Plant Circular RNA Database

Detail information of Solyc05g009780.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc05g009780.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_001647
					
						Alias
						5:3974975|3977801
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr5: 3974975-3977801  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Segemehl, CIRI
					
						Parent gene
						
							Solyc05g009780.2						
					
						Parent gene annotation
						
							Methionine aminopeptidase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc05g009780.2_circ_g.1 						
					
						Support reads
						5
					
						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
						Solyc05g009780.2.1:6

General Information
CircRNA Name	Solyc05g009780.2_circ_g.2
ID in PlantcircBase	sly_circ_001647
Alias	5:3974975\|3977801
Organism	Solanum lycopersicum
Position	chr5: 3974975-3977801 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	Segemehl, CIRI
Parent gene	Solyc05g009780.2
Parent gene annotation	Methionine aminopeptidase
Parent gene strand	-
Alternative splicing	Solyc05g009780.2_circ_g.1
Support reads	5
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	Solyc05g009780.2.1:6

			
						 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  
						
							TCTTTGGAAATCCCCCATAGCCTAAGGGAGATGGATAAGCGCCAGCATCGATTATCATTTGATG
CACAGCTTTGTCAATTTCATTTGTTGTTACTGAAGGcgatagtaaatgtttgcccttcaaccat
ggagccggacttgtcattccctgccgtaaatgattacattaggaaaaccagtacctttaataca
gcttgaat

									
								

					

						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: 502
Transcript exons: 3974975-3975022,3976553-3976650,3976968-3977047,3977273-
3977344,3977520-3977561,3977640-3977801
CGATAGTAAATGTTTGCCCTTCAACCATGGAGCCGGACTTGTCATTCCGGTGATGAAATATGAG
TGGTTCAGAGTGAAATACTGTCCCAATACCATGTCCAACAAAACGATCAACAACACCATAACCA
AATTTTTCAGCATGTTCACTGATCCTCTTTCCTATCTTCCTATAAAGAGCACCATCTCTGCAAA
CAGCAATTCCATAGTGCAAGCACTCCTCAGTCACCTTTACAAGCCGCTTTATGGATTCACTCAC
GTCACCACAGAAAAAGGTCTTTGACGTATCTCCATGATAACCATTCAGGTAAACGGTCACGTCA
ATGTTTATTATGTCTCCATCCTGCAGCTGCCGTGAGTCAGGTATTCCATGACACATACACTCAT
TGACGGATGTGCACACACTCTTTGGAAATCCCCCATAGCCTAAGGGAGATGGATAAGCGCCAGC
ATCGATTATCATTTGATGCACAGCTTTGTCAATTTCATTTGTTGTTACTGAAGG
						
					

