Plant Circular RNA Database

Detail information of Solyc04g082560.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc04g082560.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001593
					
						Alias
						4:63794638|63796662
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr4: 66201268-66203292  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc04g082560.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc04g082560.2_circ_g.1 						
					
						Support reads
						10
					
						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
						Solyc04g082560.2.1:7

General Information
CircRNA Name	Solyc04g082560.2_circ_g.2
ID in PlantcircBase	sly_circ_001593
Alias	4:63794638\|63796662
Organism	Solanum lycopersicum
Position	chr4: 66201268-66203292 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc04g082560.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc04g082560.2_circ_g.1
Support reads	10
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	Solyc04g082560.2.1:7

			
						 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  
						
							AGGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAACCATTT
CGGCAAGAGCTTTAAAACGGAATCTGAAACTGATAGgatgaaagcaaggacaagatgcttctgg
attctaaggagaagcttgaattctaccgcacaaaaatgcaggatcttgtgagtagttgccgcct
tcaatgta

									
								

					

						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: 803
Transcript exons: 66201268-66201342,66201496-66201567,66201676-66201774,66
202095-66202166,66202272-66202386,66202805-66202873,6620
2992-66203292
GATGAAAGCAAGGACAAGATGCTTCTGGATTCTAAGGAGAAGCTTGAATTCTACCGCACAAAAA
TGCAGGATCTTGTTTTGTATAAAAGTAGATGTGATAACCGGCTTAATGAAATCACTGAAAGGGC
ATTGGCTGATAAACGTGAGGCCGAGCTTCTTGGCAAAAAATATGAAGAGAAGTACAAGCAAGTT
GCAGAAATTGCTTCTAAACTGACAATTGAAGAAGCATCATTTCGTGATACTCAAGAGAGAAAGC
TGGAGTTGCAACAGGCAATCACTAAAATGGAACAAGGTGGCAGCACTGATGGTATTCTTCAGGT
CCGTGCTGATCGCATACAACATGATCTTGAGGAGCTACTGAAGGCCTTGGTGGATCGTTGCAAG
AAACACGAGCTTAATATGAAGTCAACTGCGTTAATTGAACTCCCCCCTGGCTGGCAACCTGGAA
TTCCGGAGATATCAGCTGTTTGGGATGAAGATTGGGATAAATTCGAAGATGAAGGATTTTCTTT
TGATGTAGCTGTGCCTGAAAATTCCAAATCCACATCTGTTCAGAAGGAAAGTTCTCCGACTCAT
CGCGAATCCTCTGATTCTATGTCAAATGCTGATGCCAAGTCAGAAAACCATTCCGCTAAAGGAA
ACAATAGTACTGTTGAGACTGATTTGATGTATATGCATAGCGACGAAGAGTCAAAAAGTCCACA
GGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAACCATTTC
GGCAAGAGCTTTAAAACGGAATCTGAAACTGATAG
						
					

