Plant Circular RNA Database

Detail information of PGSC0003DMG400003512_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400003512_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000334
					
						Alias
						chr02:40342613|40346852
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr2: 40342614-40346852  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400003512						
					
						Parent gene annotation
						
							Laccase
							
						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  
						
							CT-CA							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
						PGSC0003DMT400009041:1
PGSC0003DMT400009039:2
PGSC0003DMT400009042:4
PGSC0003DMT400009040:2

General Information
CircRNA Name	PGSC0003DMG400003512_circ_g.1
ID in PlantcircBase	stu_circ_000334
Alias	chr02:40342613\|40346852
Organism	Solanum tuberosum
Position	chr2: 40342614-40346852 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400003512
Parent gene annotation	Laccase
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	CT-CA 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	PGSC0003DMT400009041:1 PGSC0003DMT400009039:2 PGSC0003DMT400009042:4 PGSC0003DMT400009040:2

			
						 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  
						
							GTATGATTAGCCAGGGCAAAAAAGAGTTCATCATTGAGAGCAGCATTGATAATTCTCAACAGGT
ATGTCTTTCCTTTTTCAACTTCCATGGCAAAAGTATtttctctgaacatgggaaaagaggccct
ggctttccgttaatcgtgtgagcatcagacatattaggaggaatacccaaggcatttccttgtt
tctcgact

									
								

					

