Plant Circular RNA Database

Detail information of Solyc02g083450.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc02g083450.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_000742
					
						Alias
						2:41428283|41429579
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr2: 46850433-46851729  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc02g083450.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						4
					
						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
						Solyc02g083450.2.1:2

General Information
CircRNA Name	Solyc02g083450.2_circ_g.1
ID in PlantcircBase	sly_circ_000742
Alias	2:41428283\|41429579
Organism	Solanum lycopersicum
Position	chr2: 46850433-46851729 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc02g083450.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	NA
Support reads	4
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	Solyc02g083450.2.1:2

			
						 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  
						
							CGGAAACTTCAACTTCAGGAATTTTGGTGGATGATATTTTGCACTTGAGAACAGATGATAGTGA
GGAAAAAAATTTTGTCCAGGCGCGTGTGATCTTTGGcttgcattacaccacggtgactttgggg
acacctgggttgaagtttcttgtggctcttgatactgggagtgacttattttgggtgccttgtg
aatgcggc

									
								

					

						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: 378
Transcript exons: 46850433-46850571,46851491-46851729
CTTGCATTACACCACGGTGACTTTGGGGACACCTGGGTTGAAGTTTCTTGTGGCTCTTGATACT
GGGAGTGACTTATTTTGGGTGCCTTGTGAATGCGGCAGATGTGCTTCTACTGATGATCCTACAC
TTTACAGCTCTGATATTGAGCTTAGCATATACAGCCTGAATGGATCGTCAACTAGCAAGAAGGT
CACCTGCAGTGATAGCTTGTGTACAGACCGCAATAATTGTCTCAGTTCAAATAACCACTGCCCT
TATTCAGTATCCTATGTCTCCTCGGAAACTTCAACTTCAGGAATTTTGGTGGATGATATTTTGC
ACTTGAGAACAGATGATAGTGAGGAAAAAAATTTTGTCCAGGCGCGTGTGATCTTTGG
						
					

						Genomic sequence
						
							CTTGCATTACACCACGGTGACTTTGGGGACACCTGGGTTGAAGTTTCTTGTGGCTCTTGATACT
GGGAGTGACTTATTTTGGGTGCCTTGTGAATGCGGCAGATGTGCTTCTACTGATGATCCTACAC
TTTACAGCTCTGTATGTTTTACTCACTTTCCCCCCTTTTTAGGGTTATCTTATATCTTTATGAA
ATGATATATTGAGCGAAACGTTGTGGTGTATAACTTAAAGGGTTGATGAAAAGTGCCTTTGACA
GCTACAACATTTTGTTGCATCCATATATTCTATGCTATTTTGCACAAGATGTATATGATGGAAA
TATGAGGAGCTTATTCGAGAGCTTCCCTCTGACGTAGTAAATGATGACTTTTTTCGTGTGAGAA
GTGAAAACAACTGTCATTCATTGCAAGCCTGCAATAGTATCCACAAACATCTTTGCCTTTAGGA
ATGTGGTATACCATGACTCTCATGAGTGGAATTAGATGCTCTGATAAGACATTGGTACAGTAAA
CTAGACAATGATCACTTGCCAAAGAGATAATATTTACGGGTCCTACTCTTTTGGATGCCATTAT
TTTGTGAAGCGGTCAAGGAGAATTTTATAACCAAACTTTCACGAGAGTATGCACGATCGTAGAA
TTCTGTATCTAATTCACTTGTACATTGTTGTCAACTGTGAACAGACAACTAAGTAGTTCTACCC
AATGGAACTTTATGGGAACTGATGAACAATTGATTTGTGAAGTGACAGACTTTTATTGCCTAGT
TTTCCAGTTCGGATTACCATTTTACTATTAATTGTTCGATTCCATCACATCCTTACTCCAAACT
TTGTACATTCATTTTGTCATTTCCTTCTCTAAGCCATGGTTTGATAGAATTATCTTCCTCAAAT
TTTAAGATGGCAAGGTTAAATATACTGTTAACTTTGATTTGCAAGATAATTTATAAGGTGGTTA
GACGGACTGTTGTAGAAATGAGATGCACTTTATTTTGTGGTTCTCTTATATTTTTTCCTTTTCA
CTCCGGCTGAAGTGGATAATGTCTTTTGCTTCAGGATATTGAGCTTAGCATATACAGCCTGAAT
GGATCGTCAACTAGCAAGAAGGTCACCTGCAGTGATAGCTTGTGTACAGACCGCAATAATTGTC
TCAGTTCAAATAACCACTGCCCTTATTCAGTATCCTATGTCTCCTCGGAAACTTCAACTTCAGG
AATTTTGGTGGATGATATTTTGCACTTGAGAACAGATGATAGTGAGGAAAAAAATTTTGTCCAG
GCGCGTGTGATCTTTGG
						