						Genomic sequence
						
							GATGAAAGCAAGGACAAGATGCTTCTGGATTCTAAGGAGAAGCTTGAATTCTACCGCACAAAAA
TGCAGGATCTTGTGAGTAGTTGCCGCCTTCAATGTACAGCATTGTTGCATTTTTAATTTCGAGT
TGCTTTTTCTCAACTATCACCTGCTCTTTATGTTATATTTATCTCTTCATTTTTGTTTCCTATC
TCATCCATTTTCTTTATTTATTGGGCTTTCCTCCAGGTTTTGTATAAAAGTAGATGTGATAACC
GGCTTAATGAAATCACTGAAAGGGCATTGGCTGATAAACGTGAGGTACAATTCAGTCCATTGAT
CTCTCTCTCTCTCTCTTTGAAGTTCATAATTTGTTTGGTTTCAGTTTCTCCCTTCTTATGCACT
TTGTCAATTGATGAGTTATTTTAGGCCGAGCTTCTTGGCAAAAAATATGAAGAGAAGTACAAGC
AAGTTGCAGAAATTGCTTCTAAACTGACAATTGAAGAAGCATCATTTCGTGATACTCAAGTAAG
ACTTTGCTCCATATATTCTTTCAAATGTGTACTATAGTTATGTATCCAGCTCCTTCACAAATCG
AAAGATTTGAGTTTACTGCTGCAAGATGCTATACACATAAGAATAAACCATTCCTCACTGCATC
TCTATGAATTAAACGCCTTCCCGGCTTCTTCTAGTGTTTCAATTCTTTAATTGTTTAGCTGGCT
TGTTTATAGCATTTTCTAGCTTGTCATTTGTTTTATTCTTTTCCTAGTCTTTAGTGCTCGTTGA
CTTGTTGGAGCATATTAGTTTATATTCTTGAGATAAAAGGAAAAAATCCCCTTATTCAGGAGAG
AAAGCTGGAGTTGCAACAGGCAATCACTAAAATGGAACAAGGTGGCAGCACTGATGGTATTCTT
CAGGTGAATATAACAGACCTTATTACTTTGGTTACTCGGGTAAACTGTTGGGAAGTATGTGTTT
CCATAGGAACTTATGCTATGTTTCGTTCACTGTTGGTTGTCCAGGTCCGTGCTGATCGCATACA
ACATGATCTTGAGGAGCTACTGAAGGCCTTGGTGGATCGTTGCAAGAAACACGAGCTTAATATG
AAGTCAACTGCGTTAATTGAACTCCCCCCTGGTGAGTTCTTTTCCCCTTGTTTTTCTACGTCTT
GACAGCTTGTTCTCTGTTTGTTATGTTTTTATTGCTCCTATTGAGTCTCTTATGAACTCTGAAC
ATCCTACCCTGGTTAAGAAGTCAACTCTACTAATTTCATCTGCATATGGGCATAATGTCATATC
AGTTCTTGAGGTCCTATGTTTTCTGTGTTTGCTACTTAGATAATACAATTGGAATTTATTCTTG
CTCAATTCTTGCAGTTATTATTGAAAATTGAATATTTTTCAATGGATTTTGAATTTATTGTGTT
GATGTTGTTTATCAAATAAAAATAGGTAACTTGAAGAAAGTTGGCAACTTTTCAATTTGTTGCA
TCACATTTGTTTATTATGTTTTCGATCTAACTTTTTTGGTCTGAAATGGTCTTCTCCTTCTCAA
GGCTGGCAACCTGGAATTCCGGAGATATCAGCTGTTTGGGATGAAGATTGGGATAAATTCGAAG
ATGAAGGTTTGCTTTCTTGAATATATTCCCTCCCGCTTTTCCCGTTCTTCATTGGTTGTCTTTC
TGGCACCATATAAGTTGCATAGTGTTTGACGTATGTGCATCCCTATATCACTTTCTGCAGGATT
TTCTTTTGATGTAGCTGTGCCTGAAAATTCCAAATCCACATCTGTTCAGAAGGAAAGTTCTCCG
ACTCATCGCGAATCCTCTGATTCTATGTCAAATGCTGATGCCAAGTCAGAAAACCATTCCGCTA
AAGGAAACAATAGTACTGTTGAGACTGATTTGATGTATATGCATAGCGACGAAGAGTCAAAAAG
TCCACAGGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAAC
CATTTCGGCAAGAGCTTTAAAACGGAATCTGAAACTGATAG
						
					

			
		