						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
						
							TTTCTCTGAACATGGGAAAAGAGGCCCTGGCTTTCCGTTAATCGTGTGAGCATCAGACATATTA
GGAGGAATACCCAAGGCATTTCCTTGTTTCTCGACTGCTTCAACATCAGCATTCCACCATTCCC
CTGCATCACAATCACATAGAAGTATTGCTGTCATTTTCTTTTATTCTTTGCCATAAGAGAACTT
TGAGAAATTTTGGGGATGAATACTATATATATTAACGAATGTCAATGCTCACCTAGAACAAGCA
CTTCTTCCCTATCTGGCTGAGGAAAAGGGAAGGGAGTTCCTTGTTGTGGCATTATCACTATTGC
ACCATAGACAGTTGCCCTTAGCCAAAGAATATGTGCATGCCACCATAAGGTTCCTCTTTGTCCT
GTTACATTGAAATCATAAACATAGCTATTTCCTGTCTGGATAGGGCATTGAGTTATGTAAGCTG
GACCGTCTGCCCAACCATTGCGATATTGTTTCAAACCATGCCTACAAGAATCAGAACAAAAACA
TTCTGTTTTAGCACCTGAAAGTTTTGAGACTTCAATTTTCATCTAATTCTAGCTTATCTTACCA
ATGGATGGACAAGTTATATTGTACATAGTTAGTAACATTGATTTGAACTCTATCTCCTTCTCTA
GCATATATAGTTGGCCCCGGAAATCCGCCATTTACTGTAACCATTTGTTTTGCATTGCACAATC
TGCTCACATTTGACAATTTCACCTGTAAACCACAGAAAGTTTACCATGATGAAAAGAAAAGAAC
CAAAAGTAAACAAAGTTCAAAAATTGAAAGCACTAACATCAAATTGATATTTCTTAAGGGCAGC
CTCAACAGGTAGACAAATGAAACAGAGAAATCCAAAGACAAGTAAGCCTATAAAACTTGTCTGC
TTTGCCATTTTCCTTAATTGGCTAAAAGGTGTATGACAAGTATGTGGAATGGGATGAGACAAGC
GTATTTATACAAGTGAAATGTCATATAGTTTGTTAAGGGAAGAGATATATTAGGTACAAAAAGT
ATTTCAATTTGCTGTAGTGCTGTTACTGCAAAGCCTTTAAGCAATACACAGATGTAGACATTTT
TAAAGCCATTGACTGACGTAGAGGCTAAATTCAAAATCCACCACATTCAAGCTAAGAAAAATAT
AAATTAGTTTTATGAACTTTACCTTAACGGTAAAGGAAAGAAGTTGCCCTAGCTATAGTATAAG
AAGGTGCATGTTAATTAGCATGTAGAATGTAGGTATATTTTTTGACGGCAGTTTTATTGGTTGG
TCAAAAAATAGCATATTGATTTAGACATAGGAAGGAAAGAAATTATTATATTATTACTAAAATA
AATAAATGTTCGTTGTGCTATTGTAGTCATGTAAACCTACTATGAGTATCACCATTTACATATG
TTTTTATGGCTACTCAATTTTATTATCTATGACACTGAAATACCACCTTCATTCATTAATTTAA
TCCTCTCAACTAGGCGCTTCACTTTTTTTTCCTTGCATGGTATGTTAACTAAAAAAATAATTTT
GATAACTCAGAACTGTAATTGGGGGTGACTCAAGCACTTTCATGGCCTAAAATCAAAAACAAAT
CGGATCTCTTAAATTTTTGAGTAATAATAATACTTTTTTTTAATTTAAAATCTGTTATTCTAGT
TTTTTTAAAATGCAAAGTGTTTGTAAATATATATTTTAAAAAATTATTTTGAGATGCAAACTTG
TTTTCTCTTTCTATATGAAAAAATTATTTTGTTTTGTAAATAGTACTCTCTCCATTTCAATTTG
TTTGTCTAATTTTGACTTGACATGGAGTTTGAAGTTTAATAAGAAATAAATAATATTTTTTGAA
TCGTATAGTCTTAAACTAAAGATTGAAACTAACTATATAATTTTTTCTAATTTTTAAGAGTACT
TGTAAAAATCTTAGTATTTTTTAATGGGATCTTTAAATTTGGAGGCCTAAAGTAAGTGACTTAT
TTTTCAATACATATAGAGCCGTCCTGACTTACCAACACTATAACTTTTTGGGGGTAAAATCACA
ATCAATCTATTTTACGAGTAAAATGAACCACTAACAGATATGTGAAATTCAGTAAAATTATTGT
