Plant Circular RNA Database

Detail information of Solyc07g017510.2_circ_g.1

			
						 General Information
					
						CircRNA Name
						Solyc07g017510.2_circ_g.1
					
						ID in PlantcircBase
						sly_circ_002233
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 7408758-7411930  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc07g017510.2						
					
						Parent gene annotation
						
							1-phosphatidylinositol-3-phosphate 5-kinase FAB1A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Solyc07g017510.2.1:2

General Information
CircRNA Name	Solyc07g017510.2_circ_g.1
ID in PlantcircBase	sly_circ_002233
Alias	NA
Organism	Solanum lycopersicum
Position	chr7: 7408758-7411930 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc07g017510.2
Parent gene annotation	1-phosphatidylinositol-3-phosphate 5-kinase FAB1A
Parent gene strand	+
Alternative splicing	NA
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	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	Solyc07g017510.2.1:2

			
						 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  
						
							TAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTGACAAAGACCTTGATG
TTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACTtatggtggttaaaggcgttgtttgtaag
aaaaatgtggcgcaccgacgaatgaactcaaaattcaaaaagcctagactcctaattcttggag
gagcactg

									
								

					

						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: 499
Transcript exons: 7408758-7408911,7411586-7411930
TATGGTGGTTAAAGGCGTTGTTTGTAAGAAAAATGTGGCGCACCGACGAATGAACTCAAAATTC
AAAAAGCCTAGACTCCTAATTCTTGGAGGAGCACTGGAATATCAAAGGGTGGCTAATCACTTGT
CAAGTTTTGACACTTTATTGCAGCAGGAAATGGACCATCTGAAGATGGCTGTTGCAAAGATTGA
TGCTCATCATCCAAACATTTTGTTAGTAGAGAAATCAGTATCTCGATTTGCGCAGGAATACCTG
CTTGTGAAAAACATATCTCTAGTTCTCAATGTGAAGCGGCCGCTTTTAGAGCGTATTGCCCGTT
GTACAGGTGCACAAGTAGTCCCTTCAATTGATAATCTTACAACGCCAAAGTTAGGGTACTGTGA
TTCATTTCATGTTGATAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTG
ACAAAGACCTTGATGTTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACT
						
					

