Plant Circular RNA Database

Detail information of PGSC0003DMG400003838_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400003838_circ_g.1
					
						ID in PlantcircBase
						stu_circ_001136
					
						Alias
						chr09:51059204|51059731
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr9: 51059205-51059731  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400003838						
					
						Parent gene annotation
						
							Elongation factor Tu
							
						Parent gene strand
						-
					
						Alternative splicing
						
							PGSC0003DMG400046431_circ_ag.1 PGSC0003DMG400016849_circ_ig.1 PGSC0003DMG400011384_circ_ig.1 PGSC0003DMG400011384_circ_ig.2 PGSC0003DMG400011384_circ_ig.3 PGSC0003DMG400011384_circ_ig.4 PGSC0003DMG400011398_circ_g.1 PGSC0003DMG402011400_circ_igg.1 PGSC0003DMG401011400_circ_igg.1 PGSC0003DMG402031803_circ_ig.1 PGSC0003DMG402031803_circ_ig.2 PGSC0003DMG400031808_circ_g.1 PGSC0003DMG400031808_circ_g.2 PGSC0003DMG400036103_circ_ag.1 PGSC0003DMG403006439_circ_ag.1 PGSC0003DMG403006439_circ_ag.2 PGSC0003DMG403006439_circ_igg.1 PGSC0003DMG403006439_circ_igg.2 PGSC0003DMG403006439_circ_igg.3 PGSC0003DMG400006075_circ_g.1 PGSC0003DMG400015117_circ_ig.1 PGSC0003DMG400015117_circ_ig.2 PGSC0003DMG400015117_circ_ig.3 PGSC0003DMG400015117_circ_ig.4 PGSC0003DMG400015117_circ_ig.5 PGSC0003DMG400015117_circ_ig.6 PGSC0003DMG400017245_circ_igg.1 PGSC0003DMG402017241_circ_ag.1 PGSC0003DMG402017241_circ_ag.2 PGSC0003DMG402017239_circ_igg.1 PGSC0003DMG402017239_circ_igg.2 PGSC0003DMG400017219_circ_ig.1 PGSC0003DMG400017219_circ_ig.2 PGSC0003DMG400017202_circ_ig.1 PGSC0003DMG400017202_circ_ig.2 PGSC0003DMG400001557_circ_g.1 PGSC0003DMG402001494_circ_ag.1 PGSC0003DMG400029644_circ_igg.1 PGSC0003DMG400029643_circ_g.1 PGSC0003DMG400029620_circ_ag.1 PGSC0003DMG400007743_circ_igg.1 PGSC0003DMG401026432_circ_igg.1 PGSC0003DMG400026434_circ_ag.1 						
					
						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
						PGSC0003DMT400009804:2

General Information
CircRNA Name	PGSC0003DMG400003838_circ_g.1
ID in PlantcircBase	stu_circ_001136
Alias	chr09:51059204\|51059731
Organism	Solanum tuberosum
Position	chr9: 51059205-51059731 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400003838
Parent gene annotation	Elongation factor Tu
Parent gene strand	-
Alternative splicing	PGSC0003DMG400046431_circ_ag.1 PGSC0003DMG400016849_circ_ig.1 PGSC0003DMG400011384_circ_ig.1 PGSC0003DMG400011384_circ_ig.2 PGSC0003DMG400011384_circ_ig.3 PGSC0003DMG400011384_circ_ig.4 PGSC0003DMG400011398_circ_g.1 PGSC0003DMG402011400_circ_igg.1 PGSC0003DMG401011400_circ_igg.1 PGSC0003DMG402031803_circ_ig.1 PGSC0003DMG402031803_circ_ig.2 PGSC0003DMG400031808_circ_g.1 PGSC0003DMG400031808_circ_g.2 PGSC0003DMG400036103_circ_ag.1 PGSC0003DMG403006439_circ_ag.1 PGSC0003DMG403006439_circ_ag.2 PGSC0003DMG403006439_circ_igg.1 PGSC0003DMG403006439_circ_igg.2 PGSC0003DMG403006439_circ_igg.3 PGSC0003DMG400006075_circ_g.1 PGSC0003DMG400015117_circ_ig.1 PGSC0003DMG400015117_circ_ig.2 PGSC0003DMG400015117_circ_ig.3 PGSC0003DMG400015117_circ_ig.4 PGSC0003DMG400015117_circ_ig.5 PGSC0003DMG400015117_circ_ig.6 PGSC0003DMG400017245_circ_igg.1 PGSC0003DMG402017241_circ_ag.1 PGSC0003DMG402017241_circ_ag.2 PGSC0003DMG402017239_circ_igg.1 PGSC0003DMG402017239_circ_igg.2 PGSC0003DMG400017219_circ_ig.1 PGSC0003DMG400017219_circ_ig.2 PGSC0003DMG400017202_circ_ig.1 PGSC0003DMG400017202_circ_ig.2 PGSC0003DMG400001557_circ_g.1 PGSC0003DMG402001494_circ_ag.1 PGSC0003DMG400029644_circ_igg.1 PGSC0003DMG400029643_circ_g.1 PGSC0003DMG400029620_circ_ag.1 PGSC0003DMG400007743_circ_igg.1 PGSC0003DMG401026432_circ_igg.1 PGSC0003DMG400026434_circ_ag.1
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	PGSC0003DMT400009804:2

