Plant Circular RNA Database

Detail information of PGSC0003DMG401010374_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG401010374_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000409
					
						Alias
						chr03:18927151|18947412
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr3: 18927212-18931157  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG401010374						
					
						Parent gene annotation
						
							Sugar transporter
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							AT-AA							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
						PGSC0003DMT400026887:1
PGSC0003DMT400026885:12
PGSC0003DMT400026884:11
PGSC0003DMT400026895:2
PGSC0003DMT400026893:11
PGSC0003DMT400026894:8
PGSC0003DMT400026890:11
PGSC0003DMT400026892:10
PGSC0003DMT400026889:8
PGSC0003DMT400026891:11
PGSC0003DMT400026888:11

General Information
CircRNA Name	PGSC0003DMG401010374_circ_g.1
ID in PlantcircBase	stu_circ_000409
Alias	chr03:18927151\|18947412
Organism	Solanum tuberosum
Position	chr3: 18927212-18931157 JBrowse»
Reference genome	3.0.38
Type	ui-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG401010374
Parent gene annotation	Sugar transporter
Parent gene strand	+
Alternative splicing	NA
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	AT-AA 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	PGSC0003DMT400026887:1 PGSC0003DMT400026885:12 PGSC0003DMT400026884:11 PGSC0003DMT400026895:2 PGSC0003DMT400026893:11 PGSC0003DMT400026894:8 PGSC0003DMT400026890:11 PGSC0003DMT400026892:10 PGSC0003DMT400026889:8 PGSC0003DMT400026891:11 PGSC0003DMT400026888:11

			
						 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  
						
							TCAAAATTAATTAATTCTTCTACCCGATCAGTCAATCAACTAAACCTCAATCCTAACTTGTGTC
TGGCAAATGAATTCTCTGCATCCAATCCGTTATATTatgggttggtataatccgacaatggcac
tctcaaaaccaccattgctagttccatccaactcgtgggttttgaggggtaagaaggtaattga
atgtagaa

									
								

					

