Plant Circular RNA Database

Detail information of PGSC0003DMG400044842_circ_ag.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400044842_circ_ag.1
					
						ID in PlantcircBase
						stu_circ_000440
					
						Alias
						chr03:45827890|45833388
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr3: 48001878-48006298  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
						
							PGSC0003DMG402018519_circ_igg.1 						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							Yes-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  
						
							GG-TG							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	PGSC0003DMG400044842_circ_ag.1
ID in PlantcircBase	stu_circ_000440
Alias	chr03:45827890\|45833388
Organism	Solanum tuberosum
Position	chr3: 48001878-48006298 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	PGSC0003DMG402018519_circ_igg.1
Support reads	NA
Tissues	stem
Exon boundary	Yes-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	GG-TG 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  
						
							CAACTGATTCTGAAGTTTCTCTAGCACTTAGAGTTCTGGAAGGTTGTTGTCTGATTCACTGCGA
GAGTAATGTTTTGGCCCATCAGTACAAGGCAATCCCttagttgaataacaaagtagaggtagaa
gagggaaaagatgggtcttccactggcgcagcagctttaggactcccgtgtaccattgcaatgt
gttggtta

									
								

					

						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
						
							TTAGTTGAATAACAAAGTAGAGGTAGAAGAGGGAAAAGATGGGTCTTCCACTGGCGCAGCAGCT
TTAGGACTCCCGTGTACCATTGCAATGTGTTGGTTAGGAGGAGGGTGATTATGTTGGCCTCTAT
AAGTTACAATCACCTTGTTTGGATCTGTTGAGCTTTTCTGAATATGTCTCCTTGCCGGACAATC
GTTAGCTTCATTACACCTATAGTAGCTCTTCAGAAAAGTCGAATCACCAGTTCGCTTCATCCCA
TACTTTCTCCATCTCCATTGATCTGCCTCACTCAATTTCTCAGCCAATAGTTCATATCTTTCAG
TGCTCTTCCCGCGGTAACAAAACGCCTTGCCTGCCTCAGTACTTGGACTCTGCATCGAGTATCT
CACCTTCTTGTTCTTCTTCTTCTCCTCCTCGTGTTCTACAATCACCAGTGGTGTGTTTGGAATA
GTTTCAGTTTGGTTTTCTTGGTTGTGGGGTTGAATTCTTGAATTGGTATTCAGGTTCTTGGAAA
GACTGATAACTTCATCTAACCCAAAGTAATGCTTGTTTTCCGTGACGAACGAGTCAGTAAAATC
