Plant Circular RNA Database

Detail information of PGSC0003DMG400001856_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400001856_circ_g.1
					
						ID in PlantcircBase
						stu_circ_001079
					
						Alias
						chr08:50539836|50542152
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr8: 50539837-50542152  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400001856						
					
						Parent gene annotation
						
							Placental protein 11
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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-GG							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
						PGSC0003DMT400004688:3

General Information
CircRNA Name	PGSC0003DMG400001856_circ_g.1
ID in PlantcircBase	stu_circ_001079
Alias	chr08:50539836\|50542152
Organism	Solanum tuberosum
Position	chr8: 50539837-50542152 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400001856
Parent gene annotation	Placental protein 11
Parent gene strand	+
Alternative splicing	NA
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-GG 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	PGSC0003DMT400004688:3

			
						 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  
						
							TTCTCAGCCGTCTCAAAACATGCAGGCTTCACCTCAGGGGTACCAAAGAAATGAAGATGAGAGG
AGAGACAATGTCAACCAAAGCAGTTGGAAGCAAAAGaagatgatggggttaacagtgatcatag
aactggatataatagacaggttaatttggtttttcttgattttttagaatattagtgtggaatt
tgatttta

									
								

					

						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
						
							AAGATGATGGGGTTAACAGTGATCATAGAACTGGATATAATAGACAGGTTAATTTGGTTTTTCT
TGATTTTTTAGAATATTAGTGTGGAATTTGATTTTAAAGTTTTGATTTTTTTTAATCCCTTTTT
GATAATAATAATAACAAACATAGTGTATCCCACGAGTGGTTCTAAGGAGGATAGAGTGTATGCA
GATCTTATCTATCTTGGGAAGATAGAGTGTTTGTTTTCGATAGGCCGTCGGTTTTAATACCTTT
ATAAAAGTTTGAATTTTTGGCAGGATGAGAGATATGGGAGAAATGAGGAATCAAGGCCTCACAT
GATTCCCCAAAAGGTACATACAAGTTTTTTTTTATTATTGGTTCTTCTTTGTTTTATAGTGTCT
TTAAGATTCTATGGTGTAAATGTCATGAATATGGGACTCCCAATTCTTGAATTATATGTTTTTT
TGTCTCAAGTTTTCCTGTTTATAGAGTAGCTTTTGTGGTCAAATTGTAGTTTTTTTGGTAAACT
TTGAATATTTACAGTACTGATTAACTTGCTATTGATCTCTAGATTGAGTCTGTTTTTGTAGTGT
GATGGGATTTCTTGCTTCATAGAATAACCCAAATACAGTGAGACTGGCCCGAATAGAGTGCGAA
TGGATATAGAGGACTCATATAGCTGAAGGTGAAGCCAAGGATTTTTAATATATGGGTTCTGGAC
CATTGTTCTTGTTGCTTACTAGGTTCTAGATAGATTATTGTACATATCAAATGAATTTTTTTAA
CACAAATACAGAATTTGAGCCAAAGCTATTGGGTTCGAACCAGGGGAGGAGTTAGGATACCTCT
AAACCCCCTTAGTCTAAAAATTATACTATATTTACATTGTCGAAATTATTCTATATATANNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNTATATATATATATAGTAGATATTGAACCCCTTGGCTTCTTCATA
CATTTACTTCCTTATATTTTGTATCCCCTTGGTGAAAATCCCATTTCTGCCACGTGTTTGAACC
CAGTTACTAAAATTGTGCCTTTGCCCCTGCATATAACAATTCCCAACTATTTTGTGACCGATTT
ATAGTCATCCTTGTTGTTTTATTAGTTAATCCAAAGAATTCGTTTGGTGGTGTGATGGGATGGG
GAAGGAGAAGTGTGATTGTTTTTCTCTTCTTGTTTGTGCAAAGAAGGTGCAGGGCTGCTTGTAC
AGTTGATTTATGCAATATGAGAGAACAAGATGCTAGTGCTGAATTGATAAGAAAAAGCTCTTGG
AATGGTATTGCATATGATGCAAATTTTTACAACAAGTAACTGTTTGAAAGGCAATAAAACTCGG
CTTTAATTTTTTCATACGGAAATTAGTTCTAAACTAAAAGAACAATCGTCTTGTATAAGATCTC
AAGTGAGTTGAAGAATGAAGCGATAAGTATAATCATGTCACGAGTGTGAAATATTCATGTAATC
ACTGTGTAGTAGTATGTGGTTTCTGTTTGAACAATAATTGTTCTCAGCCGTCTCAAAACATGCA
GGCTTCACCTCAGGGGTACCAAAGAAATGAAGATGAGAGGAGAGACAATGTCAACCAAAGCAGT
TGGAAGCAAAAG
						