						Genomic sequence
						
							TATGGTGGTTAAAGGCGTTGTTTGTAAGAAAAATGTGGCGCACCGACGAATGAACTCAAAATTC
AAAAAGCCTAGACTCCTAATTCTTGGAGGAGCACTGGAATATCAAAGGGTGGCTAATCACTTGT
CAAGTTTTGACACTTTATTGCAGCAGGTCTTCACTCAATCCAATTCTTTATTGATATTTTTAGT
TACTTGATAGGATGCGGAAATGCTATCTGGCCTCCAGACTGCAGGATCTTTGGGACCTTGAACA
CATGATTGTTTCTTCCCTGTTGCTGGAGGGAGTTGAGGTGTGTGCATGTTGGCGTGGACATCAC
GGTTATTAGAAAGAGAGGATATCTCCATATCACTGTTTATCCTTCACTAGACCTTTTTTAAGTT
TGTGTAGAGATGAAGCATTTATGCTAAATGGACCATCTTGTTAGTTATTTTTCCATGTACATGA
CATCACACCATATCTACTTAATAAAACTGTAGGAGCCTTTTCCTCATAGAAAAGCCTTGAATTG
GCTTTAGATCTTATACATAGCATGATTATGAAATTACAAAATTAATGATTGAAATACATGGATA
AGATAATGGCTGAATGTACCCTAGGGTTTGACTTAGTGGTCAATGAAGTGGTTGAGAGCCATGA
GGTGTCTTGCAGGTGGGAGGTGACGAGTATCCCGTGGAATTAGTCGTGGTGCACAAAAGCTATT
CTGGACACCATAATCATCCAAAAGAAAAGATAATGGCTGAACCGTGATACAGAATCATTTCCTT
TAAGATTCAGAACTGAACTATTTAAAAGAAGCTGGGGAGCTAATATGTACACTATCATTGCTAT
TGCTTTGGAGGTCTTCTTGAATTCTAGGATCCATTTCCTATACATTTATTTGCTGGGTAGTACC
TCCAATTTGGGAAATTTTTTAAATCTCGTTGGTCTCTCCTCTCTCTCCTCTCCCTCCCTCTCTC
TCTCTCTCTCTCTCTCTTTTTTGGGCTAGGAGGAGGAACAATTGGTGGAGGGGAACAGAGTGGA
AAGATAAGAGGTATTTCCCTTGTTCGCTTAGCAAATAAACTAGAAGTAAAGGTAAAAGTGGAGG
GTTATACTTCATACATCATCTACTTTTTGATCTTGCCAAAATTAGACAGAAAGAAGAAAAAAAT
ATATATTAGTTCCTTTCCAGCTAGTACTGAACAAGTAATGGGATATGAAATACATTCCTTGATG
AAGGTAACTCAGAAAGTTCCCTCCTCATACTCTAGTTAAACTTAGTTTACCCCAAAATTTGAAT
TTTGTTGGCCATACCTGTTGTCGATCAGCTTAATCATTTTTATTGAGATGTTGCAACTGTACCT
GCTGCAGCATAAAAAAATATGATATGGGGAAGTTGGGTAACAGTAGAAGGGTAATAAGGATTGT
TTTTTTTTTTAATGTGTGGGGGGGCGGGATGAGGAAGGCATGTAAATAAGAGGATGTAGGTCAC
AGGGGAAAGCTGGTCAGTGAGTCTATGTAGTGATGCAAATGAGATAGGCTCAAGGAGGGAGGTC
TCTTGTATGTGCAAGTGTTTATGCATTGTAGTTCATGTTATTCTTTAAATTTCTGGTATTACAA
GTTTTTTTTTATTCTGTTTCTGTTATCAGTTTGTTCTGGTTTTGCTTGTCCTTCATCAAAATAG
TAGACTGGTTCTCTGATGACTTATACAATGTCCTTTCTAAGTATTCACTAGATAAGACATTAGA
GACTGAGGGAGAAATAGTTTTTTCAAGGGATCAATTAAAATGATAGTTAGGTGCTACGGTGCCC
GTCATTCTTATTGTAGTATGTGTATGATTTTAAAAAGATTGTGCAGCAAAAGAATTTGGAAGAA
TAATTAAAAAATGTCTTTGAATAATTTTATCAAGCATGGAGGGCTTTAAATAGACAACTTGAAA
ACAGAATTGTCAAAAATATGCATAATGAAAATTCAAAAAAACCACTAACAAACTAAACCAATCT
ACTAGAAATTTGAAATTAAGAAAAGTAGATTCATTCTAAAACTAAGCAACTTATTATGCTAAAT
TAAAAAAATGCTTCAGTAACTGAAGCAAATTTCAACCTAAGTTGTGCAGACTCTTCATTTTTGT
TATCGACATGTGACGGGTGTGGGTGCAGGATACAAGTGGGGTTCGGTCAACCCACATTGTATAC
TTTGACCATAGTCCATAAACAATTTTGATCCACTAAGAAAATAAGATTTGATCTTCACTGACCA
AATCTGATAGATTTCACCTGTGAAAGTTTGTGGGGCATTCAAAGAGATATTGCAGCTTGCAATG
TTTGAAAAATAGGTTGAATATTAGTATTGGTTAAAAGCGGATTGAAAATGGTTCTTTAGATGAA
CTCTCAGATCCCTTAGGACTAGTGAAACTCTGACTACTATTGGTTTTTAAAAGATGGTGCAGCA
AAAAGATTGGAGGAATAATTTTAAATCTCTCTCAATAATTTTAAACATAATCTGCAGAAAATAT
GTATAGCAAAAATTTAAAAACACTAAAATAACTCAACTAAGAAAATCTAATGGAAATTAAAGAT
TCAAAAGTATGTTCATCCTAAAACTAAGCAATTTATTATGATAAAAGATGCTGCAGTGACTGAA
GCAAATATCTACAGTATGTCATTGGTTTCTTGTTTTATCGAACCATTCAGATTTGCTAGAATGC
TCTAGTTTCTTGTTATCTTGGTTTTGACCAGGGAGAGAAGACTTTCTAATAAAAGCACATTGCG
TTATTTGGGTTATCAGTTTTATTTGGATTAACACTGTTTGGTTCATCACTTTTACTTGGATCAT
TCTTTCTTCTAGGAAATGGACCATCTGAAGATGGCTGTTGCAAAGATTGATGCTCATCATCCAA
ACATTTTGTTAGTAGAGAAATCAGTATCTCGATTTGCGCAGGAATACCTGCTTGTGAAAAACAT
ATCTCTAGTTCTCAATGTGAAGCGGCCGCTTTTAGAGCGTATTGCCCGTTGTACAGGTGCACAA
GTAGTCCCTTCAATTGATAATCTTACAACGCCAAAGTTAGGGTACTGTGATTCATTTCATGTTG
ATAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTGACAAAGACCTTGAT
GTTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACT
						
					

			
		