						Genomic sequence
						
							CGATAGTAAATGTTTGCCCTTCAACCATGGAGCCGGACTTGTCATTCCCTGCCGTAAATGATTA
CATTAGGAAAACCAGTACCTTTAATACAGCTTGAATATCTTATATCACATTCAGCAGTCAGATA
AAAAATTGTCCATGTTCTAATCAAGATAACCTCGTGAAAAGGAACAAATCAAAGTCAGACTTGA
ACGAGACCTGATAAGCAAAGATAAAACCAAATTGATCATATATACCTGAAAGGATCATCAGCCT
TGACACACAGTAATTATTATATATTATGAACTAATTTTATTTTTATGATTTGTGTTCATCTCAA
AGGGATTAGTATTAAACAAGAATGAGACGCTAAAGATGAACAAGGGGACCTGGAAGAACTTAAG
AAATCATTTTTCTCAAAAAAAGAAGTTAAAGAACTCATTTTTCTCAAAAAAAAAGAAGTTAAGG
AACTCATGAGCCATGAGAACGTAAAATGATCCATCTATTGAAGTGTCTAGCGTCCAATGGGTCA
TGATCACTATGACCCAATGAATACAACTAGTGATCTAAGTTTCAGTCAAGGAATTACTTAAGAG
ATAGCAATTCAAAAATCAGGGCATCCATTCCTTGAAAAATGGGACTAAAGTGGTGCTGAAACAA
TCTTTTCACTTGAAGGTGACATTCAATTTAAAGGCCAAATGTCGTGATGCTAAGAGAGGTAAGT
GACCACTCCCTTTGAAGTCTATGCATTTTATATTAGTTGCAAATAAGCAATGAAAAGAGGAGAT
TCAGTTAACCATAAAATAATGTATTAGCAACTAAGAAGTCCGTGGAAATAGAACAAGCCAACTA
GTGGCTTTTGCATGTTAATATAAATGTTTCTTCAAGTAAAGAACCAATTTTTGAACATGTTCTG
ATATCATTTCATATAAACTATAATCTACATTGTTATTTATTATATTGTTAATACATGATAGTGA
AGCTGTGTGACCTATAGGTCACGAATTCGAACCGTGGAAGCAACCACTAATGCTTGCTTGCATT
GTGGTAGGCTGTCTACATCACAATCCTAGGGTGCGGCCCTTCCCCTGAGCCTGCGCAAATGTGG
GATGTTGTGTGCACAGGGCTGCCCTGTTATTTTATTTTAACATAAGACGGTGATATCTTTGGAT
CAGGATAAACAGGGATCACACAAAGGACAACTTATTTTGTGTCATTTCGTCCAACTTTCTTAAT
CTAGTTATAGCTTGATGTTGACTGTTAAGAGCTAATCCAGATTTTGCTAAGCTCTAGCAAAGAA
AATCCAATTATCCGCAGAACAATCAACTCAACTGATATGCAATGAATGGCAATGTCAATTAGCG
TTCTCTATAAGATATTTACGCGTATACATACACAACCTGTTCTTCAGAGAAACGCAAGGACAGG
ACAGACACAACCAACTCCTCCAAAAGTAAACCTATTTAGTATTAGTTTTATGTTAGATTAAGCA
TGGTCTTCACAATTCTAGCGAATCTTCCACAACTTTCAGAGATTTTACAGGATGAACACAAAGG
CAGTAGTAAATGTCAAAGTCGATAAAAATGAGAGTAACTTACGGTGATGAAATATGAGTGGTTC
AGAGTGAAATACTGTCCCAATACCATGTCCAACAAAACGATCAACAACACCATAACCAAATTTT
TCAGCATGTTCACTGAAACAAAAGTCCAAAACGTTCAATGTCCAAGACAGAGTGTCCACAAAAA
ATAAGGTACATACACAAGAAATGACATTAATTGTTTGCAAACAATATTTAAGAAAATCACAGTA
AATTATTCAAAGTTTCATCAGAAGAAGGAAATTTCACTACCGACGTTTTTTAGTGATAACTAAA
AGTTTTTGAATCTGATAAACAGAAACAGTTTGACACCTATAGGAACTTCAAAATAGATAGACTG
TTGAAGCTTCAAAATATCCATATCACAAAATAATATTCACAAATTCACGATAATATCATATTCA
TAAAATTACCTGATCCTCTTTCCTATCTTCCTATAAAGAGCACCATCTCTGCAAACAGCAATTC
CATAGTGCAAGCACTCCTCAGTCACCTGCCACAGTAGGATATACAGATATAATTAATATAATGA
GCATCGGATGATAAAAGAGACATTAGTTCTATTGCTAATACTGACTGGTATCTTAAATCTTAAC
CAGTCTTACCACAGCAGAGTTCAATTTCAAATAGCAGTGATCTGATTAAGTTTAAGCAAAACTT
TGTTAAACTAATAACCAGAAAGTTTCAGCATTCCTTTCATAATTGAAGAAATCTATACCTTTAC
AAGCCGCTTTATGGATTCACTCACGTCACCACAGAAAAAGGTCTTTGACGTATCTCCATGATAA
CCCTAAAAAAGGAACAAAGCAATGATCCTTACAATTTACAAGGTTCATCCAGAATCCAACAGCA
GAAATTTCAGAGAAGACAAATGTCCTTCTAAATACTAGGGTAAAGACCGGCTAGCAGTAAAAAA
GATAGCACATGTAGCCTATTACAATAATGAAGGGGCATCGACAACTTACATTCAGGTAAACGGT
CACGTCAATGTTTATTATGTCTCCATCCTGCACATTATATTAATATTTGTCTTGAATACACATA
TAAAAAGTTTAAGCAAGAGGATGATATGAAAAGATAAAGACCTGCAGCTGCCGTGAGTCAGGTA
TTCCATGACACATACACTCATTGACGGATGTGCACACACTCTTTGGAAATCCCCCATAGCCTAA
GGGAGATGGATAAGCGCCAGCATCGATTATCATTTGATGCACAGCTTTGTCAATTTCATTTGTT
GTTACTGAAGG
						
					

			
		

