Plant Circular RNA Database

Detail information of PGSC0003DMG400024874_circ_ag.4

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400024874_circ_ag.4
					
						ID in PlantcircBase
						stu_circ_000192
					
						Alias
						chr01:79950534|79954313
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr1: 79950535-79954313  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
						
							PGSC0003DMG400024874_circ_ag.1 PGSC0003DMG400024874_circ_ag.2 PGSC0003DMG400024874_circ_ag.3 						
					
						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-GA							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	PGSC0003DMG400024874_circ_ag.4
ID in PlantcircBase	stu_circ_000192
Alias	chr01:79950534\|79954313
Organism	Solanum tuberosum
Position	chr1: 79950535-79954313 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	PGSC0003DMG400024874_circ_ag.1 PGSC0003DMG400024874_circ_ag.2 PGSC0003DMG400024874_circ_ag.3
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-GA 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  
						
							TTTTTCTTCTGTACTTAGGGTTTTTTTCTTCTTCTCCCGATTCTCACTGGATACAAGAAGATTC
AGAATTTGCGCTTTTCAGATCAAGATTCTCCGTCTGtaattgaagagtttcagaaatgtcatac
agaccacccactaggaaaattccttgggcaatgcacagaactgaaagtaaagcttgaccggtgc
tttaggca

									
								

					