					

			
		

Sequences
Splice junction sequence	TTCTCAGCCGTCTCAAAACATGCAGGCTTCACCTCAGGGGTACCAAAGAAATGAAGATGAGAGG AGAGACAATGTCAACCAAAGCAGTTGGAAGCAAAAGaagatgatggggttaacagtgatcatag aactggatataatagacaggttaatttggtttttcttgattttttagaatattagtgtggaatt tgatttta
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	AAGATGATGGGGTTAACAGTGATCATAGAACTGGATATAATAGACAGGTTAATTTGGTTTTTCT TGATTTTTTAGAATATTAGTGTGGAATTTGATTTTAAAGTTTTGATTTTTTTTAATCCCTTTTT GATAATAATAATAACAAACATAGTGTATCCCACGAGTGGTTCTAAGGAGGATAGAGTGTATGCA GATCTTATCTATCTTGGGAAGATAGAGTGTTTGTTTTCGATAGGCCGTCGGTTTTAATACCTTT ATAAAAGTTTGAATTTTTGGCAGGATGAGAGATATGGGAGAAATGAGGAATCAAGGCCTCACAT GATTCCCCAAAAGGTACATACAAGTTTTTTTTTATTATTGGTTCTTCTTTGTTTTATAGTGTCT TTAAGATTCTATGGTGTAAATGTCATGAATATGGGACTCCCAATTCTTGAATTATATGTTTTTT TGTCTCAAGTTTTCCTGTTTATAGAGTAGCTTTTGTGGTCAAATTGTAGTTTTTTTGGTAAACT TTGAATATTTACAGTACTGATTAACTTGCTATTGATCTCTAGATTGAGTCTGTTTTTGTAGTGT GATGGGATTTCTTGCTTCATAGAATAACCCAAATACAGTGAGACTGGCCCGAATAGAGTGCGAA TGGATATAGAGGACTCATATAGCTGAAGGTGAAGCCAAGGATTTTTAATATATGGGTTCTGGAC CATTGTTCTTGTTGCTTACTAGGTTCTAGATAGATTATTGTACATATCAAATGAATTTTTTTAA CACAAATACAGAATTTGAGCCAAAGCTATTGGGTTCGAACCAGGGGAGGAGTTAGGATACCTCT AAACCCCCTTAGTCTAAAAATTATACTATATTTACATTGTCGAAATTATTCTATATATANNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNTATATATATATATAGTAGATATTGAACCCCTTGGCTTCTTCATA CATTTACTTCCTTATATTTTGTATCCCCTTGGTGAAAATCCCATTTCTGCCACGTGTTTGAACC CAGTTACTAAAATTGTGCCTTTGCCCCTGCATATAACAATTCCCAACTATTTTGTGACCGATTT ATAGTCATCCTTGTTGTTTTATTAGTTAATCCAAAGAATTCGTTTGGTGGTGTGATGGGATGGG GAAGGAGAAGTGTGATTGTTTTTCTCTTCTTGTTTGTGCAAAGAAGGTGCAGGGCTGCTTGTAC AGTTGATTTATGCAATATGAGAGAACAAGATGCTAGTGCTGAATTGATAAGAAAAAGCTCTTGG AATGGTATTGCATATGATGCAAATTTTTACAACAAGTAACTGTTTGAAAGGCAATAAAACTCGG CTTTAATTTTTTCATACGGAAATTAGTTCTAAACTAAAAGAACAATCGTCTTGTATAAGATCTC AAGTGAGTTGAAGAATGAAGCGATAAGTATAATCATGTCACGAGTGTGAAATATTCATGTAATC ACTGTGTAGTAGTATGTGGTTTCTGTTTGAACAATAATTGTTCTCAGCCGTCTCAAAACATGCA GGCTTCACCTCAGGGGTACCAAAGAAATGAAGATGAGAGGAGAGACAATGTCAACCAAAGCAGT TGGAAGCAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.068271319

Conservation Information
Conserved circRNAs	NA
PMCS	0.068271319

			
						 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 PGSC0003DMG400001856_circ_g.1

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