Sequences
Splice junction sequence	TAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTGACAAAGACCTTGATG TTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACTtatggtggttaaaggcgttgtttgtaag aaaaatgtggcgcaccgacgaatgaactcaaaattcaaaaagcctagactcctaattcttggag gagcactg
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: 499 Transcript exons: 7408758-7408911,7411586-7411930 TATGGTGGTTAAAGGCGTTGTTTGTAAGAAAAATGTGGCGCACCGACGAATGAACTCAAAATTC AAAAAGCCTAGACTCCTAATTCTTGGAGGAGCACTGGAATATCAAAGGGTGGCTAATCACTTGT CAAGTTTTGACACTTTATTGCAGCAGGAAATGGACCATCTGAAGATGGCTGTTGCAAAGATTGA TGCTCATCATCCAAACATTTTGTTAGTAGAGAAATCAGTATCTCGATTTGCGCAGGAATACCTG CTTGTGAAAAACATATCTCTAGTTCTCAATGTGAAGCGGCCGCTTTTAGAGCGTATTGCCCGTT GTACAGGTGCACAAGTAGTCCCTTCAATTGATAATCTTACAACGCCAAAGTTAGGGTACTGTGA TTCATTTCATGTTGATAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTG ACAAAGACCTTGATGTTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACT
Genomic sequence	TATGGTGGTTAAAGGCGTTGTTTGTAAGAAAAATGTGGCGCACCGACGAATGAACTCAAAATTC AAAAAGCCTAGACTCCTAATTCTTGGAGGAGCACTGGAATATCAAAGGGTGGCTAATCACTTGT CAAGTTTTGACACTTTATTGCAGCAGGTCTTCACTCAATCCAATTCTTTATTGATATTTTTAGT TACTTGATAGGATGCGGAAATGCTATCTGGCCTCCAGACTGCAGGATCTTTGGGACCTTGAACA CATGATTGTTTCTTCCCTGTTGCTGGAGGGAGTTGAGGTGTGTGCATGTTGGCGTGGACATCAC GGTTATTAGAAAGAGAGGATATCTCCATATCACTGTTTATCCTTCACTAGACCTTTTTTAAGTT TGTGTAGAGATGAAGCATTTATGCTAAATGGACCATCTTGTTAGTTATTTTTCCATGTACATGA CATCACACCATATCTACTTAATAAAACTGTAGGAGCCTTTTCCTCATAGAAAAGCCTTGAATTG GCTTTAGATCTTATACATAGCATGATTATGAAATTACAAAATTAATGATTGAAATACATGGATA AGATAATGGCTGAATGTACCCTAGGGTTTGACTTAGTGGTCAATGAAGTGGTTGAGAGCCATGA GGTGTCTTGCAGGTGGGAGGTGACGAGTATCCCGTGGAATTAGTCGTGGTGCACAAAAGCTATT CTGGACACCATAATCATCCAAAAGAAAAGATAATGGCTGAACCGTGATACAGAATCATTTCCTT TAAGATTCAGAACTGAACTATTTAAAAGAAGCTGGGGAGCTAATATGTACACTATCATTGCTAT TGCTTTGGAGGTCTTCTTGAATTCTAGGATCCATTTCCTATACATTTATTTGCTGGGTAGTACC TCCAATTTGGGAAATTTTTTAAATCTCGTTGGTCTCTCCTCTCTCTCCTCTCCCTCCCTCTCTC TCTCTCTCTCTCTCTCTTTTTTGGGCTAGGAGGAGGAACAATTGGTGGAGGGGAACAGAGTGGA AAGATAAGAGGTATTTCCCTTGTTCGCTTAGCAAATAAACTAGAAGTAAAGGTAAAAGTGGAGG GTTATACTTCATACATCATCTACTTTTTGATCTTGCCAAAATTAGACAGAAAGAAGAAAAAAAT ATATATTAGTTCCTTTCCAGCTAGTACTGAACAAGTAATGGGATATGAAATACATTCCTTGATG AAGGTAACTCAGAAAGTTCCCTCCTCATACTCTAGTTAAACTTAGTTTACCCCAAAATTTGAAT TTTGTTGGCCATACCTGTTGTCGATCAGCTTAATCATTTTTATTGAGATGTTGCAACTGTACCT GCTGCAGCATAAAAAAATATGATATGGGGAAGTTGGGTAACAGTAGAAGGGTAATAAGGATTGT TTTTTTTTTTAATGTGTGGGGGGGCGGGATGAGGAAGGCATGTAAATAAGAGGATGTAGGTCAC AGGGGAAAGCTGGTCAGTGAGTCTATGTAGTGATGCAAATGAGATAGGCTCAAGGAGGGAGGTC TCTTGTATGTGCAAGTGTTTATGCATTGTAGTTCATGTTATTCTTTAAATTTCTGGTATTACAA GTTTTTTTTTATTCTGTTTCTGTTATCAGTTTGTTCTGGTTTTGCTTGTCCTTCATCAAAATAG TAGACTGGTTCTCTGATGACTTATACAATGTCCTTTCTAAGTATTCACTAGATAAGACATTAGA GACTGAGGGAGAAATAGTTTTTTCAAGGGATCAATTAAAATGATAGTTAGGTGCTACGGTGCCC GTCATTCTTATTGTAGTATGTGTATGATTTTAAAAAGATTGTGCAGCAAAAGAATTTGGAAGAA TAATTAAAAAATGTCTTTGAATAATTTTATCAAGCATGGAGGGCTTTAAATAGACAACTTGAAA ACAGAATTGTCAAAAATATGCATAATGAAAATTCAAAAAAACCACTAACAAACTAAACCAATCT ACTAGAAATTTGAAATTAAGAAAAGTAGATTCATTCTAAAACTAAGCAACTTATTATGCTAAAT TAAAAAAATGCTTCAGTAACTGAAGCAAATTTCAACCTAAGTTGTGCAGACTCTTCATTTTTGT TATCGACATGTGACGGGTGTGGGTGCAGGATACAAGTGGGGTTCGGTCAACCCACATTGTATAC TTTGACCATAGTCCATAAACAATTTTGATCCACTAAGAAAATAAGATTTGATCTTCACTGACCA AATCTGATAGATTTCACCTGTGAAAGTTTGTGGGGCATTCAAAGAGATATTGCAGCTTGCAATG TTTGAAAAATAGGTTGAATATTAGTATTGGTTAAAAGCGGATTGAAAATGGTTCTTTAGATGAA CTCTCAGATCCCTTAGGACTAGTGAAACTCTGACTACTATTGGTTTTTAAAAGATGGTGCAGCA AAAAGATTGGAGGAATAATTTTAAATCTCTCTCAATAATTTTAAACATAATCTGCAGAAAATAT GTATAGCAAAAATTTAAAAACACTAAAATAACTCAACTAAGAAAATCTAATGGAAATTAAAGAT TCAAAAGTATGTTCATCCTAAAACTAAGCAATTTATTATGATAAAAGATGCTGCAGTGACTGAA GCAAATATCTACAGTATGTCATTGGTTTCTTGTTTTATCGAACCATTCAGATTTGCTAGAATGC TCTAGTTTCTTGTTATCTTGGTTTTGACCAGGGAGAGAAGACTTTCTAATAAAAGCACATTGCG TTATTTGGGTTATCAGTTTTATTTGGATTAACACTGTTTGGTTCATCACTTTTACTTGGATCAT TCTTTCTTCTAGGAAATGGACCATCTGAAGATGGCTGTTGCAAAGATTGATGCTCATCATCCAA ACATTTTGTTAGTAGAGAAATCAGTATCTCGATTTGCGCAGGAATACCTGCTTGTGAAAAACAT ATCTCTAGTTCTCAATGTGAAGCGGCCGCTTTTAGAGCGTATTGCCCGTTGTACAGGTGCACAA GTAGTCCCTTCAATTGATAATCTTACAACGCCAAAGTTAGGGTACTGTGATTCATTTCATGTTG ATAAGTTTGTGGAAGAGCATGGTAGTGCTGGGCAAGCTGGAAAGAAACTGACAAAGACCTTGAT GTTTTTCGAAGGATGCCCAAAGCCTTTTGGCTGTACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.335402556

