Plant Circular RNA Database

Detail information of PGSC0003DMG400000776_circ_g.4

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400000776_circ_g.4
					
						ID in PlantcircBase
						stu_circ_000552
					
						Alias
						chr04:59015512|59015698
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr4: 59015513-59015698  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400000776						
					
						Parent gene annotation
						
							Extensin (ext)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							PGSC0003DMG400000776_circ_g.1 PGSC0003DMG400000776_circ_g.2 PGSC0003DMG400000776_circ_g.3 PGSC0003DMG400000776_circ_g.5 PGSC0003DMG400000776_circ_g.6 PGSC0003DMG400000776_circ_ag.1 PGSC0003DMG400000776_circ_g.7 PGSC0003DMG400000776_circ_ag.2 PGSC0003DMG400000776_circ_g.8 PGSC0003DMG400000776_circ_g.9 PGSC0003DMG400000776_circ_g.10 PGSC0003DMG400000776_circ_ag.3 PGSC0003DMG400000776_circ_ag.4 PGSC0003DMG400000776_circ_g.11 PGSC0003DMG400000776_circ_g.12 PGSC0003DMG400000776_circ_g.13 PGSC0003DMG400000776_circ_g.14 PGSC0003DMG400000776_circ_ag.5 PGSC0003DMG400000776_circ_ag.6 PGSC0003DMG400000776_circ_g.15 PGSC0003DMG400000776_circ_g.16 PGSC0003DMG400000776_circ_g.17 PGSC0003DMG400000776_circ_g.18 PGSC0003DMG400000776_circ_ag.7 PGSC0003DMG400000776_circ_ag.8 PGSC0003DMG400000776_circ_ag.9 PGSC0003DMG400000776_circ_ag.10 PGSC0003DMG400000776_circ_g.19 PGSC0003DMG400000776_circ_g.20 PGSC0003DMG400000776_circ_ag.11 PGSC0003DMG400000776_circ_igg.1 PGSC0003DMG400000776_circ_igg.2 PGSC0003DMG400000776_circ_g.21 PGSC0003DMG400000776_circ_g.22 PGSC0003DMG400000776_circ_g.23 PGSC0003DMG400000776_circ_ag.12 PGSC0003DMG400000776_circ_igg.3 PGSC0003DMG400000776_circ_igg.4 PGSC0003DMG400000776_circ_g.24 PGSC0003DMG400000776_circ_g.25 PGSC0003DMG400000776_circ_g.26 PGSC0003DMG400000776_circ_g.27 PGSC0003DMG400000776_circ_g.28 PGSC0003DMG400000776_circ_ag.13 PGSC0003DMG400000776_circ_g.29 PGSC0003DMG400000776_circ_g.30 PGSC0003DMG400000776_circ_g.31 PGSC0003DMG400000776_circ_g.32 PGSC0003DMG400000777_circ_ag.1 PGSC0003DMG400000777_circ_g.1 PGSC0003DMG400000777_circ_g.2 PGSC0003DMG400000779_circ_ag.1 PGSC0003DMG400000779_circ_ag.2 PGSC0003DMG400000779_circ_ag.3 PGSC0003DMG400000779_circ_ag.4 PGSC0003DMG400000779_circ_ag.5 PGSC0003DMG400000794_circ_g.1 PGSC0003DMG400000794_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							No-No							"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-CC							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
						PGSC0003DMT400002035:1