ACCGACACAATCAGTTTCTTCTTGCAGAAGAGTTGTGTTTTGTGTGTTGTTAACAGAGTTAGCA
TGAGTAGGATCCTCATGAACACTGTGATCGACAAGAACAGAGGTATTATTAACGTTGATATCAT
CATGAACAGAGTTGTTCGTCCTACCGCAACTTCTCACAACTGCCCATAAATCCCAATCGTTTTC
GTTTTCAGCCATTGAAAGCCTTGTTGAAGGGGAAGGCTTCATTCATTAATGTAGGATTGTCTCT
CTGTATATATGGATTTAGTTTCCATTGAAAACTTTCTTCTAGGGGAAGGCTTCATTAATGCTGG
ATTCTATATATATGGATTTTGTTTCCATTGGGAAATGGAGTTTAAACAAACTGTTTGGATCCGT
TCCTATACAAGGCGAGAGATTTATTACTAATTCGATTCTTGAACTATTATTTAGGTAAGGAAAT
TTGAAGAGTTATGGAAATAAATTTAGAAACTTAATTACATTGTTTTCTAACCCTTTTTTTAAGT
GATTGGAGGCACCATATTTTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTA
TTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTATTACTTTTTAAATATTTC
CTTATTTGAACTATATTAGAAAATCCTATTACTTTTTAAATATTTCCTTATTTGAACTATATTA
GAAAATCCTATTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTATTACTTTT
TAAATATTTCCTTATTTGAACTATATTAGAAGTCCTAAACATTTATTACTTTAAAATTAATAGT
TTTTTACTTTATATTAATTTTACTTAAATTATGGTAAATAGAAGAAATAAAAATATTAAAGAAA
GACGTTCACTTTTATTATTTAGATCTATATAACATTTATTATTAGGGAAAAGAACTCATATATC
CCAAAAAGAGAAATTATTTACAAGGATATATATTTTGATGGTATCAAAGAGGAAGAAACAATGT
TTCAATGAAAACATTAAAATTGTTCAATTATTGTTTGATATATATATATGACGGTATCAAGGAT
TAGTGGTTCAATAAATAAAACAAAGGGGCAGTCGGATAAATAGTTTGAGCGGTGAGTCTAATCA
GTTAAATATATTTGATTGGATCGAATTTGTGTAGCTTTTCCTTTATTATAATGTCAATAGTTAT
TATTTTTAATAATTTTATTGATTGATGTGACACACATGCCATGTATACTAAACTATCTACTACA
AACATATCACCGACCATATGGATACACCATTCTCGTTCATGCTACCCAAAAACAATTTACCAGA
ACATACCACCAGGCACCAGCAATGCTCCTTTGTTTTGGTTTTTGGACTCTTTGGAACAACTGCA
ATGACAACTATTTCAACCGTATAGATAATTCCCGAACCATAGGCTAACCTCTACCGCTCTTTCA
CATAATTTTCATTCGATAATTATTTAAACAGATGCTAAGGAAATTAACCGAATACTGCAATATT
TTCATCACATTTATGATTGCAGGTGGCTCCTCCGCCAGCTTCTTGATTTGAGAATGGTGCACTC
GTACAGAGAGGCAAATGAAGTAGCAGATCTACTCACGAAAATTATCTCTGCATCTGTTTTTTTT
TTTTAACACTATCTTTTTTGCAAGAACCATCCACTCCTTGTGACTGCCGCTCTCGAAGTTGATC
AATGAGGGGATGTCAAACAACGGCTTATACAACCTTCACTTCTACTGCTATTTCTAGGCCTTTG
ACGTTTGCTGTAATAGTTTTAAGTTTTGTATAAAAGTATCTTTCATGACAACTATTGAAAAATA
TGAGTCGTCGGAGTGGTGATGTATATGAAAAAAGTATTTGAATATATAGGTTAAAATTTCTCCC
