCATCATCAACATCGAATAGAATATTCAACTTCCTCAATCAGC AGTAT
Genomic sequence	CTGACAGCCAATACTTTGTGGTACTATATCTTCAACACGCTTTAGACTATCTTCAAGAGCACAT CTTGCTCTCTCAAATTTCAGAACTATAGAGTCACCTGTTATGGCCTGAAAACAAAGACATTTCA ATAAATATAAATTGTCAGAAAAAGAAAGTTTAGTGGACAGACATTGTAACCATTAAGAAAAATT CGGTAGCGTCTCTTCTTACTACTTCTGTTTGGTAATAAACATACTGCATGAGCAAATAAATTAT AGTTATATCTTTACGAAATAGCACTTTACATTTAAAAACTTTCAAGTTGATCAAGTATTCCATT TGGAAACTGTTGTTAGATATTAACAACTACAAGACGTCAACCCCAAGCAACTTGGGAAGTGGTT AGGAAACATAATAAATAGGAAATCTTGTTATGTAGGATCCGGACCCAAGGTAACTCACCAGAGG AATAAGAAGGCACATTCATATCCCTCTTAAGAAATTAATAATACAGTACAGTCGAAGATTGCCA AAAAACATTCTCTCAATATTGACAATCAAAACTAAAAAGGTACCATCATTACCAGGTAAAGTTT ACTGCATTCAGCACAATGTTGAAGAACAGTCTTTGTTTTCTCAAGGGCTATATGCAAAGCACAC AATGCTTGAATACCAGATGTGCTTCTTGGTCTTGCAGCTTCTAGTTCAGGAAATATTCCCAGCA CTTTTGCATATACAGCCGATAAGCTCTTGCACATTCCTCCATGTAACTATGTAACACAAAACTT TATTACTTATAGAAATATGATAAATGAACATCAAGAAACCCATATAAGTATCAAACAAGTATAA ACTTAGATGATATAAAAGAACTACTTAAACCATCATATCCACCGACAGGTTGTAAAAAGTCAAC TAGATAAGAAAAGGTTATTGAAAAAGCTAATCAGCGTCGAGTATACAAGGTGTTTTCATTTCAA AACCCAACTTTAAAAATTTTCCTAGTTGTAAGTCTACATAGATCCAATAAAATGGAAAATGAAA GCAACCATTTGTACATTAAGTGTTTCATAAGCATACCTTAGGCTCACCGATAGATAACAAGTTC TCCTCAACCTCACTATTCTCCATCATCAACATCGAATAGAATATTCAACTTCCTCAATCAGCAG TAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.545105562

Conservation Information
Conserved circRNAs	NA
PMCS	0.545105562

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9779600-9779594(-)
						
						Potential amino acid sequence
						
							MLMMENSEVEENLLSIGEPKLHGGMCKSLSAVYAKVLGIFPELEAARPRSTSGIQALCALHIAL
EKTKTVLQHCAECSKLYLAITGDSIVLKFERARCALEDSLKRVEDIVPQSIGCQILLIEEVEYS
IRC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9779600-9779594(-)
Potential amino acid sequence	MLMMENSEVEENLLSIGEPKLHGGMCKSLSAVYAKVLGIFPELEAARPRSTSGIQALCALHIAL EKTKTVLQHCAECSKLYLAITGDSIVLKFERARCALEDSLKRVEDIVPQSIGCQILLIEEVEYS IRC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc05g015070.2_circ_g.3

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