Sequences
Splice junction sequence	AGGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAACCATTT CGGCAAGAGCTTTAAAACGGAATCTGAAACTGATAGgatgaaagcaaggacaagatgcttctgg attctaaggagaagcttgaattctaccgcacaaaaatgcaggatcttgtgagtagttgccgcct tcaatgta
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: 803 Transcript exons: 66201268-66201342,66201496-66201567,66201676-66201774,66 202095-66202166,66202272-66202386,66202805-66202873,6620 2992-66203292 GATGAAAGCAAGGACAAGATGCTTCTGGATTCTAAGGAGAAGCTTGAATTCTACCGCACAAAAA TGCAGGATCTTGTTTTGTATAAAAGTAGATGTGATAACCGGCTTAATGAAATCACTGAAAGGGC ATTGGCTGATAAACGTGAGGCCGAGCTTCTTGGCAAAAAATATGAAGAGAAGTACAAGCAAGTT GCAGAAATTGCTTCTAAACTGACAATTGAAGAAGCATCATTTCGTGATACTCAAGAGAGAAAGC TGGAGTTGCAACAGGCAATCACTAAAATGGAACAAGGTGGCAGCACTGATGGTATTCTTCAGGT CCGTGCTGATCGCATACAACATGATCTTGAGGAGCTACTGAAGGCCTTGGTGGATCGTTGCAAG AAACACGAGCTTAATATGAAGTCAACTGCGTTAATTGAACTCCCCCCTGGCTGGCAACCTGGAA TTCCGGAGATATCAGCTGTTTGGGATGAAGATTGGGATAAATTCGAAGATGAAGGATTTTCTTT TGATGTAGCTGTGCCTGAAAATTCCAAATCCACATCTGTTCAGAAGGAAAGTTCTCCGACTCAT CGCGAATCCTCTGATTCTATGTCAAATGCTGATGCCAAGTCAGAAAACCATTCCGCTAAAGGAA ACAATAGTACTGTTGAGACTGATTTGATGTATATGCATAGCGACGAAGAGTCAAAAAGTCCACA GGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAACCATTTC GGCAAGAGCTTTAAAACGGAATCTGAAACTGATAG
Genomic sequence	GATGAAAGCAAGGACAAGATGCTTCTGGATTCTAAGGAGAAGCTTGAATTCTACCGCACAAAAA TGCAGGATCTTGTGAGTAGTTGCCGCCTTCAATGTACAGCATTGTTGCATTTTTAATTTCGAGT TGCTTTTTCTCAACTATCACCTGCTCTTTATGTTATATTTATCTCTTCATTTTTGTTTCCTATC TCATCCATTTTCTTTATTTATTGGGCTTTCCTCCAGGTTTTGTATAAAAGTAGATGTGATAACC GGCTTAATGAAATCACTGAAAGGGCATTGGCTGATAAACGTGAGGTACAATTCAGTCCATTGAT CTCTCTCTCTCTCTCTTTGAAGTTCATAATTTGTTTGGTTTCAGTTTCTCCCTTCTTATGCACT TTGTCAATTGATGAGTTATTTTAGGCCGAGCTTCTTGGCAAAAAATATGAAGAGAAGTACAAGC AAGTTGCAGAAATTGCTTCTAAACTGACAATTGAAGAAGCATCATTTCGTGATACTCAAGTAAG ACTTTGCTCCATATATTCTTTCAAATGTGTACTATAGTTATGTATCCAGCTCCTTCACAAATCG AAAGATTTGAGTTTACTGCTGCAAGATGCTATACACATAAGAATAAACCATTCCTCACTGCATC TCTATGAATTAAACGCCTTCCCGGCTTCTTCTAGTGTTTCAATTCTTTAATTGTTTAGCTGGCT TGTTTATAGCATTTTCTAGCTTGTCATTTGTTTTATTCTTTTCCTAGTCTTTAGTGCTCGTTGA CTTGTTGGAGCATATTAGTTTATATTCTTGAGATAAAAGGAAAAAATCCCCTTATTCAGGAGAG AAAGCTGGAGTTGCAACAGGCAATCACTAAAATGGAACAAGGTGGCAGCACTGATGGTATTCTT CAGGTGAATATAACAGACCTTATTACTTTGGTTACTCGGGTAAACTGTTGGGAAGTATGTGTTT CCATAGGAACTTATGCTATGTTTCGTTCACTGTTGGTTGTCCAGGTCCGTGCTGATCGCATACA ACATGATCTTGAGGAGCTACTGAAGGCCTTGGTGGATCGTTGCAAGAAACACGAGCTTAATATG AAGTCAACTGCGTTAATTGAACTCCCCCCTGGTGAGTTCTTTTCCCCTTGTTTTTCTACGTCTT GACAGCTTGTTCTCTGTTTGTTATGTTTTTATTGCTCCTATTGAGTCTCTTATGAACTCTGAAC ATCCTACCCTGGTTAAGAAGTCAACTCTACTAATTTCATCTGCATATGGGCATAATGTCATATC AGTTCTTGAGGTCCTATGTTTTCTGTGTTTGCTACTTAGATAATACAATTGGAATTTATTCTTG CTCAATTCTTGCAGTTATTATTGAAAATTGAATATTTTTCAATGGATTTTGAATTTATTGTGTT GATGTTGTTTATCAAATAAAAATAGGTAACTTGAAGAAAGTTGGCAACTTTTCAATTTGTTGCA TCACATTTGTTTATTATGTTTTCGATCTAACTTTTTTGGTCTGAAATGGTCTTCTCCTTCTCAA GGCTGGCAACCTGGAATTCCGGAGATATCAGCTGTTTGGGATGAAGATTGGGATAAATTCGAAG ATGAAGGTTTGCTTTCTTGAATATATTCCCTCCCGCTTTTCCCGTTCTTCATTGGTTGTCTTTC TGGCACCATATAAGTTGCATAGTGTTTGACGTATGTGCATCCCTATATCACTTTCTGCAGGATT TTCTTTTGATGTAGCTGTGCCTGAAAATTCCAAATCCACATCTGTTCAGAAGGAAAGTTCTCCG ACTCATCGCGAATCCTCTGATTCTATGTCAAATGCTGATGCCAAGTCAGAAAACCATTCCGCTA AAGGAAACAATAGTACTGTTGAGACTGATTTGATGTATATGCATAGCGACGAAGAGTCAAAAAG TCCACAGGGAAGTCCACGAGAACAAACAGCATTTGATAGTCCTTCTGGTGAATACTCTGATAAC CATTTCGGCAAGAGCTTTAAAACGGAATCTGAAACTGATAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.578093669

