Plant Circular RNA Database

Detail information of Solyc02g050260.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc02g050260.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_000573
					
						Alias
						2:24946338|24955965
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr2: 4511928-4521555  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc02g050260.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc02g050260.2_circ_g.1 Solyc02g050260.2_circ_g.2 						
					
						Support reads
						13
					
						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
						Solyc02g050260.2.1:6

General Information
CircRNA Name	Solyc02g050260.2_circ_g.3
ID in PlantcircBase	sly_circ_000573
Alias	2:24946338\|24955965
Organism	Solanum lycopersicum
Position	chr2: 4511928-4521555 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc02g050260.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc02g050260.2_circ_g.1 Solyc02g050260.2_circ_g.2
Support reads	13
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	Solyc02g050260.2.1:6

			
						 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  
						
							CTGCAAAGTTTGTGGCCAAGTTGAGAGAAATGAAGACGAATGATAATTTACTCTTGTTCAAATG
TGAAATGGGTGCAGGACATTTTTCAAAATCTGGAAGcatcaagctccaggacatacaacttttt
accaaccatcttgctgttcatgaacgtgaaaatggtttacccagaattactgtatatcgccttc
cttctgtt

						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: 1056
Transcript exons: 4511928-4512219,4518110-4518268,4518938-4519303,4519648-
4519713,4519848-4519896,4521432-4521555
CATCAAGCTCCAGGACATACAACTTTTTACCAACCATCTTGCTGTTCATGAACGTGAAAATGGT
TTACCCAGAATTACTGTATATCGCCTTCCTTCTGTTGGAGAGCCACTAAAAAGACTTCAAGGTG
GTTTTGCCGTTGATTTTATTGATCCTGTATACTCTGTGGATCCATTAGAATCAGAATTTGAATC
CGGTGTACTCAAGTTTTCTTATAGCTCAATGAGAACCCCACCTTCTGTATATGATTATGATATG
GACACAGGGATTTCGGTGTTGAAGAAGATTGAAACGGTACTGGGAGGCTTTGATGCATCAAATT
ATGTAACTGAGAGGCAATGGGCTACTGCTTCAGATGGCACACAGATACCTATATCAATAATCTA
TCAAAAAAATCTTGTAAAACTTGATAGTTCAGACCCGTTGCTTCTTTATGGTTATGGATCCTAC
GAGATATGCATTGATCCCACTTTCAAGGCGTCACGCTTTTCTCTGTTAGACAGGGGTTTCATTT
ACGCTATTGCTCACATTCGTGGAGGTGGTGAAATGGGGAGGCAGTGGTATGAAAATGGGAAACT
GTTGAAAAAGAAAAATACTTTCACAGATTTCATTGCTTGTGCAGAATATTTAATAGACAAGAAG
TACTGTTCCAAGGAAAAGCTTTGTATCAACGGAAGAAGTGCAGGTGGATTGCTGATCGGTGCTG
TTATTAACATGCGTCCTAATTTGTTCAAAGCCGCTGTTGCTGGGGTTCCTTTTGTAGATGTTGT
AACTACAATGCTTGATCCAACTATTCCTTTAACAACTTCAGAGTGGGAGGAATGGGGTGATCCA
CGTCAGGAAGAATTCTATTCCTACATGAAGTCGTATTCCCCTGTTGATAATGTCAAAGCACAGA
ATTATCCAGACATTCTTGTTACAGCTGGCTTGAATGATCCACGTGTTATGTACTCTGAGCCTGC
AAAGTTTGTGGCCAAGTTGAGAGAAATGAAGACGAATGATAATTTACTCTTGTTCAAATGTGAA
ATGGGTGCAGGACATTTTTCAAAATCTGGAAG
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CTGCAAAGTTTGTGGCCAAGTTGAGAGAAATGAAGACGAATGATAATTTACTCTTGTTCAAATG TGAAATGGGTGCAGGACATTTTTCAAAATCTGGAAGcatcaagctccaggacatacaacttttt accaaccatcttgctgttcatgaacgtgaaaatggtttacccagaattactgtatatcgccttc cttctgtt
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: 1056 Transcript exons: 4511928-4512219,4518110-4518268,4518938-4519303,4519648- 4519713,4519848-4519896,4521432-4521555 CATCAAGCTCCAGGACATACAACTTTTTACCAACCATCTTGCTGTTCATGAACGTGAAAATGGT TTACCCAGAATTACTGTATATCGCCTTCCTTCTGTTGGAGAGCCACTAAAAAGACTTCAAGGTG GTTTTGCCGTTGATTTTATTGATCCTGTATACTCTGTGGATCCATTAGAATCAGAATTTGAATC CGGTGTACTCAAGTTTTCTTATAGCTCAATGAGAACCCCACCTTCTGTATATGATTATGATATG GACACAGGGATTTCGGTGTTGAAGAAGATTGAAACGGTACTGGGAGGCTTTGATGCATCAAATT ATGTAACTGAGAGGCAATGGGCTACTGCTTCAGATGGCACACAGATACCTATATCAATAATCTA TCAAAAAAATCTTGTAAAACTTGATAGTTCAGACCCGTTGCTTCTTTATGGTTATGGATCCTAC GAGATATGCATTGATCCCACTTTCAAGGCGTCACGCTTTTCTCTGTTAGACAGGGGTTTCATTT ACGCTATTGCTCACATTCGTGGAGGTGGTGAAATGGGGAGGCAGTGGTATGAAAATGGGAAACT GTTGAAAAAGAAAAATACTTTCACAGATTTCATTGCTTGTGCAGAATATTTAATAGACAAGAAG TACTGTTCCAAGGAAAAGCTTTGTATCAACGGAAGAAGTGCAGGTGGATTGCTGATCGGTGCTG TTATTAACATGCGTCCTAATTTGTTCAAAGCCGCTGTTGCTGGGGTTCCTTTTGTAGATGTTGT AACTACAATGCTTGATCCAACTATTCCTTTAACAACTTCAGAGTGGGAGGAATGGGGTGATCCA CGTCAGGAAGAATTCTATTCCTACATGAAGTCGTATTCCCCTGTTGATAATGTCAAAGCACAGA ATTATCCAGACATTCTTGTTACAGCTGGCTTGAATGATCCACGTGTTATGTACTCTGAGCCTGC AAAGTTTGTGGCCAAGTTGAGAGAAATGAAGACGAATGATAATTTACTCTTGTTCAAATGTGAA ATGGGTGCAGGACATTTTTCAAAATCTGGAAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.513598503