General Information
CircRNA Name	PGSC0003DMG400000776_circ_g.4
ID in PlantcircBase	stu_circ_000552
Alias	chr04:59015512\|59015698
Organism	Solanum tuberosum
Position	chr4: 59015513-59015698 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400000776
Parent gene annotation	Extensin (ext)
Parent gene strand	+
Alternative splicing	PGSC0003DMG400000776_circ_g.1 PGSC0003DMG400000776_circ_g.2 PGSC0003DMG400000776_circ_g.3 PGSC0003DMG400000776_circ_g.5 PGSC0003DMG400000776_circ_g.6 PGSC0003DMG400000776_circ_ag.1 PGSC0003DMG400000776_circ_g.7 PGSC0003DMG400000776_circ_ag.2 PGSC0003DMG400000776_circ_g.8 PGSC0003DMG400000776_circ_g.9 PGSC0003DMG400000776_circ_g.10 PGSC0003DMG400000776_circ_ag.3 PGSC0003DMG400000776_circ_ag.4 PGSC0003DMG400000776_circ_g.11 PGSC0003DMG400000776_circ_g.12 PGSC0003DMG400000776_circ_g.13 PGSC0003DMG400000776_circ_g.14 PGSC0003DMG400000776_circ_ag.5 PGSC0003DMG400000776_circ_ag.6 PGSC0003DMG400000776_circ_g.15 PGSC0003DMG400000776_circ_g.16 PGSC0003DMG400000776_circ_g.17 PGSC0003DMG400000776_circ_g.18 PGSC0003DMG400000776_circ_ag.7 PGSC0003DMG400000776_circ_ag.8 PGSC0003DMG400000776_circ_ag.9 PGSC0003DMG400000776_circ_ag.10 PGSC0003DMG400000776_circ_g.19 PGSC0003DMG400000776_circ_g.20 PGSC0003DMG400000776_circ_ag.11 PGSC0003DMG400000776_circ_igg.1 PGSC0003DMG400000776_circ_igg.2 PGSC0003DMG400000776_circ_g.21 PGSC0003DMG400000776_circ_g.22 PGSC0003DMG400000776_circ_g.23 PGSC0003DMG400000776_circ_ag.12 PGSC0003DMG400000776_circ_igg.3 PGSC0003DMG400000776_circ_igg.4 PGSC0003DMG400000776_circ_g.24 PGSC0003DMG400000776_circ_g.25 PGSC0003DMG400000776_circ_g.26 PGSC0003DMG400000776_circ_g.27 PGSC0003DMG400000776_circ_g.28 PGSC0003DMG400000776_circ_ag.13 PGSC0003DMG400000776_circ_g.29 PGSC0003DMG400000776_circ_g.30 PGSC0003DMG400000776_circ_g.31 PGSC0003DMG400000776_circ_g.32 PGSC0003DMG400000777_circ_ag.1 PGSC0003DMG400000777_circ_g.1 PGSC0003DMG400000777_circ_g.2 PGSC0003DMG400000779_circ_ag.1 PGSC0003DMG400000779_circ_ag.2 PGSC0003DMG400000779_circ_ag.3 PGSC0003DMG400000779_circ_ag.4 PGSC0003DMG400000779_circ_ag.5 PGSC0003DMG400000794_circ_g.1 PGSC0003DMG400000794_circ_g.2
Support reads	NA
Tissues	stem
Exon boundary	No-No "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-CC 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	PGSC0003DMT400002035:1

			
						 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  
						
							CAGTTTACAAGTCTCCTCCACCACACCATATTCACCATCCCGTTTACAAGTCTCCACCACCTCC
AACTCCTATTTACAAGTCGCCACCACCACatccagtgtataagtctcctccaccacaccatcat
catcccgtttacaagtctccaccaccatctgagaagccacactaccctccacacaccc

						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
						
							ATCCAGTGTATAAGTCTCCTCCACCACACCATCATCATCCCGTTTACAAGTCTCCACCACCATC
TGAGAAGCCACACTACCCTCCACACACCCCAGTTTACAAGTCTCCTCCACCACACCATATTCAC
CATCCCGTTTACAAGTCTCCACCACCTCCAACTCCTATTTACAAGTCGCCACCACCAC

Sequences
Splice junction sequence	CAGTTTACAAGTCTCCTCCACCACACCATATTCACCATCCCGTTTACAAGTCTCCACCACCTCC AACTCCTATTTACAAGTCGCCACCACCACatccagtgtataagtctcctccaccacaccatcat catcccgtttacaagtctccaccaccatctgagaagccacactaccctccacacaccc
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	ATCCAGTGTATAAGTCTCCTCCACCACACCATCATCATCCCGTTTACAAGTCTCCACCACCATC TGAGAAGCCACACTACCCTCCACACACCCCAGTTTACAAGTCTCCTCCACCACACCATATTCAC CATCCCGTTTACAAGTCTCCACCACCTCCAACTCCTATTTACAAGTCGCCACCACCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.921082079

Conservation Information
Conserved circRNAs	NA
PMCS	0.921082079

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhou et al., 2018

circRNA

Detail information of PGSC0003DMG400000776_circ_g.4

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