Conservation Information
Conserved circRNAs	NA
PMCS	0.578093669

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							66201287-66201739(+)
						
						Potential amino acid sequence
						
							MLLDSKEKLEFYRTKMQDLVLYKSRCDNRLNEITERALADKREAELLGKKYEEKYKQVAEIASK
LTIEEASFRDTQERKLELQQAITKMEQGGSTDGILQVRADRIQHDLEELLKALVDRCKKHELNM
KSTALIELPPGWQPGIPEISAVWDEDWDKFEDEGFSFDVAVPENSKSTSVQKESSPTHRESSDS
MSNADAKSENHSAKGNNSTVETDLMYMHSDEESKSPQGSPREQTAFDSPSGEYSDNHFGKSFKT
ESETDRMKARTRCFWILRRSLNSTAQKCRILFCIKVDVITGLMKSLKGHWLINVRPSFLAKNMK
RSTSKLQKLLLN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						fruit ripening

Functional Information
Coding potential	Y
Potential coding position	66201287-66201739(+)
Potential amino acid sequence	MLLDSKEKLEFYRTKMQDLVLYKSRCDNRLNEITERALADKREAELLGKKYEEKYKQVAEIASK LTIEEASFRDTQERKLELQQAITKMEQGGSTDGILQVRADRIQHDLEELLKALVDRCKKHELNM KSTALIELPPGWQPGIPEISAVWDEDWDKFEDEGFSFDVAVPENSKSTSVQKESSPTHRESSDS MSNADAKSENHSAKGNNSTVETDLMYMHSDEESKSPQGSPREQTAFDSPSGEYSDNHFGKSFKT ESETDRMKARTRCFWILRRSLNSTAQKCRILFCIKVDVITGLMKSLKGHWLINVRPSFLAKNMK RSTSKLQKLLLN*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	fruit ripening

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc04g082560.2_circ_g.2

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