Sequences
Splice junction sequence	TCTTTGGAAATCCCCCATAGCCTAAGGGAGATGGATAAGCGCCAGCATCGATTATCATTTGATG CACAGCTTTGTCAATTTCATTTGTTGTTACTGAAGGcgatagtaaatgtttgcccttcaaccat ggagccggacttgtcattccctgccgtaaatgattacattaggaaaaccagtacctttaataca gcttgaat
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: 502 Transcript exons: 3974975-3975022,3976553-3976650,3976968-3977047,3977273- 3977344,3977520-3977561,3977640-3977801 CGATAGTAAATGTTTGCCCTTCAACCATGGAGCCGGACTTGTCATTCCGGTGATGAAATATGAG TGGTTCAGAGTGAAATACTGTCCCAATACCATGTCCAACAAAACGATCAACAACACCATAACCA AATTTTTCAGCATGTTCACTGATCCTCTTTCCTATCTTCCTATAAAGAGCACCATCTCTGCAAA CAGCAATTCCATAGTGCAAGCACTCCTCAGTCACCTTTACAAGCCGCTTTATGGATTCACTCAC GTCACCACAGAAAAAGGTCTTTGACGTATCTCCATGATAACCATTCAGGTAAACGGTCACGTCA ATGTTTATTATGTCTCCATCCTGCAGCTGCCGTGAGTCAGGTATTCCATGACACATACACTCAT TGACGGATGTGCACACACTCTTTGGAAATCCCCCATAGCCTAAGGGAGATGGATAAGCGCCAGC ATCGATTATCATTTGATGCACAGCTTTGTCAATTTCATTTGTTGTTACTGAAGG
Genomic sequence	CGATAGTAAATGTTTGCCCTTCAACCATGGAGCCGGACTTGTCATTCCCTGCCGTAAATGATTA CATTAGGAAAACCAGTACCTTTAATACAGCTTGAATATCTTATATCACATTCAGCAGTCAGATA AAAAATTGTCCATGTTCTAATCAAGATAACCTCGTGAAAAGGAACAAATCAAAGTCAGACTTGA ACGAGACCTGATAAGCAAAGATAAAACCAAATTGATCATATATACCTGAAAGGATCATCAGCCT TGACACACAGTAATTATTATATATTATGAACTAATTTTATTTTTATGATTTGTGTTCATCTCAA AGGGATTAGTATTAAACAAGAATGAGACGCTAAAGATGAACAAGGGGACCTGGAAGAACTTAAG AAATCATTTTTCTCAAAAAAAGAAGTTAAAGAACTCATTTTTCTCAAAAAAAAAGAAGTTAAGG AACTCATGAGCCATGAGAACGTAAAATGATCCATCTATTGAAGTGTCTAGCGTCCAATGGGTCA TGATCACTATGACCCAATGAATACAACTAGTGATCTAAGTTTCAGTCAAGGAATTACTTAAGAG ATAGCAATTCAAAAATCAGGGCATCCATTCCTTGAAAAATGGGACTAAAGTGGTGCTGAAACAA TCTTTTCACTTGAAGGTGACATTCAATTTAAAGGCCAAATGTCGTGATGCTAAGAGAGGTAAGT GACCACTCCCTTTGAAGTCTATGCATTTTATATTAGTTGCAAATAAGCAATGAAAAGAGGAGAT TCAGTTAACCATAAAATAATGTATTAGCAACTAAGAAGTCCGTGGAAATAGAACAAGCCAACTA GTGGCTTTTGCATGTTAATATAAATGTTTCTTCAAGTAAAGAACCAATTTTTGAACATGTTCTG ATATCATTTCATATAAACTATAATCTACATTGTTATTTATTATATTGTTAATACATGATAGTGA AGCTGTGTGACCTATAGGTCACGAATTCGAACCGTGGAAGCAACCACTAATGCTTGCTTGCATT GTGGTAGGCTGTCTACATCACAATCCTAGGGTGCGGCCCTTCCCCTGAGCCTGCGCAAATGTGG GATGTTGTGTGCACAGGGCTGCCCTGTTATTTTATTTTAACATAAGACGGTGATATCTTTGGAT CAGGATAAACAGGGATCACACAAAGGACAACTTATTTTGTGTCATTTCGTCCAACTTTCTTAAT CTAGTTATAGCTTGATGTTGACTGTTAAGAGCTAATCCAGATTTTGCTAAGCTCTAGCAAAGAA AATCCAATTATCCGCAGAACAATCAACTCAACTGATATGCAATGAATGGCAATGTCAATTAGCG TTCTCTATAAGATATTTACGCGTATACATACACAACCTGTTCTTCAGAGAAACGCAAGGACAGG ACAGACACAACCAACTCCTCCAAAAGTAAACCTATTTAGTATTAGTTTTATGTTAGATTAAGCA TGGTCTTCACAATTCTAGCGAATCTTCCACAACTTTCAGAGATTTTACAGGATGAACACAAAGG CAGTAGTAAATGTCAAAGTCGATAAAAATGAGAGTAACTTACGGTGATGAAATATGAGTGGTTC AGAGTGAAATACTGTCCCAATACCATGTCCAACAAAACGATCAACAACACCATAACCAAATTTT TCAGCATGTTCACTGAAACAAAAGTCCAAAACGTTCAATGTCCAAGACAGAGTGTCCACAAAAA ATAAGGTACATACACAAGAAATGACATTAATTGTTTGCAAACAATATTTAAGAAAATCACAGTA AATTATTCAAAGTTTCATCAGAAGAAGGAAATTTCACTACCGACGTTTTTTAGTGATAACTAAA AGTTTTTGAATCTGATAAACAGAAACAGTTTGACACCTATAGGAACTTCAAAATAGATAGACTG TTGAAGCTTCAAAATATCCATATCACAAAATAATATTCACAAATTCACGATAATATCATATTCA TAAAATTACCTGATCCTCTTTCCTATCTTCCTATAAAGAGCACCATCTCTGCAAACAGCAATTC CATAGTGCAAGCACTCCTCAGTCACCTGCCACAGTAGGATATACAGATATAATTAATATAATGA GCATCGGATGATAAAAGAGACATTAGTTCTATTGCTAATACTGACTGGTATCTTAAATCTTAAC CAGTCTTACCACAGCAGAGTTCAATTTCAAATAGCAGTGATCTGATTAAGTTTAAGCAAAACTT TGTTAAACTAATAACCAGAAAGTTTCAGCATTCCTTTCATAATTGAAGAAATCTATACCTTTAC AAGCCGCTTTATGGATTCACTCACGTCACCACAGAAAAAGGTCTTTGACGTATCTCCATGATAA CCCTAAAAAAGGAACAAAGCAATGATCCTTACAATTTACAAGGTTCATCCAGAATCCAACAGCA GAAATTTCAGAGAAGACAAATGTCCTTCTAAATACTAGGGTAAAGACCGGCTAGCAGTAAAAAA GATAGCACATGTAGCCTATTACAATAATGAAGGGGCATCGACAACTTACATTCAGGTAAACGGT CACGTCAATGTTTATTATGTCTCCATCCTGCACATTATATTAATATTTGTCTTGAATACACATA TAAAAAGTTTAAGCAAGAGGATGATATGAAAAGATAAAGACCTGCAGCTGCCGTGAGTCAGGTA TTCCATGACACATACACTCATTGACGGATGTGCACACACTCTTTGGAAATCCCCCATAGCCTAA GGGAGATGGATAAGCGCCAGCATCGATTATCATTTGATGCACAGCTTTGTCAATTTCATTTGTT GTTACTGAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.335480737

