Plant Circular RNA Database

Detail information of PGSC0003DMG400003691_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400003691_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000664
					
						Alias
						chr04:69954240|69957355
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr4: 69954241-69957357  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400003691						
					
						Parent gene annotation
						
							Phenylcoumaran benzylic ether reductase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							PGSC0003DMG400003691_circ_igg.1 PGSC0003DMG400003691_circ_igg.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  
						
							AA-GC							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
						PGSC0003DMT400009473:1
PGSC0003DMT400009471:2
PGSC0003DMT400009470:1

General Information
CircRNA Name	PGSC0003DMG400003691_circ_g.1
ID in PlantcircBase	stu_circ_000664
Alias	chr04:69954240\|69957355
Organism	Solanum tuberosum
Position	chr4: 69954241-69957357 JBrowse»
Reference genome	3.0.38
Type	ei-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400003691
Parent gene annotation	Phenylcoumaran benzylic ether reductase
Parent gene strand	+
Alternative splicing	PGSC0003DMG400003691_circ_igg.1 PGSC0003DMG400003691_circ_igg.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	AA-GC 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	PGSC0003DMT400009473:1 PGSC0003DMT400009471:2 PGSC0003DMT400009470:1

			
						 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  
						
							CTGTTTTGCTGGTTATTTTTTAGCAACTTTGGTCCAGCCAGGAGCCACTGCTCCTCCTCGAGAC
AAAGTCATCATTACCGGAGATGGAATTGTTAAGGGTtgtattcaatgaagaacatgacattggc
acctacaccattaaggctgttgatgacccgagaacgttgaacaagaccctttacatcaggcctc
ccaagaac

									
								

					