			
						 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  
						
							AGAATGGTTTATCAAGCTGACGCACTGGATCTGGAATGTATTCATCTACAGCATCCATCAACTT
TAAAATAGCTTTCTTTCCAATTTCTTCATTAGTTCCtgcatcagccctaaaatctccacatctt
ctccaacttttattgttccctgttcaatacggccagtagcaacagttccacgtcccttcaaaac
attaacgg

						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
						
							TGCATCAGCCCTAAAATCTCCACATCTTCTCCAACTTTTATTGTTCCCTGTTCAATACGGCCAG
TAGCAACAGTTCCACGTCCCTTCAAAACATTAACGGTAACTGATCAGTATCACATTAGAAGCAA
GGTTCAAGCATTATTATTTTTCCTCTTTTGGAAATGAAAGATGGACTGCTGCAAAAAAAATATT
TTTCTACCTTTCTCAGAGCAAAGGATTGTACTAAAATAAGCAGAAAGAGGTATAGCATCACAGC
ACAAAGGCTATGAACATATGGAAGTAAAAGATAAACCTCAAAAATGAAGTAGAATTCAAGGGAT
CGGAAAGAAACTGAAAAAAGCAAAGTCGTTTAACTGATCTCTGGCTAAACATGAGCTACTAGAA
TATCAGATTACCTGAATTGAGAATACATCTTCTACTGGCATTAAGAATGGTTTATCAAGCTGAC
GCACTGGATCTGGAATGTATTCATCTACAGCATCCATCAACTTTAAAATAGCTTTCTTTCCAAT
TTCTTCATTAGTTCC

Sequences
Splice junction sequence	AGAATGGTTTATCAAGCTGACGCACTGGATCTGGAATGTATTCATCTACAGCATCCATCAACTT TAAAATAGCTTTCTTTCCAATTTCTTCATTAGTTCCtgcatcagccctaaaatctccacatctt ctccaacttttattgttccctgttcaatacggccagtagcaacagttccacgtcccttcaaaac attaacgg
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	TGCATCAGCCCTAAAATCTCCACATCTTCTCCAACTTTTATTGTTCCCTGTTCAATACGGCCAG TAGCAACAGTTCCACGTCCCTTCAAAACATTAACGGTAACTGATCAGTATCACATTAGAAGCAA GGTTCAAGCATTATTATTTTTCCTCTTTTGGAAATGAAAGATGGACTGCTGCAAAAAAAATATT TTTCTACCTTTCTCAGAGCAAAGGATTGTACTAAAATAAGCAGAAAGAGGTATAGCATCACAGC ACAAAGGCTATGAACATATGGAAGTAAAAGATAAACCTCAAAAATGAAGTAGAATTCAAGGGAT CGGAAAGAAACTGAAAAAAGCAAAGTCGTTTAACTGATCTCTGGCTAAACATGAGCTACTAGAA TATCAGATTACCTGAATTGAGAATACATCTTCTACTGGCATTAAGAATGGTTTATCAAGCTGAC GCACTGGATCTGGAATGTATTCATCTACAGCATCCATCAACTTTAAAATAGCTTTCTTTCCAAT TTCTTCATTAGTTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.238057717

Conservation Information
Conserved circRNAs	NA
PMCS	0.238057717

			
						 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 PGSC0003DMG400003838_circ_g.1

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