Plant Circular RNA Database

Detail information of PGSC0003DMG402002659_circ_ag.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG402002659_circ_ag.1
					
						ID in PlantcircBase
						stu_circ_001105
					
						Alias
						chr09:3190168|3193651
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr9: 3190169-3193651  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							PGSC0003DMG400008482_circ_ag.1 PGSC0003DMG400020343_circ_g.1 PGSC0003DMG400020347_circ_g.1 PGSC0003DMG400002168_circ_ag.1 PGSC0003DMG400024261_circ_ag.1 PGSC0003DMG400008917_circ_g.1 PGSC0003DMG400008917_circ_g.2 PGSC0003DMG400008917_circ_g.3 PGSC0003DMG400008924_circ_ag.1 PGSC0003DMG400008926_circ_g.1 PGSC0003DMG400008934_circ_g.1 PGSC0003DMG401008964_circ_igg.1 PGSC0003DMG402002659_circ_igg.1 PGSC0003DMG400002662_circ_ig.1 PGSC0003DMG400002662_circ_ig.2 PGSC0003DMG400002706_circ_ig.1 PGSC0003DMG400021562_circ_g.1 PGSC0003DMG400020909_circ_ig.1 PGSC0003DMG400020913_circ_ig.1 PGSC0003DMG400020913_circ_ig.2 PGSC0003DMG400027903_circ_g.1 						
					
						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
						NA

General Information
CircRNA Name	PGSC0003DMG402002659_circ_ag.1
ID in PlantcircBase	stu_circ_001105
Alias	chr09:3190168\|3193651
Organism	Solanum tuberosum
Position	chr9: 3190169-3193651 JBrowse»
Reference genome	3.0.38
Type	ag-circRNA
Identification method	CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	PGSC0003DMG400008482_circ_ag.1 PGSC0003DMG400020343_circ_g.1 PGSC0003DMG400020347_circ_g.1 PGSC0003DMG400002168_circ_ag.1 PGSC0003DMG400024261_circ_ag.1 PGSC0003DMG400008917_circ_g.1 PGSC0003DMG400008917_circ_g.2 PGSC0003DMG400008917_circ_g.3 PGSC0003DMG400008924_circ_ag.1 PGSC0003DMG400008926_circ_g.1 PGSC0003DMG400008934_circ_g.1 PGSC0003DMG401008964_circ_igg.1 PGSC0003DMG402002659_circ_igg.1 PGSC0003DMG400002662_circ_ig.1 PGSC0003DMG400002662_circ_ig.2 PGSC0003DMG400002706_circ_ig.1 PGSC0003DMG400021562_circ_g.1 PGSC0003DMG400020909_circ_ig.1 PGSC0003DMG400020913_circ_ig.1 PGSC0003DMG400020913_circ_ig.2 PGSC0003DMG400027903_circ_g.1
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	NA

			
						 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  
						
							AAGGAAAAAAAAAAAATGGCAACAAAGAAGATTTCAGCAGCTTCAGCTAGGGCTCATACTCGTA
AAGCTAAGCAAAAAAGTTCTTTTCCTCTTCCTTCTGaatgatgagaaatatggtagcccttttt
ggaattgtgatattggcactgatttatagggcaattatgccaccatcaccaaagatttgtggtt
caccaaat

									
								

					

