Plant Circular RNA Database

Detail information of Solyc07g042550.2_circ_g.2

			
						 General Information
					
						CircRNA Name
						Solyc07g042550.2_circ_g.2
					
						ID in PlantcircBase
						sly_circ_002315
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr7: 55978886-55981020  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc07g042550.2						
					
						Parent gene annotation
						
							Sucrose synthase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Solyc07g042550.2_circ_g.3 						
					
						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  
						
							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
						Solyc07g042550.2.1:7

General Information
CircRNA Name	Solyc07g042550.2_circ_g.2
ID in PlantcircBase	sly_circ_002315
Alias	NA
Organism	Solanum lycopersicum
Position	chr7: 55978886-55981020 JBrowse»
Reference genome	SL2.50.38
Type	ue-circRNA
Identification method	CIRI
Parent gene	Solyc07g042550.2
Parent gene annotation	Sucrose synthase
Parent gene strand	-
Alternative splicing	Solyc07g042550.2_circ_g.3
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	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	Solyc07g042550.2.1:7

			
						 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  
						
							GATGAGCATCCAAAGTAGCATCAAGACGTTCACGAAGACTGTGAACACGAGTTAGAACACGTTG
AGCCATTGCACCTGCAAATCCTCAGATGACTTTCAActcaatgaaagtctccatgtatggccag
acttcaaaacgagagatccatttgcgaacaatgcccttttcagtcctaaaggggaccctaagaa
tatgtgaa

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTCAATGAAAGTCTCCATGTATGGCCAGACTTCAAAACGAGAGATCCATTTGCGAACAATGCCC
TTTTCAGTCCTAAAGGGGACCCTAAGAATATGTGAATGCTCAGTTCCAAATACCTTCTCGAGTC
GCTGACCACAAGTGGTACCAACTGCATCAGGGAGAAGCCGAGTAACCTGAGAATTTAAACAAAG
ATCAGATGTTGCATTAGAACAAATCAAAATCCTGCATAATCATAATCTATAAGCACAATCTCTG
AGAATACTAACAATAAGAATACGCGGTTTGATATCAAGTCCTTGCTCCTTTATGCGCTTGAGCA
TCTCACGCTCCAAGGCAGGAACTTGATCCAAAATATAGACAACCTGCAAATTAAAGGAACGGGA
ACTCAGCACTTGCCCCAATAGGTTTCTAAGGAGTAAGACAAAGTGATCACAAATAAGCAATGCA
CCTGACCACCAGTGTCGGGGTAACCCAAGACATTTTCCTGGGCGAAATATCCATGAGGTGAAAG
TATAACTACATTGAAAACCATAGGAATTCTACTAAGGAACTTCTCAAGAGTACATGAGTCAGGA
GCCTCAAGGAGATCCAGGAGCATGCAGATCATCTCTAGAACACGCTCTGCGGTGTCACCCCAAC
CTCTCTCCAAGCCAATTTCTTGGAACTTGTGCTCAAATGAGGAGTATGAAGTTTCTGGCGAAAG
GGTGGTGAGGTATTCCTCGGCCTTCCTCAGGACTTTTTGGAGAGTATACAAATTCTGAATTCTA
TCATTCAGCATCATTGACTGCACAGAAAATGATTGTTCGAACATGTTAATCATTTGTTGGATGC
AAAAATCAGTAACTCCATACTCGAAATTTATCGGAGAAAAACCACCATAACACTAAATTTACCT
TTCCATTGTAGTGGTGAACTCGAAGAAACTCGAGAAGAGGGGTCATGCTTTCCTTGTCATGGAA
CATTTTAGCAGAGAGGTGCCTGTTGAGGAATTCAACTCCATTTCCAATTGATTTCGTGAGGGTT
GGTTTTGGAAATGATGCAGTGAAGGGCTCAAAATCCAATTCAAGAACAAAGTTATCACTGGAAC
TGCATCAGGGAAAATCACAACATTAATCAAAAAGATTCTAAGAACATGTTGATTAGATAACTCA
TCATCAAATTCAAACGTAAAACTTACGTTCCGTTAACAAGTTCTTCCTTGAATTGCAAAAACTC
AGGCACAGTCAGCTCCTCAACACTAAGAGCATTAACATTCACACGGACATATTCCCACACACCG
GGCCTCAAACGAATAGCAAGTGCAACCCATGGGGGCAAAACAATTGCTTCCTAGTATGACGAAC
AACGCAAAAGAAAATTTCAAATGCAAGTACAAACAGATACACATGTTAGCTTAGTAAGAAAATT
AAATATAATCAACCTAACAACAAAACCAAGTTACCTGAGTGGATTTCAGGACTTCTTCAAAGGC
ATGATCATTCAGTTTGTCTTTGTCTTCTTTCTGAATTGATTCAAACTCAGCCAGTAGCTGGTGA
GGTTTCAAGATCCCTTTCCCGTGGCTTTCGATCCTGATACAGCCAAAAACAGCAAGAATAACTC
ATGATGTACTTGATGGAACCATATATTTGTCCGTCAATTAGGGGTCGTTTGGTTTGAAGACAAG
TTTTACTAGGACAAACATTCATTGCATAATTTTTAAGAACGAAAGTTATTTGTTTACGAGAATA
CCTTCCACCTTATTAAGTAAAAAAGGATCTAAGGGACCTCTGGGGGATTTTTGTCATTTTCATT
GTATTGTTCCAGGATTACTAGTTAACAGTACTATTATTCCATCAGAGATAACTTATCGAGGTAC
TAATTACTAATTCTGATATAACTTATTCCGAGATCAATAACCAAACAAAGGAATAAGGCAGTAC
TAAGTTTGTATCCCCAAAACTATTTAGGCTTGCGAAACATACCAAACGAAAATTACAAAAAGCG
AAAACATGGCTGTAAGACCATACCTTGAAAGAAAGAGCAAAATTTCATTGCGATGAGCATCCAA
AGTAGCATCAAGACGTTCACGAAGACTGTGAACACGAGTTAGAACACGTTGAGCCATTGCACCT
GCAAATCCTCAGATGACTTTCAA
						