Conservation Information
Conserved circRNAs	NA
PMCS	0.513598503

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							4512149-4521552(+)
4521496-4512037(+)
4511947-4519864(-)
4511978-4521544(-)
						
					

						Potential amino acid sequence
						
							MRTPPSVYDYDMDTGISVLKKIETVLGGFDASNYVTERQWATASDGTQIPISIIYQKNLVKLDS
SDPLLLYGYGSYEICIDPTFKASRFSLLDRGFIYAIAHIRGGGEMGRQWYENGKLLKKKNTFTD
FIACAEYLIDKKYCSKEKLCINGRSAGGLLIGAVINMRPNLFKAAVAGVPFVDVVTTMLDPTIP
LTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKAQNYPDILVTAGLNDPRVMYSEPAKFVAKLREM
KTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLFTNHLAVHERENGLPRITVYRLPSVGEPLKRLQ
GGFAVDFIDPVYSVDPLESEFESGVLKFSYSSMRTPPSVYDYDMDTGISVLKKIETVLGGFDAS
NYVTERQWATASDGTQIPISIIYQKNLVKLDSSDPLLLYGYGSYEICIDPTFKASRFSLLDRGF
IYAIAHIRGGGEMGRQWYENGKLLKKKNTFTDFIACAEYLIDKKYCSKEKLCINGRSAGGLLIG
AVINMRPNLFKAAVAGVPFVDVVTTMLDPTIPLTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKA
QNYPDILVTAGLNDPRVMYSEPAKFVAKLREMKTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLF
TNHLAVHERENGLPRITVYRLPSVGEPLKRLQGGFAVDFIDPVYSVDPLESEFESGVLKFSYSS
MRTPPSVYDYDMDTGISVLKKIETVLGGFDASNYVTERQWATASDGTQIPISIIYQKNLVKLDS
SDPLLLYGYGSYEICIDPTFKASRFSLLDRGFIYAIAHIRGGGEMGRQWYENGKLLKKKNTFTD
FIACAEYLIDKKYCSKEKLCINGRSAGGLLIGAVINMRPNLFKAAVAGVPFVDVVTTMLDPTIP
LTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKAQNYPDILVTAGLNDPRVMYSEPAKFVAKLREM
KTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLFTNHLAVHERENGLPRITVYRLPSVGEPLKRLQ
GGFAVDFIDPVYSVDPLESEFESGVLKFSYSSMRTPPSVYDYDMDTGISVLKKIETVLGGFDAS
NYVTERQWATASDGTQIPISIIYQKNLVKLDSSDPLLLYGYGSYEICIDPTFKASRFSLLDRGF
IYAIAHIRGGGEMGRQWYENGKLLKKKNTFTDFIACAEYLIDKKYCSKEKLCINGRSAGGLLIG
AVINMRPNLFKAAVAGVPFVDVVTTMLDPTIPLTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKA
QNYPDILVTAGLNDPRVMYSEPAKFVAKLREMKTNDNLLLFKCEMGAGHFSKSG(+)
MIIYSCSNVKWVQDIFQNLEASSSRTYNFLPTILLFMNVKMVYPELLYIAFLLLESH*(+)
MSWSLMLPDFEKCPAPISHLNKSKLSFVFISLNLATNFAGSEYITRGSFKPAVTRMSG*(-)
MNSKMVGKKLYVLELDASRF*(-)
						