						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
						
							AATGATGAGAAATATGGTAGCCCTTTTTGGAATTGTGATATTGGCACTGATTTATAGGGCAATT
ATGCCACCATCACCAAAGATTTGTGGTTCACCAAATGGACCTCTAATTACAGCACCGAGAGTGA
AGCTTTCTGATGGGAGATATTTGACATATAAAGAAAATGGTGTTCCTAGAGACCAAGCAAAACA
CAAATTTGTTTTCATCCATGGCTTTGATTGTGTTAGACATGATGTTGCTTTGCACACAACTACT
TCTCCTGTATGTATGTTTCATCTTTACTTGTTCTCCCCTCGCCCTCCCTTAGAATAGTTTTTAG
TTTCTTTTTCGTTTTGTTTGTGTCCGATATTTGTTTTGGGGTCCGACTAATTTAGATTTGTGTT
GGGAGGTTTCACTTTTAAGGCTCCCGACCAAAGATTACTCTATTTTCAGAGCTCAACCCCCAAG
AGTCTGGTGATTCTAGTTAAGGATGAAGGGATACTTTTAAAGGTTGTTTGAGTATTCGTCTTGG
TTTCCCATCCGGTGTCCGGCATCTATTGGAGCCCTACTAATCTGAATTTGTGTCCGGAAGTCCT
AGTTTTAAGGCTCCCGGCCCAATGCAACTACATTTTCAGAGTTCAAACCTTAGATCTCTGGTTA
ATTATTGAGGGGTACTTATAAAGGTTGTGTTTAGTATTCTTTTTAGTTTCCCACCCGGTGTCCA
ACATCCGATTTGGTGCATGACTAGTCCGAATTCACATCTGGAAGTCCCACTTTGAGGGTTAAGG
CTCCTAACAACAGCGACTTTATTTCTAGAGCTTGGATCCGGAGCTTGATTAAGGATGGAGGGAC
ACTTACCGTCTGCTTGAATATATTTGTGGCTGCAATTAATGAAATTTTGTTTGTGGTTGCAGGA
GCTTATGCAAAGCTTGGGAATATATATTGTGTCAATTGATAGACCTGGTTATGGTGAAAGTGAT
CCTCATCCAAAAAGAACGCCAAAGACCTTAGCTCTTGATATAGAGGAATTAGCTGATCAATTGG
AATTGGGATCTAAATTTTATGTTATGGGATTTTCTATGGGTGGACAAGCTGTTTGGGGCCTTCT
CAAATATATTCCTCACAGGTATCATTTAGTTTCCTCGCACCTCAACTATTTAACAAGGTACATG
TTACGTCCCACCAGCGCATATATGGGTAACTTTGTCTACCAATGCTTAAGCAGATGAGGAGAAG
TCATCTTATGAATTGACTTGATTGTTCAGAGAAAGTAGTTTAGTTCTTTGGGTTTAACTTATAG
ACACTGACGGTGCCACTGATTTTTATAGTATTAGTGTATGTTAATCTGTTGTAGTTATCTTTTA
GATGACTTTCTCAGTGTCCGTATTAGCTTGTCGTATTAGTTGTACCACATAGGACTGAACTTCC
CACTAGTATAAGTTAAATTTATGGTGTCTGGATTAGTTTGTTCGCACCTCAACTATTTAACAGA
GTACCTGCTAACTCCCACCAGCGCATACATGGGTAACTTTGTCTATCAATGCTTAAGCAGGTGC
GGAGAAATCATCTTACGGATTGGCTTTTTTTTTCCTTTTCTATGTGTATAAATTGATTTTTCAG
AGAAAGTAGTTTAGTTCTTCAGATTTAACTTATAGACACTGACGATGCTAACGACTTTTACATT
ATTAGTTTACATTAATCTGTCGTAGTTATCTTTTAGGTGACCTTCTCGGGTGCATATAGGTTTC
CATCTTAACTTGTGACATTTGAAATGTGTAACAGATTGGCTGGAGCAATTCTTCTAACACCTGT
GACTAACTACTGGTGGGGTAGTTTTCCTGCAAACTTGACTAAACAAGCGTACTACGAACAGCTC
GTGCAGGATCAATGGACACTTCGGATTGCACACTATTTTCCATGGCTGACTTACTGGTGGAACA
CTCAAAAATTGTTTCCTTCTTCCAGCGTTGCAACGGGCAGCGAGGATATTCTTTTAGAGCAAGA
CAGAGTTCTAATGCCTATCTTTGATTCATATCAGAGTAAATATCGGGTGAGTACTCCTTTAGCT
TCTTAGCATATCCACATTTCATTTTCACGCGACTTTGAAGTAAGATCAATGGTGGATCAACAAT
GGATTCGCGAATTTGGAAAAACTCTGTGCTTCAAATAGAGTTACATATAAGTTTTTTGCATCAT
TAGCGACAGTAGGAGACGCTTCATATCAAATCTGATATAGTAACACCGTAACACGCAAGATAGA
GTCATAACTTGTTATAACTAGTTAAATTACGCTGATAGTATTGTATATAACTTAATTCCACAAT
TATATGTGTTGATTTTGATTAGCAAATTGTTTGAGTTAATTCTCCTAATTCTTGTTCTTGCCTA
ATGCATACTAGCAACTAACAAGTACTTAACTCTGAGTTCTGTTCTGTTTTTTGATTTGAGGTTA
GGACTTGGTAAGACAGCAAGGGGAGTATGAGTCCATCCATCGCGACCTAATGGTAGGTTTCGGG
ACATGGGAATTTGATCCGATGGAACTAGAAAACCCATTCCCTAACGGGGAAGGGTCCGTTCACA
TTTGGCAAGGTGATGAAGACGGGCATGTACCAGTCATTCTACAACGATTCATCGCGAAGAAACT
CCCATGGATTCACTATCATGAAATGAAAGGAGGAGGTCATATGTTTCCATGGGCTGAAGGAATG
GGAGATAAAGTCATGAAGACATTTTTACTTGGAGAGCCTTTTGTTATGTAAAAGCTATAAAGGG
CTATTGGTTTTACTATTGGATTCAATGACTCTTTTGGTCATTGAACAAATTTGAATATTTTGTT
AATAATTAAATTCTACTCAAGTCGTTGGGACTCTTCAAAAATATTATTGTATGTATGTCGAATC
TTCTAAATGCTATACATTTTTGAAGAGTTCGACCAACATTGTTTTTTTCGATCAAGTAGTAGAT
ATAGTCATAAACACTTTCTAACTTGTGAAGCTCTTGTCATTGAACAAACTTGAATATTTGTTAA
TAATTAATAAGGTCATAATACATCAAACATATACTTAAACTTTGTTGTGTAATTAATTAAGGTG
TACGTAAGTTAATACGAATACTATTAATATTTAGTAATAGTACTATATATTAAAAATAAATTAT
TCATTGTTTCCAGTTCCACAGTCCTAAACTTTTTTTTTTAAAAAAGGGAAAAAAATAGAAAGAA
AGGAAAAAAGGTTTTTGCCAAATGTTATGGATAGATCATATGCTAAAAATAGCAACACTTTTAG
ATCAGAGAGATGAGACACAGATCTCTTCAATCTTCCTTTTTGTATAATTTTTGTAAATTTAGAC
TGTAAAATACAGAATTTGTAATTTCAAAATCAAGAATTTGATTCAGCTGAAAAAGAAGGAAAAA
AAAAAAATGGCAACAAAGAAGATTTCAGCAGCTTCAGCTAGGGCTCATACTCGTAAAGCTAAGC
AAAAAAGTTCTTTTCCTCTTCCTTCTG
						