						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
						
							TGTATTCAATGAAGAACATGACATTGGCACCTACACCATTAAGGCTGTTGATGACCCGAGAACG
TTGAACAAGACCCTTTACATCAGGCCTCCCAAGAACACCTTATCGTTCAACGAGCTTGTGGCTA
TATGGGAGAAACTGATTGGTAAAACTCTCGAGAAAATCTACGTTCCAGGGGAGCAAATTCTCAA
AGACATCCAGAGTTAGTAATCTTTATATCATTCATCTGTTTCTTTCAATTTAACATAGGTAATC
CTGACAATGTATATTGCATACTGTTGCAGCATCTCCGATACCAATCAATATCATACTATCAGTC
AACCACTCAACATTCGTGAACGGTGATCATACCAATTTTGAGATAGAGCCATCGTTTGGGGTTG
AGGCCTCGGAAATTTATCCAGATGTTAAGTACACCACCGTGGAGGAGACCTTGGTCACGTTGTC
TGAACTACACGTTTGATGTCTTCGATAACTCGAATAAACTGTTAGATGATGAGTGTTGTCAGAC
ATTTTGTCTGGAAGTATGAGTGCTTGTTAACTATGTCATCAGAGACGGGTTGAATGGTATGTTT
TAAGTCTGTTTTTTCTGTCCATACTGCATAGTACTATAATGAATATGGAAGACATTCGCGTTTT
TCTTCTTTTTGCATTGTTGCTCTACCATCTTGTGCCAGATTTTAAGGTGTTATGTAATAGGGGT
GGCAAATGGTTGGATTGGATCGGATTTGGATGGATTGAACAAAAATGGTTTGGATTACAATCCA
CCCAAATATAATATGGGTAAATATGGATTTGATCAAATATGGTTTGGGTAAAATGGTTCTAACA
CATTTAAAACCTCTCCATATTTCCTTGACTAAGTGAACTGGGACTTCATGACATCAATTTACCC
CCTTCCCCGGGGCGCCCCCCACCTTCCACCAACCGACCCCTAATTTTTTTTTGTTTTCCAAAAA
CAAAAAAAAATATTTTGTTTTTCAAAAAAAAAAAAAATTTACCCCCTCCCCCCGTCCCCCTCCC
TTCCACCAACCTACCCTTAAATTTTTTTTTGTTTTTCAAAAACAAAAATAAATGTTTTTTCAGT
TAAGTTTGAAAATTAATTGAATTTTTGAAAATTAATCTTAAATTCTTTTATTTTTTAGCACAAT
TAAGAATTTTGAGTGAAAGTGAAAACTAAGTGATCTATCCATATTTTATCTATTTTGATCATAT
CTGTAGAGACTCTTAATATAGCTTGAAGCCCATATTTACCCAATTAAAATATGAGTGATCCAAG
TCATTAAATATGAATAAAATAGACTCATTTCGTTAATATGGGCTGAAATTGTCACCCTAATATG
AAAGAGTCTTGTTGTCAATAAAGATCAATCACAGAGGACTCTCTCCTGTTTATATATGAGGCTC
ACTCATTTCAGTTATCTCTAGCTTTCTTATGAGTTCAGGTATCGTATGGAATATAATCCACGGA
TCATTAGGAACCTATGTAATAGTATCCCAATCAAATAGCTGATGAGCGGATAAATAGTGATTGG
AAAATATTGTCAATTTGGTCTGATGATTTTACGTGATGAGTTATTACCCTACCAATCTAACATT
ATCATTCATGCTTTAGTCATACGCCAGGAAAACCTTCCAACTTCACCTAACTTTTGTTAGGAAG
AATATGCTGCTTCACTCTAGAATGGATCATGATCCTTTCTTAAGTAAAGTGGAGATCTTTACGC
GAATAGCCGAGCAGATTTACTGTTTACTTTTTAGAAGGCCACATTTTATGATCTTTGTTTGGAG
CTCACTCAAGCTATAATTATGCTATGAATTATATATATTGAAAAAATAATGAGTATTGAACGTA
TCGTTTCAAGTTTCTCCCATTCTTTTTGGCACATTACACTATGAAGTGAACATCTCCCACATTC
ATCAACAAATTCAATTTTTATACCACTTCTTCTTTAAAAATCCCAAAATTCATCCGTCTGCCTA
TTTACGCTATCGGAGAACCCACAAGCTTTGTCAACCTATGGTAGCATCTAGCGAAGCAATTATC
GATGCATTTTAAGAAAAAGTTCAAGCTCTTCTAAATCTTGTTCATGATCGTTTCCATGGAATGA
TTAATAGTTAATATTCTGAACTCATCGATTTAATATTTTCGTCAATAGATTCACTCATATTTTT
TGCCAATGGTGGTGTAGTGATTTGGAAGAAGCAAGATATAAGTAAAATGAAAGTGCAGGTTAGG
TTAGTAATGGTGTAATGGGTGTGGTGAGTTTGCAGGAAGAGTGGAGAAGAAGAGAAATAAATTA
GAAGTTAATATTAAAGAAAATGAAGAGTTTGTTGAAGGCTATAAAACAAGTGGATCTGGTGATA
TCAACTGTTGGTGCAATGCAATTCCGCTGATCAAGTTAAGATCATTGATGCTATCAAAGAAGCT
GGCAATATTAAGGTTAATTACTTCTTGTTTTTCGAAACGGGGTTGAACTCGAGACCTCTGGTTA
AGGATGGAGGGATCTTATTTATCTGTATGCAACATGGGACAGAGGGGATAATGGAGTATGGGGA
TCTTGATTACAGTAATTGTTGATGAAAATTCTTGAATTTATCGATAAACATTTGAATTAGAGAA
TTTGGCTTAAATCTATGTTGCTCAGATACTTCAATAATGTTGATGGTTGCATGTTGGATCGTCC
AAAAGTAGTGTATTTTTGGAGGATCCAACATGGGTTCAGCAACATAATTGGATAGTCCGAGCAA
CATAGCCTCCAATTAAGGGAGTATTCGTCTCGTTGATTTAAGGTTATAAAATGAGTTAGATTAC
TAATTGTTAACATGGCCTAGTGGAACATCTTGATCTGCATAACCAAGTGTATGACAGAAATATG
CAGCAAGTTCGCGTAAATGCCTCAAATTAGGAAGAGATGAACGCTGTGGAGCCAATAAAGTCTA
CATTGGCTGTGAAATCCCAAATCCGAAGAGCTATTGAGGCTGCAGAAATTCCCTATACTTATGT
CTTATGCAACTGTTTTGCTGGTTATTTTTTAGCAACTTTGGTCCAGCCAGGAGCCACTGCTCCT
CCTCGAGACAAAGTCATCATTACCGGAGATGGAATTGTTAAGGGT
						
