Plant Circular RNA Database

Detail information of PGSC0003DMG400029350_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400029350_circ_g.1
					
						ID in PlantcircBase
						stu_circ_001717
					
						Alias
						chr12:58490496|58494039
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr12: 58490497-58494039  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400029350						
					
						Parent gene annotation
						
							Glycosyltransferase
							
						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  
						
							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
						PGSC0003DMT400075462:2
PGSC0003DMT400075467:1
PGSC0003DMT400075464:1

General Information
CircRNA Name	PGSC0003DMG400029350_circ_g.1
ID in PlantcircBase	stu_circ_001717
Alias	chr12:58490496\|58494039
Organism	Solanum tuberosum
Position	chr12: 58490497-58494039 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400029350
Parent gene annotation	Glycosyltransferase
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	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	PGSC0003DMT400075462:2 PGSC0003DMT400075467:1 PGSC0003DMT400075464:1

			
						 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  
						
							TTTGTATCCAACTCTTAGAGGACTTATCTTTAGTCAGAACATCAATTTCAAGAAAGCAGATTGG
CTTTTCTTCAACACATTTAATGCATTGGAAAAGGAGtagtcgactggataaggccttgatactc
aattaaaactatcggaccaactattccatcaatgtatcttgacaagagactaaaggaagacaaa
gaatatgg

									
								

					