					

			
		

Sequences
Splice junction sequence	AAGGAAAAAAAAAAAATGGCAACAAAGAAGATTTCAGCAGCTTCAGCTAGGGCTCATACTCGTA AAGCTAAGCAAAAAAGTTCTTTTCCTCTTCCTTCTGaatgatgagaaatatggtagcccttttt ggaattgtgatattggcactgatttatagggcaattatgccaccatcaccaaagatttgtggtt caccaaat
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	AATGATGAGAAATATGGTAGCCCTTTTTGGAATTGTGATATTGGCACTGATTTATAGGGCAATT ATGCCACCATCACCAAAGATTTGTGGTTCACCAAATGGACCTCTAATTACAGCACCGAGAGTGA AGCTTTCTGATGGGAGATATTTGACATATAAAGAAAATGGTGTTCCTAGAGACCAAGCAAAACA CAAATTTGTTTTCATCCATGGCTTTGATTGTGTTAGACATGATGTTGCTTTGCACACAACTACT TCTCCTGTATGTATGTTTCATCTTTACTTGTTCTCCCCTCGCCCTCCCTTAGAATAGTTTTTAG TTTCTTTTTCGTTTTGTTTGTGTCCGATATTTGTTTTGGGGTCCGACTAATTTAGATTTGTGTT GGGAGGTTTCACTTTTAAGGCTCCCGACCAAAGATTACTCTATTTTCAGAGCTCAACCCCCAAG AGTCTGGTGATTCTAGTTAAGGATGAAGGGATACTTTTAAAGGTTGTTTGAGTATTCGTCTTGG TTTCCCATCCGGTGTCCGGCATCTATTGGAGCCCTACTAATCTGAATTTGTGTCCGGAAGTCCT AGTTTTAAGGCTCCCGGCCCAATGCAACTACATTTTCAGAGTTCAAACCTTAGATCTCTGGTTA ATTATTGAGGGGTACTTATAAAGGTTGTGTTTAGTATTCTTTTTAGTTTCCCACCCGGTGTCCA ACATCCGATTTGGTGCATGACTAGTCCGAATTCACATCTGGAAGTCCCACTTTGAGGGTTAAGG CTCCTAACAACAGCGACTTTATTTCTAGAGCTTGGATCCGGAGCTTGATTAAGGATGGAGGGAC ACTTACCGTCTGCTTGAATATATTTGTGGCTGCAATTAATGAAATTTTGTTTGTGGTTGCAGGA GCTTATGCAAAGCTTGGGAATATATATTGTGTCAATTGATAGACCTGGTTATGGTGAAAGTGAT CCTCATCCAAAAAGAACGCCAAAGACCTTAGCTCTTGATATAGAGGAATTAGCTGATCAATTGG AATTGGGATCTAAATTTTATGTTATGGGATTTTCTATGGGTGGACAAGCTGTTTGGGGCCTTCT CAAATATATTCCTCACAGGTATCATTTAGTTTCCTCGCACCTCAACTATTTAACAAGGTACATG TTACGTCCCACCAGCGCATATATGGGTAACTTTGTCTACCAATGCTTAAGCAGATGAGGAGAAG TCATCTTATGAATTGACTTGATTGTTCAGAGAAAGTAGTTTAGTTCTTTGGGTTTAACTTATAG ACACTGACGGTGCCACTGATTTTTATAGTATTAGTGTATGTTAATCTGTTGTAGTTATCTTTTA GATGACTTTCTCAGTGTCCGTATTAGCTTGTCGTATTAGTTGTACCACATAGGACTGAACTTCC CACTAGTATAAGTTAAATTTATGGTGTCTGGATTAGTTTGTTCGCACCTCAACTATTTAACAGA GTACCTGCTAACTCCCACCAGCGCATACATGGGTAACTTTGTCTATCAATGCTTAAGCAGGTGC GGAGAAATCATCTTACGGATTGGCTTTTTTTTTCCTTTTCTATGTGTATAAATTGATTTTTCAG AGAAAGTAGTTTAGTTCTTCAGATTTAACTTATAGACACTGACGATGCTAACGACTTTTACATT ATTAGTTTACATTAATCTGTCGTAGTTATCTTTTAGGTGACCTTCTCGGGTGCATATAGGTTTC