Conservation Information
Conserved circRNAs	NA
PMCS	0.335480737

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3977691-3976554(+)
3977761-3977784(-)
3976647-3977784(-)
						
						Potential amino acid sequence
						
							MCTHSLEIPHSLREMDKRQHRLSFDAQLCQFHLLLLKAIVNVCPSTMEPDLSFR*(+)
MIIDAGAYPSPLGYGGFPKSVCTSVNECMCHGIPDSRQLQDGDIINIDVTVYLNGYHGDTSKTF
FCGDVSESIKRLVKVTEECLHYGIAVCRDGALYRKIGKRISEHAEKFGYGVVDRFVGHGIGTVF
HSEPLIFHHRNDKSGSMVEGQTFTIAFSNNK*(-)
MLKNLVMVLLIVLLDMVLGQYFTLNHSYFITGMTSPAPWLKGKHLLSPSVTTNEIDKAVHQMII
DAGAYPSPLGYGGFPKSVCTSVNECMCHGIPDSRQLQDGDIINIDVTVYLNGYHGDTSKTFFCG
DVSESIKRLVKVTEECLHYGIAVCRDGALYRKIGKRISEHAEKFGYGVVDRFVGHGIGTVFHSE
PLIFHHRNDKSGSMVEGQTFTIAFSNNK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3977691-3976554(+) 3977761-3977784(-) 3976647-3977784(-)
Potential amino acid sequence	MCTHSLEIPHSLREMDKRQHRLSFDAQLCQFHLLLLKAIVNVCPSTMEPDLSFR(+) MIIDAGAYPSPLGYGGFPKSVCTSVNECMCHGIPDSRQLQDGDIINIDVTVYLNGYHGDTSKTF FCGDVSESIKRLVKVTEECLHYGIAVCRDGALYRKIGKRISEHAEKFGYGVVDRFVGHGIGTVF HSEPLIFHHRNDKSGSMVEGQTFTIAFSNNK(-) MLKNLVMVLLIVLLDMVLGQYFTLNHSYFITGMTSPAPWLKGKHLLSPSVTTNEIDKAVHQMII DAGAYPSPLGYGGFPKSVCTSVNECMCHGIPDSRQLQDGDIINIDVTVYLNGYHGDTSKTFFCG DVSESIKRLVKVTEECLHYGIAVCRDGALYRKIGKRISEHAEKFGYGVVDRFVGHGIGTVFHSE PLIFHHRNDKSGSMVEGQTFTIAFSNNK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Tan et al., 2017; Yin et al., 2018

circRNA

Detail information of Solyc05g009780.2_circ_g.2

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