AAATTATCACCATTTTGCAAGTATTTACCTAAATTATTTGGTGTTCACAAAATTATGATGAACT
CATTATGTTAAACAAATTCGTTTTTAAAGATTGTTATCCCATATGCACTCTCAACAAATTATTT
TACCATATATCCAATCGAAATTGTTTTACTCTAACGGAAATAATAGTCAAAAGAATTATAAAAA
CATACAAAAATTTTAAGTATGAAATTCACAAAACAATTCTATTCACTCGTAACATTATGTGATA
AGTGAACTTACTATAAATAAAAACAAATATTCTGGGTTATATTTTCTTTTTATCAAAGTTAATT
CTATTTCAAAACTTCTAATTAAATGATAATGTAATATCAAAAAAAAGAGGGGGAAAAAGTTTTT
TTTATTTAATTTTTAGTCTAAAGGAAAGGGGGAAAAAACGAGAAAAGAGACGAAATTTCAGTTT
CTCCTTTTAACGCCGAGCTGGAAAGAGCGGTGAAGACACCGGAGCGAAGAAATGTATCTAAAAG
CTCCGTTTTGGAGCAAAGATTCGAACTCTGAATCTCAGACGGAATCTCCGTCGGCGGTGGCGGA
GCTAATAAGCTCTCTTGAACGGCAGAGACTATACAGGGAGGTGACGCTCGCACTCCGCACAGGA
CTCAGTGATGCACGTGCTGAGTTCTCCTTCCTCCGTATTCGTGGCCTCCGCGTCATCCTCAAGT
TCCTCCGATCCGTGGCCGAGTCCGATACTACCATCAACCTCTTCTGTCACAGCCAATCCATTCC
CGATCTTCAAGGTTTTCCTCCATTCTCTTCACCCTAGGGTTTCGATGTTCAATGATTTTTCGTT
TTATTTATATTTCAATTGCAGCAACTTATGAAAATATAATTGATGTTACTTATCTCCAATTGGT
TAACCGAAACATTGATGGGGAAGTTGGTTATATAGATGTGAATGTGGAAATTCTATAATGACAT
TAATGGGAAATTGGGAATATGTAGTTGAGGTTCATCTTCTGACAAATGTGCTGCAAGTAGTTTA
GGAAAAAAGAAGTTTTGCTTGTCTAAATCCATTTATACCGCAGATGAACTCTTATGGAATTGGT
TTTGGCTTCACGGAGAGGTTCAGTTAGGTGTTATGTCAGCTCATTATAAGATCATTAGAAGGCA
TGAAATCTGAGCTGCATTTCTTGTTCTTACTACAATATTTTGAATCTACTCTGAAGTTTTCAAA
AGGTATTAAAGTCGTTCGTTTAAGATTGTTCGCACAACTGTATTAGCAGGTTACGAACAGATGT
TTGGTTTCTTCTCGAGTTGGAATGCTTGTTTAGTATTGATGAGGATTCAGGTGCAAGTAGTAAA
CGATAAATTGGTATTTGCATGTAAGGGAAGCCTGTTCAATTACTGTTCCATTCTATTTAAAACA
AGTCAAACAATGTTGTTTTTAACTTGTTCAGATTCGATAAGGATCTGAGACTTCAGCTGGACAC
AGATGAAGCCAGAACAGCTGTGAAATGCAGTAACTACTAATTAATCTTGGAACTTTAGGGGCAG
TGACACCTATTCCGTTCATATACTTATATTCTCATTGATGCTTATTCTGTAATTTTCTGGGGTG
AAACCTTCTAGTTTCTGTTGAATGGTTGAAACTTACATCAGAAAATCTTCTAGTTTCGAGATTA
CTTTGCTTAATTTAGAAAAATGGATCAGGCTATTAACTGTGTGAGCTATGTAACAGTGGTTCCA
GTTCTTTTCAAACATTCCTTGAGAGATACAGAGGACCAGAATGTTACCAGTCTAGACCACATAT
TTACTGTGGAACCTATGGAAATAACCAGCCCATCAACTGATTCTGAAGTTTCTCTAGCACTTAG
AGTTCTGGAAGGTTGTTGTCTGATTCACTGCGAGAGTAATGTTTTGGCCCATCAGTACAAGGCA
ATCCC
						