CATCTTAACTTGTGACATTTGAAATGTGTAACAGATTGGCTGGAGCAATTCTTCTAACACCTGT GACTAACTACTGGTGGGGTAGTTTTCCTGCAAACTTGACTAAACAAGCGTACTACGAACAGCTC GTGCAGGATCAATGGACACTTCGGATTGCACACTATTTTCCATGGCTGACTTACTGGTGGAACA CTCAAAAATTGTTTCCTTCTTCCAGCGTTGCAACGGGCAGCGAGGATATTCTTTTAGAGCAAGA CAGAGTTCTAATGCCTATCTTTGATTCATATCAGAGTAAATATCGGGTGAGTACTCCTTTAGCT TCTTAGCATATCCACATTTCATTTTCACGCGACTTTGAAGTAAGATCAATGGTGGATCAACAAT GGATTCGCGAATTTGGAAAAACTCTGTGCTTCAAATAGAGTTACATATAAGTTTTTTGCATCAT TAGCGACAGTAGGAGACGCTTCATATCAAATCTGATATAGTAACACCGTAACACGCAAGATAGA GTCATAACTTGTTATAACTAGTTAAATTACGCTGATAGTATTGTATATAACTTAATTCCACAAT TATATGTGTTGATTTTGATTAGCAAATTGTTTGAGTTAATTCTCCTAATTCTTGTTCTTGCCTA ATGCATACTAGCAACTAACAAGTACTTAACTCTGAGTTCTGTTCTGTTTTTTGATTTGAGGTTA GGACTTGGTAAGACAGCAAGGGGAGTATGAGTCCATCCATCGCGACCTAATGGTAGGTTTCGGG ACATGGGAATTTGATCCGATGGAACTAGAAAACCCATTCCCTAACGGGGAAGGGTCCGTTCACA TTTGGCAAGGTGATGAAGACGGGCATGTACCAGTCATTCTACAACGATTCATCGCGAAGAAACT CCCATGGATTCACTATCATGAAATGAAAGGAGGAGGTCATATGTTTCCATGGGCTGAAGGAATG GGAGATAAAGTCATGAAGACATTTTTACTTGGAGAGCCTTTTGTTATGTAAAAGCTATAAAGGG CTATTGGTTTTACTATTGGATTCAATGACTCTTTTGGTCATTGAACAAATTTGAATATTTTGTT AATAATTAAATTCTACTCAAGTCGTTGGGACTCTTCAAAAATATTATTGTATGTATGTCGAATC TTCTAAATGCTATACATTTTTGAAGAGTTCGACCAACATTGTTTTTTTCGATCAAGTAGTAGAT ATAGTCATAAACACTTTCTAACTTGTGAAGCTCTTGTCATTGAACAAACTTGAATATTTGTTAA TAATTAATAAGGTCATAATACATCAAACATATACTTAAACTTTGTTGTGTAATTAATTAAGGTG TACGTAAGTTAATACGAATACTATTAATATTTAGTAATAGTACTATATATTAAAAATAAATTAT TCATTGTTTCCAGTTCCACAGTCCTAAACTTTTTTTTTTAAAAAAGGGAAAAAAATAGAAAGAA AGGAAAAAAGGTTTTTGCCAAATGTTATGGATAGATCATATGCTAAAAATAGCAACACTTTTAG ATCAGAGAGATGAGACACAGATCTCTTCAATCTTCCTTTTTGTATAATTTTTGTAAATTTAGAC TGTAAAATACAGAATTTGTAATTTCAAAATCAAGAATTTGATTCAGCTGAAAAAGAAGGAAAAA AAAAAAATGGCAACAAAGAAGATTTCAGCAGCTTCAGCTAGGGCTCATACTCGTAAAGCTAAGC AAAAAAGTTCTTTTCCTCTTCCTTCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123737937

Conservation Information
Conserved circRNAs	NA
PMCS	0.123737937

			
						 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 PGSC0003DMG402002659_circ_ag.1

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