						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
						
							ATGGGTTGGTATAATCCGACAATGGCACTCTCAAAACCACCATTGCTAGTTCCATCCAACTCGT
GGGTTTTGAGGGGTAAGAAGGTAATTGAATGTAGAAGAAATTACCCATTGATTGGAAGGAAGAA
GGAAAATTTAGTGGGTGTACATTTTGTGGGTTGTAAGGGAATGCTCAGACTGAAGGTAGATACA
GAGAAAGTGAATACACTCTAATTTCGAATTTTACTTGTGTTTCCTCTTCTCTTCGATTGTTGTT
TTTCTTATATAGGTTTCGGCATCTTCAGGAGAAGGAGAAGAAGCCGAGCCAGGGTATATAGAGG
AATTCAGTTGGTCTTCTGTTATTTTGCCGTAAGTTCGACACCTTTTTTCTGAACAAGAGTAAAA
ATAAGCAATTATACCTATATTCAGAACTTGGGTATTTCATCATTCATTATTAGTTCTTGACCAA
TTAACTCAATAATTGACAAAATTCAATAGTCTCTATATTCATGTATGTGATATTAAAGCCACAA
GCTGTTTTCACCATCCTTGTTCTCCATTTAAATTCAAAAGGATCATGTGATCTAAAAATAATAA
TCATTTACCCAATAAAATACTACTAGTATCACGGTTTTGCCTTTTCAGATGGTATGCAAAAATA
ATACTATTGTGTCAAATACAGTTTTATCTTCCCAGCCCTAGGCGGTTTATTATTTGGCTATGAT
ATTGGTGCCACCTCAGGTGCTACCATCTCATTGCAGGTAATTCTCAGTTTCATTGACCTGCTTT
ACTCTTTATGTACAGTCAATTATGGATTTTTTTAAAAACTGATTTCTCAGTCGCCTGAGCTTAG
TGGAATGAGTTGGTACAACCTCTCAGCTGTTCAGCTTGGTCTTGTGGTATGCTTTCTATATATG
TTGCATATTCCATGACTAATCACTGCTCTCAAATATCAAATTTTTGAATATCTATTCTTGGATA
TATATATATATAGGTCAGCGGTTCCCTTTATGGGGCTCTTATTGGCTCCATACTCGCCTACCCA
TTTGCTGATTTCCTAGGTGGAGTTCAATTACTTAAAGTTTTGCTGATACACAAATAATTATATT
AATTAACTTTTCTTTTTTGGGTTTTGTAAAGGAAGGAGGAGGGAACTGATCATAGCAGCCATTT
TATATTTGGCTGGCGGTTCACTAACTGCCTGTGCTCCAGGACTAGGGGCACTCTTGTTGGGTCG
GCTTGTTTATGGACTAGGAATTGGCTTGGTAGGTTTTGGTTTGCTTTTTATTATCTCAGTTCCA
CCTTTCCATATATGTCTATCTCTGTCACAGCTTAATCTATTGGATGACCAAGTAGCTGAGATTC
TTCATCTCAATAGGCAATGCATGGGGCACCTCTATATATAGCAGAGACTTGTCCATCCCAAATC
AGAGGGACATTAATCTCTTTAAAGGAGCTGGCAATAGTACTGGGTATTTTGGTATGTGTATCTA
TCTATGTTTATCTCTTATATTCTAATATCATCTAAGAGAAATAACGGATCACATTGAACGATGG
AATTTCCAGCTGGGTTTTTTTGTAGGTAGCTATGAAATTGATGTCATTGGAGGATGGCGTTACA
TGTTTGGATTTAGTGCTCCAATTGCTTTATTGATGGGGTTTGGCATGTGGACTCTCCCACCATC
TCCCAGATGGTTACTTCTGAGGGCAATTCAAGGTAAAGGACCATTGCAGGAATACAAAGAGAAT
GCTATTGGAGCATTGAGCAAACTGAGAGGCCGCCCTGCTGGCGATAAAGTATCTGAAAAACAAA
TAGAAGATACTATTATATCATTGAAAACTGCCTACACAGATGAAGAAGCTGAAGGAAATTTTCT
CGAGGTATTGCAAGGACCAAGTTTGAAAGCATTTACAATTGGAGGAGGTTTGGTCCTATTTCAA