					

			
		

Sequences
Splice junction sequence	GATGAGCATCCAAAGTAGCATCAAGACGTTCACGAAGACTGTGAACACGAGTTAGAACACGTTG AGCCATTGCACCTGCAAATCCTCAGATGACTTTCAActcaatgaaagtctccatgtatggccag acttcaaaacgagagatccatttgcgaacaatgcccttttcagtcctaaaggggaccctaagaa tatgtgaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTCAATGAAAGTCTCCATGTATGGCCAGACTTCAAAACGAGAGATCCATTTGCGAACAATGCCC TTTTCAGTCCTAAAGGGGACCCTAAGAATATGTGAATGCTCAGTTCCAAATACCTTCTCGAGTC GCTGACCACAAGTGGTACCAACTGCATCAGGGAGAAGCCGAGTAACCTGAGAATTTAAACAAAG ATCAGATGTTGCATTAGAACAAATCAAAATCCTGCATAATCATAATCTATAAGCACAATCTCTG AGAATACTAACAATAAGAATACGCGGTTTGATATCAAGTCCTTGCTCCTTTATGCGCTTGAGCA TCTCACGCTCCAAGGCAGGAACTTGATCCAAAATATAGACAACCTGCAAATTAAAGGAACGGGA ACTCAGCACTTGCCCCAATAGGTTTCTAAGGAGTAAGACAAAGTGATCACAAATAAGCAATGCA CCTGACCACCAGTGTCGGGGTAACCCAAGACATTTTCCTGGGCGAAATATCCATGAGGTGAAAG TATAACTACATTGAAAACCATAGGAATTCTACTAAGGAACTTCTCAAGAGTACATGAGTCAGGA GCCTCAAGGAGATCCAGGAGCATGCAGATCATCTCTAGAACACGCTCTGCGGTGTCACCCCAAC CTCTCTCCAAGCCAATTTCTTGGAACTTGTGCTCAAATGAGGAGTATGAAGTTTCTGGCGAAAG GGTGGTGAGGTATTCCTCGGCCTTCCTCAGGACTTTTTGGAGAGTATACAAATTCTGAATTCTA TCATTCAGCATCATTGACTGCACAGAAAATGATTGTTCGAACATGTTAATCATTTGTTGGATGC AAAAATCAGTAACTCCATACTCGAAATTTATCGGAGAAAAACCACCATAACACTAAATTTACCT TTCCATTGTAGTGGTGAACTCGAAGAAACTCGAGAAGAGGGGTCATGCTTTCCTTGTCATGGAA CATTTTAGCAGAGAGGTGCCTGTTGAGGAATTCAACTCCATTTCCAATTGATTTCGTGAGGGTT GGTTTTGGAAATGATGCAGTGAAGGGCTCAAAATCCAATTCAAGAACAAAGTTATCACTGGAAC TGCATCAGGGAAAATCACAACATTAATCAAAAAGATTCTAAGAACATGTTGATTAGATAACTCA TCATCAAATTCAAACGTAAAACTTACGTTCCGTTAACAAGTTCTTCCTTGAATTGCAAAAACTC AGGCACAGTCAGCTCCTCAACACTAAGAGCATTAACATTCACACGGACATATTCCCACACACCG GGCCTCAAACGAATAGCAAGTGCAACCCATGGGGGCAAAACAATTGCTTCCTAGTATGACGAAC AACGCAAAAGAAAATTTCAAATGCAAGTACAAACAGATACACATGTTAGCTTAGTAAGAAAATT AAATATAATCAACCTAACAACAAAACCAAGTTACCTGAGTGGATTTCAGGACTTCTTCAAAGGC ATGATCATTCAGTTTGTCTTTGTCTTCTTTCTGAATTGATTCAAACTCAGCCAGTAGCTGGTGA GGTTTCAAGATCCCTTTCCCGTGGCTTTCGATCCTGATACAGCCAAAAACAGCAAGAATAACTC ATGATGTACTTGATGGAACCATATATTTGTCCGTCAATTAGGGGTCGTTTGGTTTGAAGACAAG TTTTACTAGGACAAACATTCATTGCATAATTTTTAAGAACGAAAGTTATTTGTTTACGAGAATA CCTTCCACCTTATTAAGTAAAAAAGGATCTAAGGGACCTCTGGGGGATTTTTGTCATTTTCATT GTATTGTTCCAGGATTACTAGTTAACAGTACTATTATTCCATCAGAGATAACTTATCGAGGTAC TAATTACTAATTCTGATATAACTTATTCCGAGATCAATAACCAAACAAAGGAATAAGGCAGTAC TAAGTTTGTATCCCCAAAACTATTTAGGCTTGCGAAACATACCAAACGAAAATTACAAAAAGCG AAAACATGGCTGTAAGACCATACCTTGAAAGAAAGAGCAAAATTTCATTGCGATGAGCATCCAA AGTAGCATCAAGACGTTCACGAAGACTGTGAACACGAGTTAGAACACGTTGAGCCATTGCACCT GCAAATCCTCAGATGACTTTCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.18748792