						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
						
							TAGTCGACTGGATAAGGCCTTGATACTCAATTAAAACTATCGGACCAACTATTCCATCAATGTA
TCTTGACAAGAGACTAAAGGAAGACAAAGAATATGGTTTGAGTTTGTTCAAGCCTAACAGTGAA
ACCTGTATGAAGTGGCTAGATTCAAGGGAAATTGGCTCTGTTGTTTATGTGTATCATTTGGAAG
TGTTGCCAGTCTTGACGAACAACAAATAGAGGAACTAGCTTCGGGATTGATGACGAGCAACTGC
TACTTCTTGTGGGTTGTTAGAGCTACCGAAAAGAACAAACTCTCTGAGGAATGCATGTCCAAGT
TATCGGAAAAAGGACTAATTGTGAATTGGTGCCCTCAGCTCGATGTATTGTCTCATTGAGCAGT
TGGATGTTTCTTTACTCACTGTGGATGGAATTCGACACTGGAAGCATTGAGTTTGGGAGTGCCA
ATGGTGACCATGCCCCAATGGTCGGATCAACCAACTAACGCGAAATTTATTAGTGATGTATGGC
AAACAGGAGTTTGCGTTAAGGTTGGAGACAATGGTGTAGTTAATAGAGATGAAATCGCGTGTTC
TATAAGGGAAGTCATGAAGGAAGAGAAAGGTGCAATGCTGAAAGAGAATGCAATTAAATGGAAA
AAATTGGCTAAAGAAGCAGTAGATGAAGGAGGAAGTTCTGATAAGAATATTGAAGAATTTGTTT
CAAACTTGCCATGAACATTTGAGTGCTGCATAAATTAGTTCTATGTGGTCTGTTTATGAAAAAG
ACCTACATTACAGTGATTTATACTATTTGGTGAAGTCATTTAATCATCTACTACCACAAAGGCT
CAATAAAATTATGAACAACAAAATCAAACTAAACATTTAAATATTCTCTTTTCTTATAGAGACA
ACGACTGGTGAATAGAGAGCAATTGGTCTGCATTGGTGTGTTGGTATGATGTGTATGTCTACTT
GTTAAACTTTATACAACTTTAGTTGCCTTTTAAAATCAGGTTAAAAGAACACTTTTTATGTGTC
ACATCTTTTGTAAGTTGAAAAAAGAAAAATGTAAATCATGAACATGTGGACGCCTATTATCTAT
ATATCTAGTTTCTGGATACGTGCGTTGAACGTGTGTTCCATGAGAATTTTCATAAATTTGTTAA
AATAATTAAAATTTTATGAAAATATGTATTGAGTAATAAAATGCAATTTTAATTATTAATATAT
CTTTAAAATATGGTAAAAAGTACCAAAATAAGGAGCGTATTTTAATGTTTAAAATCAAGTTCTT
TTAAGCAACCAACTGTTAGTTTTGAATTTTGGTTAGTAGTTAGCAAACTTTCAATAAAACCACA
AATGATTAATCAATCAGAAATTTATAGAAAATTATATTTAAAAAGTCTAATAGATAGAAAACAC
AAAAAATACAGTGTACTCATCTTTTTTAAGACTTTAATCATACAATATAGATGTAAACAGAAAT
ATAGAAATAGTACACAATTTTTTGATTTTTTGTCAACTCCTTCTATCACAGCCAATCAAAATTC
AAGATCCTTCTTTGTTGAGTCAAACTAAAGAATGAATCAATAGAACAAAGGCACAAAAATGATA
TAAATGTTTCATTACTTTAACTATAGAATGAAAAGGATACCTAAGGATCTCATGAAACAAAAAA
GATTGATTTATATAAATAAAATTGGAGGAACACCAAAAGTTATCTTAAAATCTTAAATTAAATA
TTTAGAGGTTGTGAGAAGTACTAGAGTTATAGATATAGATATATATATTAATGGTAGCAATTGA
ATAGGTAATTAGATATGAGATATAAATGTGGATATTTAAAGCAAATAAAAGAAAATAATAATAA
TAAATAAATGAAAGGGTATAAGTTTCATAAAACCAGAACTAAAAAAATAACAAATATATAATAT
AAGACGTACAAAAAAAAATTGAAAAAATATTAAATGTGTTAATTAAGCTTAAGAAACATTTCAG
GAAGAAAATAAAAATATGTATGCAATAACCACCATAAATGTATATGTAACTACCATTGGGTATG
CAATAATTGAGAAATATGTAGCCCTGAAATGTGGTTATTAAAATTTAGTAGGTTGTAGTTATTA
GAAAATGTTCTATTAATGAAGCAAAGAAATCAGGGGGTTTAGGTTATTAGAATTTGGGGATTGT
AGTTATTTGACTTATTTCTAAGTATTAATGCAATCAAGAAATGAGGGGTTTTGGTTATTGAAAT
TTAGGGCTTGTGTATATTCCAACGTGTAAAGTTAATCTAAATTTGTAATTCATTTAATGCATTA
AGATGAATGTATGTTACTTCATGAAAACATTAATGTCGGGAATGGACTGGTGGTCTCTTTATAT
GGACTTGGACAATCCTCCCCTCAAGAGCTAACTTTTGGGGTTGAGTTAGGTCCAAATGTCATAT
TTTTACAACTTCAACTGACATCTTACTCTTTCGTTATATTTTTGTTCTGTTCTAGACACAAAAA
CATTTAGACTTGTATTCCTTTTGAATCTAAAGTATTACTTAAAGGCTTGTACAAGTGACACCAG
TTCTTGGGGGTATTTTGAGTTATGTTATTGTTTCTGCAGATTTATATTATGCTAGTCTATTTTA
CTTCCGCATTTAATCTTGTTTCATTGGGTTTAGGCTGACCTGTCTTGATAGGATAAAATAGGTG
TCATCTCACCCGATTTTTGAATTGTAATATCTATAAAGGGGGGGCTACGCAACCACCTCTATAT
AGTTCATGGAAAGCCACATATCCTTACACATGCTCAATAATTAATATTGACTATTGAATAAAAA
AATAGACCAATTTAAGACCATATATATATATTCTTGCCCAGCCCTTTATATAGATAGCAGTAAC
TTTAAGTCAGGTTCTTGTATAGTGCAGAAAATGGAAGAAAAATCCAACAAATCTCATATTTTAG
TTCTCCCAATCCCAGTACAAGGCCACATAAATCCAATGGTTCAATTTTCCAAAAGATTGGCATC
AAAAGGAGTTAATAAAGTGACATTAGTTACCATTTACTCTATTAGCAAGAACATGCCAAAGGAG
TCTGGTTTAATCAATATTGAGTCCATTCCTCATGATGATGAGTCTCCACCACAAAATATTGACC
CAATGCTTGAATGGTTTCATCTTTTGGTATCAAAAAATTTGACAAAAATTGTTGAGAAATTATC
TGATCCAGAGTACCCTGTGAAAGTTCTTGTTTTCGATTCGATGGCAACTTGGGCAATTGATCTT
GCACATCAATTAGGACTAAAAGGGGCTGCTTTTTTCACACAATCTTGTTCTCTTAGTGCCATTT
ACTATCATATGGATTTAGAGACTACCAAAGTTTCTTTGGATGGCTCTGATGTCTCTTTGCCTTC
ACTTCCATTGCTAGCAAAGGAAGATTTGCCTTCTATCATCTATGATACTGATTTGTATCCAACT
CTTAGAGGACTTATCTTTAGTCAGAACATCAATTTCAAGAAAGCAGATTGGCTTTTCTTCAACA
CATTTAATGCATTGGAAAAGGAG
						