CAGGTAAAAACAGTTTGAGATTGAGCTACTCCTTTTTTCTTGTCATACTCTGCGGTTTTCATCA
AAATAGTTTCTTGGTTTCAAGCTTATGTGGTAGTTTTTACAGATAACTGGACAGCCAAGCGTTC
TGTATTATGCTGGTTCAATTCTTCAGGTAGCTACACTCTTTTAACTTTCTCCTTATAATAATAT
GATCTTACATAATGTAATTTTAAAGCAATTTGTTCCTAGAGTGCTGGTTTTTCTGCGGCTGCAG
ATGCTGCTCGAGTTTCAGTCGTTATTGGTATATTTAAGGTAAGTTGAGTAACTGGAACCAGGAA
AAGTCTTTTATCTCTCGTTCAAGAATATTAACCTGAGTCGCCCCCAAGGCCTAGCTCAAGTGGC
AAAAGGTGGAGGATTTGTGGCTTAGGTCGCAGGTTCAAGCCCCACACCATGCAAAGCGAAGCCC
GGCATTTAAGTGGAGAAGGGTAGAGGGGCGGGCCCATTATCCACCGAGTTTTGAAGGCTGTGAT
TGGTCCAAATGTCGGTTTACAGACGGATTTCTCGGTTAATCAAAAAAAAAAAGAATATTAACCT
GAGTCGCCCCAAGGCCTAGCTCAAGTGGCAAAAGGTGGAGGATTTGTGGCTTAGGTCGCAGGTT
CAAGCCCCACACCATGCAAAGCGAAGCCCGGCATTAAGTGGAGAAGGGTAGAGGGGCGGGCCCA
TTATCCACCGAGTTAGAAGGCTGTGATTGGTCCAAAGGGCGGGTCACAGACGGATTTCTCGGTT
AATCAAAAAAAAAAAGAATATTAACCTGAGTCGCCCCCAAGGCCTAGCTCAAGTGGCAAAAGGT
GGAGGATTTGTGGCTTAGGTCGCAGGTTCAAGCCCCACACCATGCAAAGCGAAGCCCGGCATTA
AGTGGAGAAGGGTAGAGGGGCGGGCCCATTATCCACCGAGGTTAGAAGGCTGTGATTGGTCCAA
AGGGCGGGTCACAGACGGATTTCTCGGTTATCAAAAAAAAAAAAAGAATATTAACCTAAGTCTT
TTTATCAGAAGGATTTATAATTTCCCTCTAATACTCTGACTCTTTGTTTGCATCGAGTTTACTT
ATTCTCCTGCAGTCACTGATGACAGCAGTCGCTGTCCTAAAAGCTGATGATCTTGGGAGAAGGC
CATTGTTGATTGGAGGAGTCAGTGGGATTGTACGCATCTAATCATAGGATTATACTCTAGATAC
TTATCATTTTATATATAGGTCATATTTCTACTTGTTGGTTTGATTTCTGAGAGAAAGTGTTGCT
ATTTGTGTGATGTGATCTACAGGCCCTGTCATTGTTTCTTCTTTCAGCTTATTATAAATTTCTC
GGCAGTTACCCTTTCGTTGCTGTTTCTGCTCTGCTTCTCTATGTGGGATGCTACCAGGTGATGC
TCTCATATATTCATACTTGCTGGCGTAAACAACTCTAATTTGTAGGTGTTTCTTGGGAAGATTC
ACTATTAACTTAAACTAGGGTATTGACCTTAATCTACTAATCATCTTCCTAGTTATTTCAGACA
ACTTGTTTCTCTTCTCTTCTCTTTAATATGTAACACGTGAATTATGATTGTTTATACCCCAGAT
CCATAATCTTGTCAGGAATTCACCTTATTGGAAGTAGTCCCCTAGTGGTAAGAGTGCAACTTGT
GATTTGTGGGTTAGGCACAGGTCATGGATTCAAACCCTGCCACAGACAAACACTTGGTATTTAA
GTGGAGAAGGGTAAAGGGGGCCACCATTATCCACCGATTTTCGAACTATACGCCACTGACCTTC
GGGGATTTCTCATTTATAAAAGAAGCTTTTGTTAATTTATTAGTAGGTCGACATAATCAATCTA
GTGTACTTGGCAAGTTAATAATATCTCACAATTGAGTAAAGTTTTTTTGATTACGTAACTTTTC
CTTATCTCAAAATTAATTAATTCTTCTACCCGATCAGTCAATCAACTAAACCTCAATCCTAACT
TGTGTCTGGCAAATGAATTCTCTGCATCCAATCCGTTATATT
						