					

			
		

Sequences
Splice junction sequence	CTGTTTTGCTGGTTATTTTTTAGCAACTTTGGTCCAGCCAGGAGCCACTGCTCCTCCTCGAGAC AAAGTCATCATTACCGGAGATGGAATTGTTAAGGGTtgtattcaatgaagaacatgacattggc acctacaccattaaggctgttgatgacccgagaacgttgaacaagaccctttacatcaggcctc ccaagaac
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	TGTATTCAATGAAGAACATGACATTGGCACCTACACCATTAAGGCTGTTGATGACCCGAGAACG TTGAACAAGACCCTTTACATCAGGCCTCCCAAGAACACCTTATCGTTCAACGAGCTTGTGGCTA TATGGGAGAAACTGATTGGTAAAACTCTCGAGAAAATCTACGTTCCAGGGGAGCAAATTCTCAA AGACATCCAGAGTTAGTAATCTTTATATCATTCATCTGTTTCTTTCAATTTAACATAGGTAATC CTGACAATGTATATTGCATACTGTTGCAGCATCTCCGATACCAATCAATATCATACTATCAGTC AACCACTCAACATTCGTGAACGGTGATCATACCAATTTTGAGATAGAGCCATCGTTTGGGGTTG AGGCCTCGGAAATTTATCCAGATGTTAAGTACACCACCGTGGAGGAGACCTTGGTCACGTTGTC TGAACTACACGTTTGATGTCTTCGATAACTCGAATAAACTGTTAGATGATGAGTGTTGTCAGAC ATTTTGTCTGGAAGTATGAGTGCTTGTTAACTATGTCATCAGAGACGGGTTGAATGGTATGTTT TAAGTCTGTTTTTTCTGTCCATACTGCATAGTACTATAATGAATATGGAAGACATTCGCGTTTT TCTTCTTTTTGCATTGTTGCTCTACCATCTTGTGCCAGATTTTAAGGTGTTATGTAATAGGGGT GGCAAATGGTTGGATTGGATCGGATTTGGATGGATTGAACAAAAATGGTTTGGATTACAATCCA CCCAAATATAATATGGGTAAATATGGATTTGATCAAATATGGTTTGGGTAAAATGGTTCTAACA CATTTAAAACCTCTCCATATTTCCTTGACTAAGTGAACTGGGACTTCATGACATCAATTTACCC CCTTCCCCGGGGCGCCCCCCACCTTCCACCAACCGACCCCTAATTTTTTTTTGTTTTCCAAAAA CAAAAAAAAATATTTTGTTTTTCAAAAAAAAAAAAAATTTACCCCCTCCCCCCGTCCCCCTCCC TTCCACCAACCTACCCTTAAATTTTTTTTTGTTTTTCAAAAACAAAAATAAATGTTTTTTCAGT TAAGTTTGAAAATTAATTGAATTTTTGAAAATTAATCTTAAATTCTTTTATTTTTTAGCACAAT TAAGAATTTTGAGTGAAAGTGAAAACTAAGTGATCTATCCATATTTTATCTATTTTGATCATAT CTGTAGAGACTCTTAATATAGCTTGAAGCCCATATTTACCCAATTAAAATATGAGTGATCCAAG TCATTAAATATGAATAAAATAGACTCATTTCGTTAATATGGGCTGAAATTGTCACCCTAATATG AAAGAGTCTTGTTGTCAATAAAGATCAATCACAGAGGACTCTCTCCTGTTTATATATGAGGCTC ACTCATTTCAGTTATCTCTAGCTTTCTTATGAGTTCAGGTATCGTATGGAATATAATCCACGGA TCATTAGGAACCTATGTAATAGTATCCCAATCAAATAGCTGATGAGCGGATAAATAGTGATTGG