Plant Circular RNA Database

Detail information of PGSC0003DMG400001069_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400001069_circ_g.1
					
						ID in PlantcircBase
						stu_circ_001649
					
						Alias
						chr12:4905392|4905579
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr12: 4905393-4905579  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400001069						
					
						Parent gene annotation
						
							Protein phosphatase 2a, regulatory subunit
							
						Parent gene strand
						+
					
						Alternative splicing
						
							PGSC0003DMG400001069_circ_g.2 PGSC0003DMG400001069_circ_g.3 						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							No-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-GT							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
						PGSC0003DMT400002757:1
PGSC0003DMT400002756:1
PGSC0003DMT400002752:1
PGSC0003DMT400002754:1
PGSC0003DMT400002758:1
PGSC0003DMT400002753:2
PGSC0003DMT400002755:1
PGSC0003DMT400002759:1

General Information
CircRNA Name	PGSC0003DMG400001069_circ_g.1
ID in PlantcircBase	stu_circ_001649
Alias	chr12:4905392\|4905579
Organism	Solanum tuberosum
Position	chr12: 4905393-4905579 JBrowse»
Reference genome	3.0.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400001069
Parent gene annotation	Protein phosphatase 2a, regulatory subunit
Parent gene strand	+
Alternative splicing	PGSC0003DMG400001069_circ_g.2 PGSC0003DMG400001069_circ_g.3
Support reads	NA
Tissues	stem
Exon boundary	No-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-GT 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	PGSC0003DMT400002757:1 PGSC0003DMT400002756:1 PGSC0003DMT400002752:1 PGSC0003DMT400002754:1 PGSC0003DMT400002758:1 PGSC0003DMT400002753:2 PGSC0003DMT400002755:1 PGSC0003DMT400002759:1

			
						 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  
						
							TGCTGAAGTTTGATTCTTTTTTGGTTTCTTGAATAGTTGTTGGTGTAGTTTTGGGCAATTCCAT
AACTTCAGAGCTGATTAGCAGAACCCCAGtttgggcaatttcataacttcagagctgattagca
gaaccccaggttctattttcactctatctgtcagatctttttgggaaatgctgtgatgt

						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
						
							TTTGGGCAATTTCATAACTTCAGAGCTGATTAGCAGAACCCCAGGTTCTATTTTCACTCTATCT
GTCAGATCTTTTTGGGAAATGCTGTGATGTTGCTGAAGTTTGATTCTTTTTTGGTTTCTTGAAT
AGTTGTTGGTGTAGTTTTGGGCAATTCCATAACTTCAGAGCTGATTAGCAGAACCCCAG

Sequences
Splice junction sequence	TGCTGAAGTTTGATTCTTTTTTGGTTTCTTGAATAGTTGTTGGTGTAGTTTTGGGCAATTCCAT AACTTCAGAGCTGATTAGCAGAACCCCAGtttgggcaatttcataacttcagagctgattagca gaaccccaggttctattttcactctatctgtcagatctttttgggaaatgctgtgatgt
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	TTTGGGCAATTTCATAACTTCAGAGCTGATTAGCAGAACCCCAGGTTCTATTTTCACTCTATCT GTCAGATCTTTTTGGGAAATGCTGTGATGTTGCTGAAGTTTGATTCTTTTTTGGTTTCTTGAAT AGTTGTTGGTGTAGTTTTGGGCAATTCCATAACTTCAGAGCTGATTAGCAGAACCCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.202621212

Conservation Information
Conserved circRNAs	NA
PMCS	0.202621212

			
						 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 PGSC0003DMG400001069_circ_g.1

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