					

			
		

Sequences
Splice junction sequence	CAACTGATTCTGAAGTTTCTCTAGCACTTAGAGTTCTGGAAGGTTGTTGTCTGATTCACTGCGA GAGTAATGTTTTGGCCCATCAGTACAAGGCAATCCCttagttgaataacaaagtagaggtagaa gagggaaaagatgggtcttccactggcgcagcagctttaggactcccgtgtaccattgcaatgt gttggtta
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	TTAGTTGAATAACAAAGTAGAGGTAGAAGAGGGAAAAGATGGGTCTTCCACTGGCGCAGCAGCT TTAGGACTCCCGTGTACCATTGCAATGTGTTGGTTAGGAGGAGGGTGATTATGTTGGCCTCTAT AAGTTACAATCACCTTGTTTGGATCTGTTGAGCTTTTCTGAATATGTCTCCTTGCCGGACAATC GTTAGCTTCATTACACCTATAGTAGCTCTTCAGAAAAGTCGAATCACCAGTTCGCTTCATCCCA TACTTTCTCCATCTCCATTGATCTGCCTCACTCAATTTCTCAGCCAATAGTTCATATCTTTCAG TGCTCTTCCCGCGGTAACAAAACGCCTTGCCTGCCTCAGTACTTGGACTCTGCATCGAGTATCT CACCTTCTTGTTCTTCTTCTTCTCCTCCTCGTGTTCTACAATCACCAGTGGTGTGTTTGGAATA GTTTCAGTTTGGTTTTCTTGGTTGTGGGGTTGAATTCTTGAATTGGTATTCAGGTTCTTGGAAA GACTGATAACTTCATCTAACCCAAAGTAATGCTTGTTTTCCGTGACGAACGAGTCAGTAAAATC ACCGACACAATCAGTTTCTTCTTGCAGAAGAGTTGTGTTTTGTGTGTTGTTAACAGAGTTAGCA TGAGTAGGATCCTCATGAACACTGTGATCGACAAGAACAGAGGTATTATTAACGTTGATATCAT CATGAACAGAGTTGTTCGTCCTACCGCAACTTCTCACAACTGCCCATAAATCCCAATCGTTTTC GTTTTCAGCCATTGAAAGCCTTGTTGAAGGGGAAGGCTTCATTCATTAATGTAGGATTGTCTCT CTGTATATATGGATTTAGTTTCCATTGAAAACTTTCTTCTAGGGGAAGGCTTCATTAATGCTGG ATTCTATATATATGGATTTTGTTTCCATTGGGAAATGGAGTTTAAACAAACTGTTTGGATCCGT TCCTATACAAGGCGAGAGATTTATTACTAATTCGATTCTTGAACTATTATTTAGGTAAGGAAAT TTGAAGAGTTATGGAAATAAATTTAGAAACTTAATTACATTGTTTTCTAACCCTTTTTTTAAGT GATTGGAGGCACCATATTTTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTA TTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTATTACTTTTTAAATATTTC CTTATTTGAACTATATTAGAAAATCCTATTACTTTTTAAATATTTCCTTATTTGAACTATATTA GAAAATCCTATTACTTTTTAAATATTTCCTTATTTGAACTATATTAGAAAATCCTATTACTTTT TAAATATTTCCTTATTTGAACTATATTAGAAGTCCTAAACATTTATTACTTTAAAATTAATAGT TTTTTACTTTATATTAATTTTACTTAAATTATGGTAAATAGAAGAAATAAAAATATTAAAGAAA GACGTTCACTTTTATTATTTAGATCTATATAACATTTATTATTAGGGAAAAGAACTCATATATC CCAAAAAGAGAAATTATTTACAAGGATATATATTTTGATGGTATCAAAGAGGAAGAAACAATGT TTCAATGAAAACATTAAAATTGTTCAATTATTGTTTGATATATATATATGACGGTATCAAGGAT TAGTGGTTCAATAAATAAAACAAAGGGGCAGTCGGATAAATAGTTTGAGCGGTGAGTCTAATCA GTTAAATATATTTGATTGGATCGAATTTGTGTAGCTTTTCCTTTATTATAATGTCAATAGTTAT TATTTTTAATAATTTTATTGATTGATGTGACACACATGCCATGTATACTAAACTATCTACTACA AACATATCACCGACCATATGGATACACCATTCTCGTTCATGCTACCCAAAAACAATTTACCAGA ACATACCACCAGGCACCAGCAATGCTCCTTTGTTTTGGTTTTTGGACTCTTTGGAACAACTGCA ATGACAACTATTTCAACCGTATAGATAATTCCCGAACCATAGGCTAACCTCTACCGCTCTTTCA CATAATTTTCATTCGATAATTATTTAAACAGATGCTAAGGAAATTAACCGAATACTGCAATATT TTCATCACATTTATGATTGCAGGTGGCTCCTCCGCCAGCTTCTTGATTTGAGAATGGTGCACTC