					

			
		

Sequences
Splice junction sequence	TCAAAATTAATTAATTCTTCTACCCGATCAGTCAATCAACTAAACCTCAATCCTAACTTGTGTC TGGCAAATGAATTCTCTGCATCCAATCCGTTATATTatgggttggtataatccgacaatggcac tctcaaaaccaccattgctagttccatccaactcgtgggttttgaggggtaagaaggtaattga atgtagaa
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	ATGGGTTGGTATAATCCGACAATGGCACTCTCAAAACCACCATTGCTAGTTCCATCCAACTCGT GGGTTTTGAGGGGTAAGAAGGTAATTGAATGTAGAAGAAATTACCCATTGATTGGAAGGAAGAA GGAAAATTTAGTGGGTGTACATTTTGTGGGTTGTAAGGGAATGCTCAGACTGAAGGTAGATACA GAGAAAGTGAATACACTCTAATTTCGAATTTTACTTGTGTTTCCTCTTCTCTTCGATTGTTGTT TTTCTTATATAGGTTTCGGCATCTTCAGGAGAAGGAGAAGAAGCCGAGCCAGGGTATATAGAGG AATTCAGTTGGTCTTCTGTTATTTTGCCGTAAGTTCGACACCTTTTTTCTGAACAAGAGTAAAA ATAAGCAATTATACCTATATTCAGAACTTGGGTATTTCATCATTCATTATTAGTTCTTGACCAA TTAACTCAATAATTGACAAAATTCAATAGTCTCTATATTCATGTATGTGATATTAAAGCCACAA GCTGTTTTCACCATCCTTGTTCTCCATTTAAATTCAAAAGGATCATGTGATCTAAAAATAATAA TCATTTACCCAATAAAATACTACTAGTATCACGGTTTTGCCTTTTCAGATGGTATGCAAAAATA ATACTATTGTGTCAAATACAGTTTTATCTTCCCAGCCCTAGGCGGTTTATTATTTGGCTATGAT ATTGGTGCCACCTCAGGTGCTACCATCTCATTGCAGGTAATTCTCAGTTTCATTGACCTGCTTT ACTCTTTATGTACAGTCAATTATGGATTTTTTTAAAAACTGATTTCTCAGTCGCCTGAGCTTAG TGGAATGAGTTGGTACAACCTCTCAGCTGTTCAGCTTGGTCTTGTGGTATGCTTTCTATATATG TTGCATATTCCATGACTAATCACTGCTCTCAAATATCAAATTTTTGAATATCTATTCTTGGATA TATATATATATAGGTCAGCGGTTCCCTTTATGGGGCTCTTATTGGCTCCATACTCGCCTACCCA TTTGCTGATTTCCTAGGTGGAGTTCAATTACTTAAAGTTTTGCTGATACACAAATAATTATATT AATTAACTTTTCTTTTTTGGGTTTTGTAAAGGAAGGAGGAGGGAACTGATCATAGCAGCCATTT TATATTTGGCTGGCGGTTCACTAACTGCCTGTGCTCCAGGACTAGGGGCACTCTTGTTGGGTCG GCTTGTTTATGGACTAGGAATTGGCTTGGTAGGTTTTGGTTTGCTTTTTATTATCTCAGTTCCA CCTTTCCATATATGTCTATCTCTGTCACAGCTTAATCTATTGGATGACCAAGTAGCTGAGATTC TTCATCTCAATAGGCAATGCATGGGGCACCTCTATATATAGCAGAGACTTGTCCATCCCAAATC AGAGGGACATTAATCTCTTTAAAGGAGCTGGCAATAGTACTGGGTATTTTGGTATGTGTATCTA TCTATGTTTATCTCTTATATTCTAATATCATCTAAGAGAAATAACGGATCACATTGAACGATGG AATTTCCAGCTGGGTTTTTTTGTAGGTAGCTATGAAATTGATGTCATTGGAGGATGGCGTTACA TGTTTGGATTTAGTGCTCCAATTGCTTTATTGATGGGGTTTGGCATGTGGACTCTCCCACCATC TCCCAGATGGTTACTTCTGAGGGCAATTCAAGGTAAAGGACCATTGCAGGAATACAAAGAGAAT GCTATTGGAGCATTGAGCAAACTGAGAGGCCGCCCTGCTGGCGATAAAGTATCTGAAAAACAAA TAGAAGATACTATTATATCATTGAAAACTGCCTACACAGATGAAGAAGCTGAAGGAAATTTTCT CGAGGTATTGCAAGGACCAAGTTTGAAAGCATTTACAATTGGAGGAGGTTTGGTCCTATTTCAA CAGGTAAAAACAGTTTGAGATTGAGCTACTCCTTTTTTCTTGTCATACTCTGCGGTTTTCATCA