					

			
		

Sequences
Splice junction sequence	CGGAAACTTCAACTTCAGGAATTTTGGTGGATGATATTTTGCACTTGAGAACAGATGATAGTGA GGAAAAAAATTTTGTCCAGGCGCGTGTGATCTTTGGcttgcattacaccacggtgactttgggg acacctgggttgaagtttcttgtggctcttgatactgggagtgacttattttgggtgccttgtg aatgcggc
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: 378 Transcript exons: 46850433-46850571,46851491-46851729 CTTGCATTACACCACGGTGACTTTGGGGACACCTGGGTTGAAGTTTCTTGTGGCTCTTGATACT GGGAGTGACTTATTTTGGGTGCCTTGTGAATGCGGCAGATGTGCTTCTACTGATGATCCTACAC TTTACAGCTCTGATATTGAGCTTAGCATATACAGCCTGAATGGATCGTCAACTAGCAAGAAGGT CACCTGCAGTGATAGCTTGTGTACAGACCGCAATAATTGTCTCAGTTCAAATAACCACTGCCCT TATTCAGTATCCTATGTCTCCTCGGAAACTTCAACTTCAGGAATTTTGGTGGATGATATTTTGC ACTTGAGAACAGATGATAGTGAGGAAAAAAATTTTGTCCAGGCGCGTGTGATCTTTGG
Genomic sequence	CTTGCATTACACCACGGTGACTTTGGGGACACCTGGGTTGAAGTTTCTTGTGGCTCTTGATACT GGGAGTGACTTATTTTGGGTGCCTTGTGAATGCGGCAGATGTGCTTCTACTGATGATCCTACAC TTTACAGCTCTGTATGTTTTACTCACTTTCCCCCCTTTTTAGGGTTATCTTATATCTTTATGAA ATGATATATTGAGCGAAACGTTGTGGTGTATAACTTAAAGGGTTGATGAAAAGTGCCTTTGACA GCTACAACATTTTGTTGCATCCATATATTCTATGCTATTTTGCACAAGATGTATATGATGGAAA TATGAGGAGCTTATTCGAGAGCTTCCCTCTGACGTAGTAAATGATGACTTTTTTCGTGTGAGAA GTGAAAACAACTGTCATTCATTGCAAGCCTGCAATAGTATCCACAAACATCTTTGCCTTTAGGA ATGTGGTATACCATGACTCTCATGAGTGGAATTAGATGCTCTGATAAGACATTGGTACAGTAAA CTAGACAATGATCACTTGCCAAAGAGATAATATTTACGGGTCCTACTCTTTTGGATGCCATTAT TTTGTGAAGCGGTCAAGGAGAATTTTATAACCAAACTTTCACGAGAGTATGCACGATCGTAGAA TTCTGTATCTAATTCACTTGTACATTGTTGTCAACTGTGAACAGACAACTAAGTAGTTCTACCC AATGGAACTTTATGGGAACTGATGAACAATTGATTTGTGAAGTGACAGACTTTTATTGCCTAGT TTTCCAGTTCGGATTACCATTTTACTATTAATTGTTCGATTCCATCACATCCTTACTCCAAACT TTGTACATTCATTTTGTCATTTCCTTCTCTAAGCCATGGTTTGATAGAATTATCTTCCTCAAAT TTTAAGATGGCAAGGTTAAATATACTGTTAACTTTGATTTGCAAGATAATTTATAAGGTGGTTA GACGGACTGTTGTAGAAATGAGATGCACTTTATTTTGTGGTTCTCTTATATTTTTTCCTTTTCA CTCCGGCTGAAGTGGATAATGTCTTTTGCTTCAGGATATTGAGCTTAGCATATACAGCCTGAAT GGATCGTCAACTAGCAAGAAGGTCACCTGCAGTGATAGCTTGTGTACAGACCGCAATAATTGTC TCAGTTCAAATAACCACTGCCCTTATTCAGTATCCTATGTCTCCTCGGAAACTTCAACTTCAGG AATTTTGGTGGATGATATTTTGCACTTGAGAACAGATGATAGTGAGGAAAAAAATTTTGTCCAG GCGCGTGTGATCTTTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.359728963

Conservation Information
Conserved circRNAs	NA
PMCS	0.359728963

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							46850441-46851646(-)
						
						Potential amino acid sequence
						
							MQAKDHTRLDKIFFLTIICSQVQNIIHQNS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	46850441-46851646(-)
Potential amino acid sequence	MQAKDHTRLDKIFFLTIICSQVQNIIHQNS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc02g083450.2_circ_g.1

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