GTACAGAGAGGCAAATGAAGTAGCAGATCTACTCACGAAAATTATCTCTGCATCTGTTTTTTTT TTTTAACACTATCTTTTTTGCAAGAACCATCCACTCCTTGTGACTGCCGCTCTCGAAGTTGATC AATGAGGGGATGTCAAACAACGGCTTATACAACCTTCACTTCTACTGCTATTTCTAGGCCTTTG ACGTTTGCTGTAATAGTTTTAAGTTTTGTATAAAAGTATCTTTCATGACAACTATTGAAAAATA TGAGTCGTCGGAGTGGTGATGTATATGAAAAAAGTATTTGAATATATAGGTTAAAATTTCTCCC AAATTATCACCATTTTGCAAGTATTTACCTAAATTATTTGGTGTTCACAAAATTATGATGAACT CATTATGTTAAACAAATTCGTTTTTAAAGATTGTTATCCCATATGCACTCTCAACAAATTATTT TACCATATATCCAATCGAAATTGTTTTACTCTAACGGAAATAATAGTCAAAAGAATTATAAAAA CATACAAAAATTTTAAGTATGAAATTCACAAAACAATTCTATTCACTCGTAACATTATGTGATA AGTGAACTTACTATAAATAAAAACAAATATTCTGGGTTATATTTTCTTTTTATCAAAGTTAATT CTATTTCAAAACTTCTAATTAAATGATAATGTAATATCAAAAAAAAGAGGGGGAAAAAGTTTTT TTTATTTAATTTTTAGTCTAAAGGAAAGGGGGAAAAAACGAGAAAAGAGACGAAATTTCAGTTT CTCCTTTTAACGCCGAGCTGGAAAGAGCGGTGAAGACACCGGAGCGAAGAAATGTATCTAAAAG CTCCGTTTTGGAGCAAAGATTCGAACTCTGAATCTCAGACGGAATCTCCGTCGGCGGTGGCGGA GCTAATAAGCTCTCTTGAACGGCAGAGACTATACAGGGAGGTGACGCTCGCACTCCGCACAGGA CTCAGTGATGCACGTGCTGAGTTCTCCTTCCTCCGTATTCGTGGCCTCCGCGTCATCCTCAAGT TCCTCCGATCCGTGGCCGAGTCCGATACTACCATCAACCTCTTCTGTCACAGCCAATCCATTCC CGATCTTCAAGGTTTTCCTCCATTCTCTTCACCCTAGGGTTTCGATGTTCAATGATTTTTCGTT TTATTTATATTTCAATTGCAGCAACTTATGAAAATATAATTGATGTTACTTATCTCCAATTGGT TAACCGAAACATTGATGGGGAAGTTGGTTATATAGATGTGAATGTGGAAATTCTATAATGACAT TAATGGGAAATTGGGAATATGTAGTTGAGGTTCATCTTCTGACAAATGTGCTGCAAGTAGTTTA GGAAAAAAGAAGTTTTGCTTGTCTAAATCCATTTATACCGCAGATGAACTCTTATGGAATTGGT TTTGGCTTCACGGAGAGGTTCAGTTAGGTGTTATGTCAGCTCATTATAAGATCATTAGAAGGCA TGAAATCTGAGCTGCATTTCTTGTTCTTACTACAATATTTTGAATCTACTCTGAAGTTTTCAAA AGGTATTAAAGTCGTTCGTTTAAGATTGTTCGCACAACTGTATTAGCAGGTTACGAACAGATGT TTGGTTTCTTCTCGAGTTGGAATGCTTGTTTAGTATTGATGAGGATTCAGGTGCAAGTAGTAAA CGATAAATTGGTATTTGCATGTAAGGGAAGCCTGTTCAATTACTGTTCCATTCTATTTAAAACA AGTCAAACAATGTTGTTTTTAACTTGTTCAGATTCGATAAGGATCTGAGACTTCAGCTGGACAC AGATGAAGCCAGAACAGCTGTGAAATGCAGTAACTACTAATTAATCTTGGAACTTTAGGGGCAG TGACACCTATTCCGTTCATATACTTATATTCTCATTGATGCTTATTCTGTAATTTTCTGGGGTG AAACCTTCTAGTTTCTGTTGAATGGTTGAAACTTACATCAGAAAATCTTCTAGTTTCGAGATTA CTTTGCTTAATTTAGAAAAATGGATCAGGCTATTAACTGTGTGAGCTATGTAACAGTGGTTCCA GTTCTTTTCAAACATTCCTTGAGAGATACAGAGGACCAGAATGTTACCAGTCTAGACCACATAT TTACTGTGGAACCTATGGAAATAACCAGCCCATCAACTGATTCTGAAGTTTCTCTAGCACTTAG AGTTCTGGAAGGTTGTTGTCTGATTCACTGCGAGAGTAATGTTTTGGCCCATCAGTACAAGGCA ATCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.119190703

Conservation Information
Conserved circRNAs	NA
PMCS	0.119190703

			
						 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 PGSC0003DMG400044842_circ_ag.1

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