AAATAGTTTCTTGGTTTCAAGCTTATGTGGTAGTTTTTACAGATAACTGGACAGCCAAGCGTTC TGTATTATGCTGGTTCAATTCTTCAGGTAGCTACACTCTTTTAACTTTCTCCTTATAATAATAT GATCTTACATAATGTAATTTTAAAGCAATTTGTTCCTAGAGTGCTGGTTTTTCTGCGGCTGCAG ATGCTGCTCGAGTTTCAGTCGTTATTGGTATATTTAAGGTAAGTTGAGTAACTGGAACCAGGAA AAGTCTTTTATCTCTCGTTCAAGAATATTAACCTGAGTCGCCCCCAAGGCCTAGCTCAAGTGGC AAAAGGTGGAGGATTTGTGGCTTAGGTCGCAGGTTCAAGCCCCACACCATGCAAAGCGAAGCCC GGCATTTAAGTGGAGAAGGGTAGAGGGGCGGGCCCATTATCCACCGAGTTTTGAAGGCTGTGAT TGGTCCAAATGTCGGTTTACAGACGGATTTCTCGGTTAATCAAAAAAAAAAAGAATATTAACCT GAGTCGCCCCAAGGCCTAGCTCAAGTGGCAAAAGGTGGAGGATTTGTGGCTTAGGTCGCAGGTT CAAGCCCCACACCATGCAAAGCGAAGCCCGGCATTAAGTGGAGAAGGGTAGAGGGGCGGGCCCA TTATCCACCGAGTTAGAAGGCTGTGATTGGTCCAAAGGGCGGGTCACAGACGGATTTCTCGGTT AATCAAAAAAAAAAAGAATATTAACCTGAGTCGCCCCCAAGGCCTAGCTCAAGTGGCAAAAGGT GGAGGATTTGTGGCTTAGGTCGCAGGTTCAAGCCCCACACCATGCAAAGCGAAGCCCGGCATTA AGTGGAGAAGGGTAGAGGGGCGGGCCCATTATCCACCGAGGTTAGAAGGCTGTGATTGGTCCAA AGGGCGGGTCACAGACGGATTTCTCGGTTATCAAAAAAAAAAAAAGAATATTAACCTAAGTCTT TTTATCAGAAGGATTTATAATTTCCCTCTAATACTCTGACTCTTTGTTTGCATCGAGTTTACTT ATTCTCCTGCAGTCACTGATGACAGCAGTCGCTGTCCTAAAAGCTGATGATCTTGGGAGAAGGC CATTGTTGATTGGAGGAGTCAGTGGGATTGTACGCATCTAATCATAGGATTATACTCTAGATAC TTATCATTTTATATATAGGTCATATTTCTACTTGTTGGTTTGATTTCTGAGAGAAAGTGTTGCT ATTTGTGTGATGTGATCTACAGGCCCTGTCATTGTTTCTTCTTTCAGCTTATTATAAATTTCTC GGCAGTTACCCTTTCGTTGCTGTTTCTGCTCTGCTTCTCTATGTGGGATGCTACCAGGTGATGC TCTCATATATTCATACTTGCTGGCGTAAACAACTCTAATTTGTAGGTGTTTCTTGGGAAGATTC ACTATTAACTTAAACTAGGGTATTGACCTTAATCTACTAATCATCTTCCTAGTTATTTCAGACA ACTTGTTTCTCTTCTCTTCTCTTTAATATGTAACACGTGAATTATGATTGTTTATACCCCAGAT CCATAATCTTGTCAGGAATTCACCTTATTGGAAGTAGTCCCCTAGTGGTAAGAGTGCAACTTGT GATTTGTGGGTTAGGCACAGGTCATGGATTCAAACCCTGCCACAGACAAACACTTGGTATTTAA GTGGAGAAGGGTAAAGGGGGCCACCATTATCCACCGATTTTCGAACTATACGCCACTGACCTTC GGGGATTTCTCATTTATAAAAGAAGCTTTTGTTAATTTATTAGTAGGTCGACATAATCAATCTA GTGTACTTGGCAAGTTAATAATATCTCACAATTGAGTAAAGTTTTTTTGATTACGTAACTTTTC CTTATCTCAAAATTAATTAATTCTTCTACCCGATCAGTCAATCAACTAAACCTCAATCCTAACT TGTGTCTGGCAAATGAATTCTCTGCATCCAATCCGTTATATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13650034

Conservation Information
Conserved circRNAs	NA
PMCS	0.13650034

			
						 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 PGSC0003DMG401010374_circ_g.1

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