AGTACACTTTTTAAGATCATTTTGGTAATGAAGAGTGTTTAATTGCCAAAAAGATACAGTACAC
TTTCATTTAAACGATGTTCTACGTTACTAATGTTTTCAATTTTATTTGTTATTTCACCAGATGA
AATATTACATAAATTCTGTAAAGGCATCCACCCAAATACTGAAATTTGAGGATAAGTTTTATAC
TTCAAAGTGCTAGTATAATCTCCCCCTAAAAACCATGGTAAAGTTCTTCATAGAACTAGAGTTA
TATATCTATGAAATTAATCCCTATTTCACTTGCATCACTTTCCAACTCAGGCACTACTAGAAAA
ATCAGAATTTTCAATAGAAAGTCCATCAGAAATAATTACGATGAGTATAATTTTAATGGAATTT
CACCGAAAATTCTAGTTTTTCTGGTAATGTCTTCCGCTTATTCCTTAAGTTCCTGTTCAACTTT
TTAACACTTCCATTTCACTAAACGTTCAGTGTCTGTATACTCAAAGAACTGTTTGTGCACTCGT
ATAAATTTTTTGTTCTCAAACTTAAAGGGATTATTGTGGGCTTTTTCTCTAAATTTACACAGTT
TTGTTGGTGACTTAGCAATTCTTATATATGGATGGATGATCGAACTCAAATTTTAGGACTTTTT
CTTAAAATAGCAGGTACTAATTCAGGTTTGCTATAATTGATAAACCTGTCAAGTCAAGTAGTAT
TAACAGACTATATTTCAATCCAAGTAGATAGGGAAGTTCATAAAAAACAACAGCCCAAAATCAC
ATTTTTATGTGTGGACCTTTATTACAACTCAAATTACATTTAAATTCTTGGGATAAAAACTCCT
TCTTCATTTTTCCAATTTTGCACATCTTTCCTATGCACACTGGCTAAAATGTGTATAATCTTCA
AAGCATTTTGCTTCCTTATGGGAAAATAAAACAAATTATGTAAAACTTTTACAAGAAATCCATC
TGGACATATAAAAGTAAAGCCTTTTGAAATTAGCATGATGGAAGGTCCTTTGGTGGAGGCAGAA
TACTATGATCTAATCCTGGTCCATTTTCCACTAAAAATGCTGTTTTCAGTCCCCAGCCTGTGTG
CAACTCCAGATGACAGTGGAAGAACCAGACCCCTTCACAAAAAATTGGATATGTTAACAATAAA
TTTTCAAAACAATAGAAAAGTTTTAACAAAATTTGGTTGAAAACTAGGTACCTGGATTATCAGC
CCTGAATCGAATAGCAGTCCAACCGCCAGTTGGAACACCTACAGTATTTCTTTCTATAGGATCA
TTCAAGTTGTATTTTGCTGGATCTTTTTTGGGGTCAAAGTTTCCAATGCCAGTTCCAACCACAA
AGAAATTGTAGCCATGGAGATGGAAAGGATGTGATTCCACCGACAACAAGTTGGTGTCTTGGAC
TACTATTTCAACAGTAGAATTGAAAGCAATTTTGCTGATCCTAGTGCCTACATTTGTCCTTAGG
TTGGCTGTAAGGGGTGCCCCTGTAAAATTGAATGGAGTAGGTGGTTTGTCTGGGAAATCTGGAG
TGTATACACCCTTAATGTTGAAGTAATGAGACTGAAGAAGTGCAGTTTCTGGCATGATGAAGGA
AATGTTGTTCAAAGAAGCTGTTAGCCTAGTTCCATTTAGACAGGTGGGACAAGGATTTATCCCA
AGGCCAACTGTTAACAAGAGGTGTCGATCAACATTTAGGGGAACGTTTGCTGGATATTTGGGAG
TATTTAAGCTTTTGAGTTTAGAATTATAGCTCAAAGCAAAGTCTGAGTCATTTTGTGCAGGCAA
AGTAGGAAGTTTTGGAATCACGGTTTCTGGGATTCCCTTGTACTGGAATATAGCAGCGGCAGTC
TTGTTATCCACACTGATTGGAGCGTCCATGAAGGCCCTTGCAGCCATGAAGTATCTTCCTGGAA
CTTGGTTGGTGCGAACCAGAACATTTGTAGTCTGGCCTGGTGCAATCAGAATGGCGTCTGTGGT
GAATGGTTTCGTGTAGACTGCATCAATTTCTACCACTGTGAAGGTATGATTAGCCAGGGCAAAA
AAGAGTTCATCATTGAGAGCAGCATTGATAATTCTCAACAGGTATGTCTTTCCTTTTTCAACTT
CCATGGCAAAAGTAT
						