					

						Sponge-miRNAs
						
							sly-miR172c 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	4512149-4521552(+) 4521496-4512037(+) 4511947-4519864(-) 4511978-4521544(-)
Potential amino acid sequence	MRTPPSVYDYDMDTGISVLKKIETVLGGFDASNYVTERQWATASDGTQIPISIIYQKNLVKLDS SDPLLLYGYGSYEICIDPTFKASRFSLLDRGFIYAIAHIRGGGEMGRQWYENGKLLKKKNTFTD FIACAEYLIDKKYCSKEKLCINGRSAGGLLIGAVINMRPNLFKAAVAGVPFVDVVTTMLDPTIP LTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKAQNYPDILVTAGLNDPRVMYSEPAKFVAKLREM KTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLFTNHLAVHERENGLPRITVYRLPSVGEPLKRLQ GGFAVDFIDPVYSVDPLESEFESGVLKFSYSSMRTPPSVYDYDMDTGISVLKKIETVLGGFDAS NYVTERQWATASDGTQIPISIIYQKNLVKLDSSDPLLLYGYGSYEICIDPTFKASRFSLLDRGF IYAIAHIRGGGEMGRQWYENGKLLKKKNTFTDFIACAEYLIDKKYCSKEKLCINGRSAGGLLIG AVINMRPNLFKAAVAGVPFVDVVTTMLDPTIPLTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKA QNYPDILVTAGLNDPRVMYSEPAKFVAKLREMKTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLF TNHLAVHERENGLPRITVYRLPSVGEPLKRLQGGFAVDFIDPVYSVDPLESEFESGVLKFSYSS MRTPPSVYDYDMDTGISVLKKIETVLGGFDASNYVTERQWATASDGTQIPISIIYQKNLVKLDS SDPLLLYGYGSYEICIDPTFKASRFSLLDRGFIYAIAHIRGGGEMGRQWYENGKLLKKKNTFTD FIACAEYLIDKKYCSKEKLCINGRSAGGLLIGAVINMRPNLFKAAVAGVPFVDVVTTMLDPTIP LTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKAQNYPDILVTAGLNDPRVMYSEPAKFVAKLREM KTNDNLLLFKCEMGAGHFSKSGSIKLQDIQLFTNHLAVHERENGLPRITVYRLPSVGEPLKRLQ GGFAVDFIDPVYSVDPLESEFESGVLKFSYSSMRTPPSVYDYDMDTGISVLKKIETVLGGFDAS NYVTERQWATASDGTQIPISIIYQKNLVKLDSSDPLLLYGYGSYEICIDPTFKASRFSLLDRGF IYAIAHIRGGGEMGRQWYENGKLLKKKNTFTDFIACAEYLIDKKYCSKEKLCINGRSAGGLLIG AVINMRPNLFKAAVAGVPFVDVVTTMLDPTIPLTTSEWEEWGDPRQEEFYSYMKSYSPVDNVKA QNYPDILVTAGLNDPRVMYSEPAKFVAKLREMKTNDNLLLFKCEMGAGHFSKSG(+) MIIYSCSNVKWVQDIFQNLEASSSRTYNFLPTILLFMNVKMVYPELLYIAFLLLESH(+) MSWSLMLPDFEKCPAPISHLNKSKLSFVFISLNLATNFAGSEYITRGSFKPAVTRMSG(-) MNSKMVGKKLYVLELDASRF*(-)
Sponge-miRNAs	sly-miR172c
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Yin et al., 2018

circRNA

Detail information of Solyc02g050260.2_circ_g.3

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