Conservation Information
Conserved circRNAs	NA
PMCS	0.335402556

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7411907-7408807(+)
7408760-7408766(+)
						
						Potential amino acid sequence
						
							MPKAFWLYLWWLKALFVRKMWRTDE*(+)
MVVKGVVCKKNVAHRRMNSKFKKPRLLILGGALEYQRVANHLSSFDTLLQQEMDHLKMAVAKID
AHHPNILLVEKSVSRFAQEYLLVKNISLVLNVKRPLLERIARCTGAQVVPSIDNLTTPKLGYCD
SFHVDKFVEEHGSAGQAGKKLTKTLMFFEGCPKPFGCTYGG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7411907-7408807(+) 7408760-7408766(+)
Potential amino acid sequence	MPKAFWLYLWWLKALFVRKMWRTDE(+) MVVKGVVCKKNVAHRRMNSKFKKPRLLILGGALEYQRVANHLSSFDTLLQQEMDHLKMAVAKID AHHPNILLVEKSVSRFAQEYLLVKNISLVLNVKRPLLERIARCTGAQVVPSIDNLTTPKLGYCD SFHVDKFVEEHGSAGQAGKKLTKTLMFFEGCPKPFGCTYGG(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017

circRNA

Detail information of Solyc07g017510.2_circ_g.1

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