						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
						
							TAATTGAAGAGTTTCAGAAATGTCATACAGACCACCCACTAGGAAAATTCCTTGGGCAATGCAC
AGAACTGAAAGTAAAGCTTGACCGGTGCTTTAGGCAGGAAGTAAGGTTTCTTGCTTTACCTATT
CGGAAATTATATGTCTTTGAAAACATATCTTCAGTGTTCCTCATGTATGAGCCATTAAAAAAAT
ATGATGTCCTTCTGCAGAAAGCTATAAAGAGGAAAGCAAATTTTGAACAGAGCAAGAAGTTGAA
AGAGAGGCTCCAAGCTTACAGGAAAGAAACTGCTGACATGCAATCTTGAATCTGATAATAGTTA
TGTTGACAAGACACTGTTGTGCAATATTTCAACACACGAAGGAAAACTTAACGGCTAGGATTTA
TCAGAGAAAGATTGGTGAATAGAATTGTCGTTCGTCTATTCTGATGTTTTCGTCAATCTCCATT
ATTTAAGTTAGTTAAAGTAAATAAGATGTATAGACACAAGAATTGATAAATTACAGGAGCAACT
TATCAGACCATTCAATTTTGGTAAAATGTCAAACATCAAAATACTGAAATAACTGTGTGAACTG
ATAGAATGTTCCTGGTGGGAGGTAGCTAGCCTCTTAATATTAGTCGAGGTGCGTGCAAGGTGAT
CCAGCACAAACATAGACCTTGTTTGGATATTTTTAGACAAAGCAAATGTGAATTGTTCTAATAC
AAGCTGTAAGCGAAGTTTTTTTTTTTTTTTTTGGGAACTTGGAGCCTGGAGTGCATACTAAACT
CTTAAGCTTGTGTTGTTGGCCAGTTGGAAGAATATTTGCCATGAATTTGCTCCACAAAAATAGA
GTTTCTGTAGGATGGCCAATGTGATATTTAAATGGACTCTTGCTGTTATTTAAATCAAACATTA
TTTCTATTCCTTTCAAAATGAATAATGTGAGTAGTAACTCTTCCTGTTGCAACACAAATGGAGG
TTTGAGAGTTCCAAATTTGTTTCTATTTTAGAAGTGCACCACTGGTAATTAACACCAGTTCTAG
CATCCAATTGTGTGACCTAGTCTTCAACGAAGTGGTTGAGAATCAAGAGGTCTCATGTTCAATT
TCGTTGAGACAAAAAACACTAGGTGATTTTTTCCATTTGTCCTAATCTTGGTGGACAGAGTTAC
ATGATACTTGTTGCTGGTGGACACTGAATATTGTTATTGGTAGGAGGTGAAAGGTATTAAGTGA
AATTAAGCCTTGATATAAAAGCAATTATGAGATGCCAAAATTGGGACATATACAAGTGTTGTAG
GTCTCTATGGTGGTATCACATGTCTAAATAGAAACTTTCATGGCTTAAAACAGAATCTTCCTAT
TCAAATTTTAAAGTTCAATGTGTCAAAGCTTAACACATCATTTTTCACACATAGGATAAGATAT
ATAATATTAATATACAGGAAATTCTAGACCCATATATAATATCAAGAATGCAATGAATTTAGTC
TTGGAAGGTAAAAAAATTTAACTCATCAAATTTTAATATTGGATTTATTCAGTCTTGGATTTCT
AACTAACCAAAACTTTGTTCCCTCCACAAGCTAAATTATCTTTGTCGATAGTGTCAAAAGAAAA
TGAAATGGATTAGGAATTAATCTGATTTGGATTAGCCGATATGTCTTTTGCCAAATATTGTTGC
ATGAAAAAAAGAATTATACTTATGACAAATGGATCTAACTCAACTGTAAAAGCTAACTCATGAG
AAAAAGATTATCAAGTCCATATAAGTAGACCTTCAATCAATTTTCCAACCAATTTTAATACCCC
TTCGTGCTCAAGCCGTCCAGCTTTAGCGTGTACTAAGAGTCCAAACAGAAATGGACTTGGCCCT
GATACTATATAAAAATATGACATATCGACTAACTCAATTTCAAAAGTTAGCTTATGAGAAAGGA
TTATATAAGTTCATATAAGCAAGCCACCAATTCATTTTCCAATCTAAAATCCCCATACAAAGTC
GAATAGCATCACTCCTTTTGTAGTGTTTGGAAGACTCAGAAATATTCCAAAAAGGTATTCATAT
GGCATTTTACATTATTTTCTATTTTTGTTTTTTTTTTCCCTTTGAAATAATGGAAGCAAATTTA
AAGTTACTTTGGGGAATTAGGTGTTTAAAAAATAGAGCATATTTTAAGAAATCTTCTTTGATTA
ATAAGTTGGTTTTTTTTTAAAGATTATATCAATTTCAATATTTGCTTTTCTAATATGTGTTTGA
TACGACATAAATTGTCATAAAAAAATTATTAATCTCCAATTATCACTTGTTCCTCCTAAGTAAA
AAAGTAACATATTTCGTTCTTGATTTGTTCACGTGTTACATGTGAGTTGAACGCACGTCATGAT
TTATGTCCGTTATAACAGAAAAAACGTTGTTCAATTGGGAGGACATACAACATGGTTCATGCCT
TACTGTAACAAGAACACTTTTATTCGATTTGAAAATGAACTGATAACTTGTTATTCAAGTAAAA
AGAATCGAGCATAGATATATTACGTATCAAAATTTGAATCAAAATACGTGCACGATTAACCTTC
CAAAATTTGTCAAATATAAAAAGAATATATAAAAAATAACATAAAATGCCAATGATTGGCCACT
ATTGGAGCATACTTTCAAATCAAGGGAAATATTCGCAACCTACATTTTTAAAGTATCTCAACTA
ATTCTATCATATTTTTTGTTAAATCAACACATTAATTAATGTCGTTTTACTACTCTAAATGAGC
AAAAAAAAAATCATTTTGCTATAAGTGATAGTGCAACTATTGTTTACACCACCAGTACAATTTA
ATTCACTCATTATTTTATCATGTTGTAGATTAACATTAAAAATAAATAAATACTTAAAACTATT
TTATGAGTAGACTTAATTTATAATATTTTTCAAACTCTACGACCAAAAATATTTGTACAATGTC
TTTAATCCTCATAGATTTTGAAGTTGAAATTTAGAAAAATATTAGAAAAAAATAGTTTTTATTT
TCAAAATGATGGTATTTAAAAGTTAAAGTTGTGTTTGGCCATGAATATAAATTGAAATTGTTTT
TGAATTTTTTAGAGTACATGACTTTTTGGTATTCTTCAAATTTTGAGTTTTATTGTCAAATTTT
GAATTTTATGTGTTTCGGAGTTTAACGATTATGACCAACACCGTCTTAAAATTATTAAAAGATT
AGATTTTCTAAATAAATTAAATTTTATGATCAAATAAATATTTAAAGATGAATTTTTAAAATTA
ACGTCAAACAAATAATCTTCAAAAACATATTACTATTGATTATTCTATTTTTTTTAACAGAAAA
TAAAAAGGAAGAGAAAAAAAATCAAAGTTAGAACATTCACCGTAAACGCCGCCAGGGTCAGGTT
TGACAACTAGACTCGGACGTATTACAAAAGCTATAGGTTCGGAACATCCAGCTGTATACAGCCT
GTTATTTTTAGTATTTCATTTTTTCATTATATTTTTGTATATTTCACATTTAAACATTATAAAT
CTCAATTATAATTTCCAATTCTGGGTTTGGTTTATTCGCTGGCGACAGCCTGTTTCCAACAAAG
CTCTCCTACCACACTACCCCCACACCCCCCTCTATCTTCTCCCCCATTTTCCCTCACTCTTCTC
TTCCATCAATCCTCTCTCTCTCTCTCTCTTTTTTTTCTTCTGTACTTAGGGTTTTTTTCTTCTT
CTCCCGATTCTCACTGGATACAAGAAGATTCAGAATTTGCGCTTTTCAGATCAAGATTCTCCGT
CTG
						
