Plant Circular RNA Database

Detail information of PGSC0003DMG400031271_circ_igg.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400031271_circ_igg.1
					
						ID in PlantcircBase
						stu_circ_000688
					
						Alias
						chr05:5068751|5219204
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr5: 5068752-5353680  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							PGSC0003DMG400025547_circ_igg.1 PGSC0003DMG400025547_circ_ig.1 PGSC0003DMG400025545_circ_igg.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  
						
							GA-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
						NA

General Information
CircRNA Name	PGSC0003DMG400031271_circ_igg.1
ID in PlantcircBase	stu_circ_000688
Alias	chr05:5068751\|5219204
Organism	Solanum tuberosum
Position	chr5: 5068752-5353680 JBrowse»
Reference genome	3.0.38
Type	igg-circRNA
Identification method	CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	PGSC0003DMG400025547_circ_igg.1 PGSC0003DMG400025547_circ_ig.1 PGSC0003DMG400025545_circ_igg.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	GA-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	NA

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: ATGCAAAGATTGGCAAGGC
 R: GGTAGCAACAGCAGCCTGAAC
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	Yes 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	F: ATGCAAAGATTGGCAAGGC R: GGTAGCAACAGCAGCCTGAAC 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  
						
							CCTTGCAATCTTTAACAGGCTTAGCTTCAAAACCTCCTTCCGGTCTCCTCTCAAGTTCATATGG
CATGTAAGTACCAAGTATCCTATCCCACGTCACAAAtgttgtatctatcagcagttttcttagc
tcggtattgtccttaaccgatgtcagctcaagatcatagacgtcatacttcaagaaattagcca
tagcagca

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CCTTGCAATCTTTAACAGGCTTAGCTTCAAAACCTCCTTCCGGTCTCCTCTCAAGTTCATATGG CATGTAAGTACCAAGTATCCTATCCCACGTCACAAAtgttgtatctatcagcagttttcttagc tcggtattgtccttaaccgatgtcagctcaagatcatagacgtcatacttcaagaaattagcca tagcagca
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	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
						0.009960469

Conservation Information
Conserved circRNAs	NA
PMCS	0.009960469

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							stu-miR7996c stu-miR172c-3p 						
					
						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	stu-miR7996c stu-miR172c-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhou et al., 2018

circRNA

Detail information of PGSC0003DMG400031271_circ_igg.1

Address

Any questions?

Supported by