					

			
		

Sequences
Splice junction sequence	TTTGTATCCAACTCTTAGAGGACTTATCTTTAGTCAGAACATCAATTTCAAGAAAGCAGATTGG CTTTTCTTCAACACATTTAATGCATTGGAAAAGGAGtagtcgactggataaggccttgatactc aattaaaactatcggaccaactattccatcaatgtatcttgacaagagactaaaggaagacaaa gaatatgg
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	TAGTCGACTGGATAAGGCCTTGATACTCAATTAAAACTATCGGACCAACTATTCCATCAATGTA TCTTGACAAGAGACTAAAGGAAGACAAAGAATATGGTTTGAGTTTGTTCAAGCCTAACAGTGAA ACCTGTATGAAGTGGCTAGATTCAAGGGAAATTGGCTCTGTTGTTTATGTGTATCATTTGGAAG TGTTGCCAGTCTTGACGAACAACAAATAGAGGAACTAGCTTCGGGATTGATGACGAGCAACTGC TACTTCTTGTGGGTTGTTAGAGCTACCGAAAAGAACAAACTCTCTGAGGAATGCATGTCCAAGT TATCGGAAAAAGGACTAATTGTGAATTGGTGCCCTCAGCTCGATGTATTGTCTCATTGAGCAGT TGGATGTTTCTTTACTCACTGTGGATGGAATTCGACACTGGAAGCATTGAGTTTGGGAGTGCCA ATGGTGACCATGCCCCAATGGTCGGATCAACCAACTAACGCGAAATTTATTAGTGATGTATGGC AAACAGGAGTTTGCGTTAAGGTTGGAGACAATGGTGTAGTTAATAGAGATGAAATCGCGTGTTC TATAAGGGAAGTCATGAAGGAAGAGAAAGGTGCAATGCTGAAAGAGAATGCAATTAAATGGAAA AAATTGGCTAAAGAAGCAGTAGATGAAGGAGGAAGTTCTGATAAGAATATTGAAGAATTTGTTT CAAACTTGCCATGAACATTTGAGTGCTGCATAAATTAGTTCTATGTGGTCTGTTTATGAAAAAG ACCTACATTACAGTGATTTATACTATTTGGTGAAGTCATTTAATCATCTACTACCACAAAGGCT CAATAAAATTATGAACAACAAAATCAAACTAAACATTTAAATATTCTCTTTTCTTATAGAGACA ACGACTGGTGAATAGAGAGCAATTGGTCTGCATTGGTGTGTTGGTATGATGTGTATGTCTACTT GTTAAACTTTATACAACTTTAGTTGCCTTTTAAAATCAGGTTAAAAGAACACTTTTTATGTGTC ACATCTTTTGTAAGTTGAAAAAAGAAAAATGTAAATCATGAACATGTGGACGCCTATTATCTAT ATATCTAGTTTCTGGATACGTGCGTTGAACGTGTGTTCCATGAGAATTTTCATAAATTTGTTAA AATAATTAAAATTTTATGAAAATATGTATTGAGTAATAAAATGCAATTTTAATTATTAATATAT CTTTAAAATATGGTAAAAAGTACCAAAATAAGGAGCGTATTTTAATGTTTAAAATCAAGTTCTT TTAAGCAACCAACTGTTAGTTTTGAATTTTGGTTAGTAGTTAGCAAACTTTCAATAAAACCACA AATGATTAATCAATCAGAAATTTATAGAAAATTATATTTAAAAAGTCTAATAGATAGAAAACAC AAAAAATACAGTGTACTCATCTTTTTTAAGACTTTAATCATACAATATAGATGTAAACAGAAAT ATAGAAATAGTACACAATTTTTTGATTTTTTGTCAACTCCTTCTATCACAGCCAATCAAAATTC AAGATCCTTCTTTGTTGAGTCAAACTAAAGAATGAATCAATAGAACAAAGGCACAAAAATGATA TAAATGTTTCATTACTTTAACTATAGAATGAAAAGGATACCTAAGGATCTCATGAAACAAAAAA GATTGATTTATATAAATAAAATTGGAGGAACACCAAAAGTTATCTTAAAATCTTAAATTAAATA