					

			
		

Sequences
Splice junction sequence	GTATGATTAGCCAGGGCAAAAAAGAGTTCATCATTGAGAGCAGCATTGATAATTCTCAACAGGT ATGTCTTTCCTTTTTCAACTTCCATGGCAAAAGTATtttctctgaacatgggaaaagaggccct ggctttccgttaatcgtgtgagcatcagacatattaggaggaatacccaaggcatttccttgtt tctcgact
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	TTTCTCTGAACATGGGAAAAGAGGCCCTGGCTTTCCGTTAATCGTGTGAGCATCAGACATATTA GGAGGAATACCCAAGGCATTTCCTTGTTTCTCGACTGCTTCAACATCAGCATTCCACCATTCCC CTGCATCACAATCACATAGAAGTATTGCTGTCATTTTCTTTTATTCTTTGCCATAAGAGAACTT TGAGAAATTTTGGGGATGAATACTATATATATTAACGAATGTCAATGCTCACCTAGAACAAGCA CTTCTTCCCTATCTGGCTGAGGAAAAGGGAAGGGAGTTCCTTGTTGTGGCATTATCACTATTGC ACCATAGACAGTTGCCCTTAGCCAAAGAATATGTGCATGCCACCATAAGGTTCCTCTTTGTCCT GTTACATTGAAATCATAAACATAGCTATTTCCTGTCTGGATAGGGCATTGAGTTATGTAAGCTG GACCGTCTGCCCAACCATTGCGATATTGTTTCAAACCATGCCTACAAGAATCAGAACAAAAACA TTCTGTTTTAGCACCTGAAAGTTTTGAGACTTCAATTTTCATCTAATTCTAGCTTATCTTACCA ATGGATGGACAAGTTATATTGTACATAGTTAGTAACATTGATTTGAACTCTATCTCCTTCTCTA GCATATATAGTTGGCCCCGGAAATCCGCCATTTACTGTAACCATTTGTTTTGCATTGCACAATC TGCTCACATTTGACAATTTCACCTGTAAACCACAGAAAGTTTACCATGATGAAAAGAAAAGAAC CAAAAGTAAACAAAGTTCAAAAATTGAAAGCACTAACATCAAATTGATATTTCTTAAGGGCAGC CTCAACAGGTAGACAAATGAAACAGAGAAATCCAAAGACAAGTAAGCCTATAAAACTTGTCTGC TTTGCCATTTTCCTTAATTGGCTAAAAGGTGTATGACAAGTATGTGGAATGGGATGAGACAAGC GTATTTATACAAGTGAAATGTCATATAGTTTGTTAAGGGAAGAGATATATTAGGTACAAAAAGT ATTTCAATTTGCTGTAGTGCTGTTACTGCAAAGCCTTTAAGCAATACACAGATGTAGACATTTT TAAAGCCATTGACTGACGTAGAGGCTAAATTCAAAATCCACCACATTCAAGCTAAGAAAAATAT AAATTAGTTTTATGAACTTTACCTTAACGGTAAAGGAAAGAAGTTGCCCTAGCTATAGTATAAG AAGGTGCATGTTAATTAGCATGTAGAATGTAGGTATATTTTTTGACGGCAGTTTTATTGGTTGG TCAAAAAATAGCATATTGATTTAGACATAGGAAGGAAAGAAATTATTATATTATTACTAAAATA AATAAATGTTCGTTGTGCTATTGTAGTCATGTAAACCTACTATGAGTATCACCATTTACATATG TTTTTATGGCTACTCAATTTTATTATCTATGACACTGAAATACCACCTTCATTCATTAATTTAA TCCTCTCAACTAGGCGCTTCACTTTTTTTTCCTTGCATGGTATGTTAACTAAAAAAATAATTTT GATAACTCAGAACTGTAATTGGGGGTGACTCAAGCACTTTCATGGCCTAAAATCAAAAACAAAT CGGATCTCTTAAATTTTTGAGTAATAATAATACTTTTTTTTAATTTAAAATCTGTTATTCTAGT TTTTTTAAAATGCAAAGTGTTTGTAAATATATATTTTAAAAAATTATTTTGAGATGCAAACTTG TTTTCTCTTTCTATATGAAAAAATTATTTTGTTTTGTAAATAGTACTCTCTCCATTTCAATTTG TTTGTCTAATTTTGACTTGACATGGAGTTTGAAGTTTAATAAGAAATAAATAATATTTTTTGAA TCGTATAGTCTTAAACTAAAGATTGAAACTAACTATATAATTTTTTCTAATTTTTAAGAGTACT TGTAAAAATCTTAGTATTTTTTAATGGGATCTTTAAATTTGGAGGCCTAAAGTAAGTGACTTAT TTTTCAATACATATAGAGCCGTCCTGACTTACCAACACTATAACTTTTTGGGGGTAAAATCACA ATCAATCTATTTTACGAGTAAAATGAACCACTAACAGATATGTGAAATTCAGTAAAATTATTGT