AAAATATTGTCAATTTGGTCTGATGATTTTACGTGATGAGTTATTACCCTACCAATCTAACATT ATCATTCATGCTTTAGTCATACGCCAGGAAAACCTTCCAACTTCACCTAACTTTTGTTAGGAAG AATATGCTGCTTCACTCTAGAATGGATCATGATCCTTTCTTAAGTAAAGTGGAGATCTTTACGC GAATAGCCGAGCAGATTTACTGTTTACTTTTTAGAAGGCCACATTTTATGATCTTTGTTTGGAG CTCACTCAAGCTATAATTATGCTATGAATTATATATATTGAAAAAATAATGAGTATTGAACGTA TCGTTTCAAGTTTCTCCCATTCTTTTTGGCACATTACACTATGAAGTGAACATCTCCCACATTC ATCAACAAATTCAATTTTTATACCACTTCTTCTTTAAAAATCCCAAAATTCATCCGTCTGCCTA TTTACGCTATCGGAGAACCCACAAGCTTTGTCAACCTATGGTAGCATCTAGCGAAGCAATTATC GATGCATTTTAAGAAAAAGTTCAAGCTCTTCTAAATCTTGTTCATGATCGTTTCCATGGAATGA TTAATAGTTAATATTCTGAACTCATCGATTTAATATTTTCGTCAATAGATTCACTCATATTTTT TGCCAATGGTGGTGTAGTGATTTGGAAGAAGCAAGATATAAGTAAAATGAAAGTGCAGGTTAGG TTAGTAATGGTGTAATGGGTGTGGTGAGTTTGCAGGAAGAGTGGAGAAGAAGAGAAATAAATTA GAAGTTAATATTAAAGAAAATGAAGAGTTTGTTGAAGGCTATAAAACAAGTGGATCTGGTGATA TCAACTGTTGGTGCAATGCAATTCCGCTGATCAAGTTAAGATCATTGATGCTATCAAAGAAGCT GGCAATATTAAGGTTAATTACTTCTTGTTTTTCGAAACGGGGTTGAACTCGAGACCTCTGGTTA AGGATGGAGGGATCTTATTTATCTGTATGCAACATGGGACAGAGGGGATAATGGAGTATGGGGA TCTTGATTACAGTAATTGTTGATGAAAATTCTTGAATTTATCGATAAACATTTGAATTAGAGAA TTTGGCTTAAATCTATGTTGCTCAGATACTTCAATAATGTTGATGGTTGCATGTTGGATCGTCC AAAAGTAGTGTATTTTTGGAGGATCCAACATGGGTTCAGCAACATAATTGGATAGTCCGAGCAA CATAGCCTCCAATTAAGGGAGTATTCGTCTCGTTGATTTAAGGTTATAAAATGAGTTAGATTAC TAATTGTTAACATGGCCTAGTGGAACATCTTGATCTGCATAACCAAGTGTATGACAGAAATATG CAGCAAGTTCGCGTAAATGCCTCAAATTAGGAAGAGATGAACGCTGTGGAGCCAATAAAGTCTA CATTGGCTGTGAAATCCCAAATCCGAAGAGCTATTGAGGCTGCAGAAATTCCCTATACTTATGT CTTATGCAACTGTTTTGCTGGTTATTTTTTAGCAACTTTGGTCCAGCCAGGAGCCACTGCTCCT CCTCGAGACAAAGTCATCATTACCGGAGATGGAATTGTTAAGGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.630857849

Conservation Information
Conserved circRNAs	NA
PMCS	0.630857849

			
						 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 PGSC0003DMG400003691_circ_g.1

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