TTTAGAGGTTGTGAGAAGTACTAGAGTTATAGATATAGATATATATATTAATGGTAGCAATTGA ATAGGTAATTAGATATGAGATATAAATGTGGATATTTAAAGCAAATAAAAGAAAATAATAATAA TAAATAAATGAAAGGGTATAAGTTTCATAAAACCAGAACTAAAAAAATAACAAATATATAATAT AAGACGTACAAAAAAAAATTGAAAAAATATTAAATGTGTTAATTAAGCTTAAGAAACATTTCAG GAAGAAAATAAAAATATGTATGCAATAACCACCATAAATGTATATGTAACTACCATTGGGTATG CAATAATTGAGAAATATGTAGCCCTGAAATGTGGTTATTAAAATTTAGTAGGTTGTAGTTATTA GAAAATGTTCTATTAATGAAGCAAAGAAATCAGGGGGTTTAGGTTATTAGAATTTGGGGATTGT AGTTATTTGACTTATTTCTAAGTATTAATGCAATCAAGAAATGAGGGGTTTTGGTTATTGAAAT TTAGGGCTTGTGTATATTCCAACGTGTAAAGTTAATCTAAATTTGTAATTCATTTAATGCATTA AGATGAATGTATGTTACTTCATGAAAACATTAATGTCGGGAATGGACTGGTGGTCTCTTTATAT GGACTTGGACAATCCTCCCCTCAAGAGCTAACTTTTGGGGTTGAGTTAGGTCCAAATGTCATAT TTTTACAACTTCAACTGACATCTTACTCTTTCGTTATATTTTTGTTCTGTTCTAGACACAAAAA CATTTAGACTTGTATTCCTTTTGAATCTAAAGTATTACTTAAAGGCTTGTACAAGTGACACCAG TTCTTGGGGGTATTTTGAGTTATGTTATTGTTTCTGCAGATTTATATTATGCTAGTCTATTTTA CTTCCGCATTTAATCTTGTTTCATTGGGTTTAGGCTGACCTGTCTTGATAGGATAAAATAGGTG TCATCTCACCCGATTTTTGAATTGTAATATCTATAAAGGGGGGGCTACGCAACCACCTCTATAT AGTTCATGGAAAGCCACATATCCTTACACATGCTCAATAATTAATATTGACTATTGAATAAAAA AATAGACCAATTTAAGACCATATATATATATTCTTGCCCAGCCCTTTATATAGATAGCAGTAAC TTTAAGTCAGGTTCTTGTATAGTGCAGAAAATGGAAGAAAAATCCAACAAATCTCATATTTTAG TTCTCCCAATCCCAGTACAAGGCCACATAAATCCAATGGTTCAATTTTCCAAAAGATTGGCATC AAAAGGAGTTAATAAAGTGACATTAGTTACCATTTACTCTATTAGCAAGAACATGCCAAAGGAG TCTGGTTTAATCAATATTGAGTCCATTCCTCATGATGATGAGTCTCCACCACAAAATATTGACC CAATGCTTGAATGGTTTCATCTTTTGGTATCAAAAAATTTGACAAAAATTGTTGAGAAATTATC TGATCCAGAGTACCCTGTGAAAGTTCTTGTTTTCGATTCGATGGCAACTTGGGCAATTGATCTT GCACATCAATTAGGACTAAAAGGGGCTGCTTTTTTCACACAATCTTGTTCTCTTAGTGCCATTT ACTATCATATGGATTTAGAGACTACCAAAGTTTCTTTGGATGGCTCTGATGTCTCTTTGCCTTC ACTTCCATTGCTAGCAAAGGAAGATTTGCCTTCTATCATCTATGATACTGATTTGTATCCAACT CTTAGAGGACTTATCTTTAGTCAGAACATCAATTTCAAGAAAGCAGATTGGCTTTTCTTCAACA CATTTAATGCATTGGAAAAGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.109055175

Conservation Information
Conserved circRNAs	NA
PMCS	0.109055175

			
						 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 PGSC0003DMG400029350_circ_g.1

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