Conservation Information
Conserved circRNAs	NA
PMCS	0.18748792

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							55981011-55979015(+)
55980992-55981008(-)
55979042-55981019(-)
						
						Potential amino acid sequence
						
							MTFNSMKVSMYGQTSKREIHLRTMPFSVLKGTLRICECSVPNTFSSR*(+)
MAQRVLTRVHSLRERLDATLDAHRNEILLFLSRIESHGKGILKPHQLLAEFESIQKEDKDKLND
HAFEEVLKSTQEAIVLPPWVALAIRLRPGVWEYVRVNVNALSVEELTVPEFLQFKEELVNGTSS
DNFVLELDFEPFTASFPKPTLTKSIGNGVEFLNRHLSAKMFHDKESMTPLLEFLRVHHYNGKSM
MLNDRIQNLYTLQKVLRKAEEYLTTLSPETSYSSFEHKFQEIGLERGWGDTAERVLEMICMLLD
LLEAPDSCTLEKFLSRIPMVFNVVILSPHGYFAQENVLGYPDTGGQVVYILDQVPALEREMLKR
IKEQGLDIKPRILIVTRLLPDAVGTTCGQRLEKVFGTEHSHILRVPFRTEKGIVRKWISRFEVW
PYMETFIELKVI*(-)
MQLVPLVVSDSRRYLELSIHIFLGSPLGLKRALFANGSLVLKSGHTWRLSLS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	55981011-55979015(+) 55980992-55981008(-) 55979042-55981019(-)
Potential amino acid sequence	MTFNSMKVSMYGQTSKREIHLRTMPFSVLKGTLRICECSVPNTFSSR(+) MAQRVLTRVHSLRERLDATLDAHRNEILLFLSRIESHGKGILKPHQLLAEFESIQKEDKDKLND HAFEEVLKSTQEAIVLPPWVALAIRLRPGVWEYVRVNVNALSVEELTVPEFLQFKEELVNGTSS DNFVLELDFEPFTASFPKPTLTKSIGNGVEFLNRHLSAKMFHDKESMTPLLEFLRVHHYNGKSM MLNDRIQNLYTLQKVLRKAEEYLTTLSPETSYSSFEHKFQEIGLERGWGDTAERVLEMICMLLD LLEAPDSCTLEKFLSRIPMVFNVVILSPHGYFAQENVLGYPDTGGQVVYILDQVPALEREMLKR IKEQGLDIKPRILIVTRLLPDAVGTTCGQRLEKVFGTEHSHILRVPFRTEKGIVRKWISRFEVW PYMETFIELKVI(-) MQLVPLVVSDSRRYLELSIHIFLGSPLGLKRALFANGSLVLKSGHTWRLSLS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc07g042550.2_circ_g.2

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