AGTACACTTTTTAAGATCATTTTGGTAATGAAGAGTGTTTAATTGCCAAAAAGATACAGTACAC TTTCATTTAAACGATGTTCTACGTTACTAATGTTTTCAATTTTATTTGTTATTTCACCAGATGA AATATTACATAAATTCTGTAAAGGCATCCACCCAAATACTGAAATTTGAGGATAAGTTTTATAC TTCAAAGTGCTAGTATAATCTCCCCCTAAAAACCATGGTAAAGTTCTTCATAGAACTAGAGTTA TATATCTATGAAATTAATCCCTATTTCACTTGCATCACTTTCCAACTCAGGCACTACTAGAAAA ATCAGAATTTTCAATAGAAAGTCCATCAGAAATAATTACGATGAGTATAATTTTAATGGAATTT CACCGAAAATTCTAGTTTTTCTGGTAATGTCTTCCGCTTATTCCTTAAGTTCCTGTTCAACTTT TTAACACTTCCATTTCACTAAACGTTCAGTGTCTGTATACTCAAAGAACTGTTTGTGCACTCGT ATAAATTTTTTGTTCTCAAACTTAAAGGGATTATTGTGGGCTTTTTCTCTAAATTTACACAGTT TTGTTGGTGACTTAGCAATTCTTATATATGGATGGATGATCGAACTCAAATTTTAGGACTTTTT CTTAAAATAGCAGGTACTAATTCAGGTTTGCTATAATTGATAAACCTGTCAAGTCAAGTAGTAT TAACAGACTATATTTCAATCCAAGTAGATAGGGAAGTTCATAAAAAACAACAGCCCAAAATCAC ATTTTTATGTGTGGACCTTTATTACAACTCAAATTACATTTAAATTCTTGGGATAAAAACTCCT TCTTCATTTTTCCAATTTTGCACATCTTTCCTATGCACACTGGCTAAAATGTGTATAATCTTCA AAGCATTTTGCTTCCTTATGGGAAAATAAAACAAATTATGTAAAACTTTTACAAGAAATCCATC TGGACATATAAAAGTAAAGCCTTTTGAAATTAGCATGATGGAAGGTCCTTTGGTGGAGGCAGAA TACTATGATCTAATCCTGGTCCATTTTCCACTAAAAATGCTGTTTTCAGTCCCCAGCCTGTGTG CAACTCCAGATGACAGTGGAAGAACCAGACCCCTTCACAAAAAATTGGATATGTTAACAATAAA TTTTCAAAACAATAGAAAAGTTTTAACAAAATTTGGTTGAAAACTAGGTACCTGGATTATCAGC CCTGAATCGAATAGCAGTCCAACCGCCAGTTGGAACACCTACAGTATTTCTTTCTATAGGATCA TTCAAGTTGTATTTTGCTGGATCTTTTTTGGGGTCAAAGTTTCCAATGCCAGTTCCAACCACAA AGAAATTGTAGCCATGGAGATGGAAAGGATGTGATTCCACCGACAACAAGTTGGTGTCTTGGAC TACTATTTCAACAGTAGAATTGAAAGCAATTTTGCTGATCCTAGTGCCTACATTTGTCCTTAGG TTGGCTGTAAGGGGTGCCCCTGTAAAATTGAATGGAGTAGGTGGTTTGTCTGGGAAATCTGGAG TGTATACACCCTTAATGTTGAAGTAATGAGACTGAAGAAGTGCAGTTTCTGGCATGATGAAGGA AATGTTGTTCAAAGAAGCTGTTAGCCTAGTTCCATTTAGACAGGTGGGACAAGGATTTATCCCA AGGCCAACTGTTAACAAGAGGTGTCGATCAACATTTAGGGGAACGTTTGCTGGATATTTGGGAG TATTTAAGCTTTTGAGTTTAGAATTATAGCTCAAAGCAAAGTCTGAGTCATTTTGTGCAGGCAA AGTAGGAAGTTTTGGAATCACGGTTTCTGGGATTCCCTTGTACTGGAATATAGCAGCGGCAGTC TTGTTATCCACACTGATTGGAGCGTCCATGAAGGCCCTTGCAGCCATGAAGTATCTTCCTGGAA CTTGGTTGGTGCGAACCAGAACATTTGTAGTCTGGCCTGGTGCAATCAGAATGGCGTCTGTGGT GAATGGTTTCGTGTAGACTGCATCAATTTCTACCACTGTGAAGGTATGATTAGCCAGGGCAAAA AAGAGTTCATCATTGAGAGCAGCATTGATAATTCTCAACAGGTATGTCTTTCCTTTTTCAACTT CCATGGCAAAAGTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.140277271

Conservation Information
Conserved circRNAs	NA
PMCS	0.140277271

			
						 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 PGSC0003DMG400003512_circ_g.1

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