					

			
		

Sequences
Splice junction sequence	TTTTTCTTCTGTACTTAGGGTTTTTTTCTTCTTCTCCCGATTCTCACTGGATACAAGAAGATTC AGAATTTGCGCTTTTCAGATCAAGATTCTCCGTCTGtaattgaagagtttcagaaatgtcatac agaccacccactaggaaaattccttgggcaatgcacagaactgaaagtaaagcttgaccggtgc tttaggca
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	TAATTGAAGAGTTTCAGAAATGTCATACAGACCACCCACTAGGAAAATTCCTTGGGCAATGCAC AGAACTGAAAGTAAAGCTTGACCGGTGCTTTAGGCAGGAAGTAAGGTTTCTTGCTTTACCTATT CGGAAATTATATGTCTTTGAAAACATATCTTCAGTGTTCCTCATGTATGAGCCATTAAAAAAAT ATGATGTCCTTCTGCAGAAAGCTATAAAGAGGAAAGCAAATTTTGAACAGAGCAAGAAGTTGAA AGAGAGGCTCCAAGCTTACAGGAAAGAAACTGCTGACATGCAATCTTGAATCTGATAATAGTTA TGTTGACAAGACACTGTTGTGCAATATTTCAACACACGAAGGAAAACTTAACGGCTAGGATTTA TCAGAGAAAGATTGGTGAATAGAATTGTCGTTCGTCTATTCTGATGTTTTCGTCAATCTCCATT ATTTAAGTTAGTTAAAGTAAATAAGATGTATAGACACAAGAATTGATAAATTACAGGAGCAACT TATCAGACCATTCAATTTTGGTAAAATGTCAAACATCAAAATACTGAAATAACTGTGTGAACTG ATAGAATGTTCCTGGTGGGAGGTAGCTAGCCTCTTAATATTAGTCGAGGTGCGTGCAAGGTGAT CCAGCACAAACATAGACCTTGTTTGGATATTTTTAGACAAAGCAAATGTGAATTGTTCTAATAC AAGCTGTAAGCGAAGTTTTTTTTTTTTTTTTTGGGAACTTGGAGCCTGGAGTGCATACTAAACT CTTAAGCTTGTGTTGTTGGCCAGTTGGAAGAATATTTGCCATGAATTTGCTCCACAAAAATAGA GTTTCTGTAGGATGGCCAATGTGATATTTAAATGGACTCTTGCTGTTATTTAAATCAAACATTA TTTCTATTCCTTTCAAAATGAATAATGTGAGTAGTAACTCTTCCTGTTGCAACACAAATGGAGG TTTGAGAGTTCCAAATTTGTTTCTATTTTAGAAGTGCACCACTGGTAATTAACACCAGTTCTAG CATCCAATTGTGTGACCTAGTCTTCAACGAAGTGGTTGAGAATCAAGAGGTCTCATGTTCAATT TCGTTGAGACAAAAAACACTAGGTGATTTTTTCCATTTGTCCTAATCTTGGTGGACAGAGTTAC ATGATACTTGTTGCTGGTGGACACTGAATATTGTTATTGGTAGGAGGTGAAAGGTATTAAGTGA AATTAAGCCTTGATATAAAAGCAATTATGAGATGCCAAAATTGGGACATATACAAGTGTTGTAG GTCTCTATGGTGGTATCACATGTCTAAATAGAAACTTTCATGGCTTAAAACAGAATCTTCCTAT TCAAATTTTAAAGTTCAATGTGTCAAAGCTTAACACATCATTTTTCACACATAGGATAAGATAT ATAATATTAATATACAGGAAATTCTAGACCCATATATAATATCAAGAATGCAATGAATTTAGTC TTGGAAGGTAAAAAAATTTAACTCATCAAATTTTAATATTGGATTTATTCAGTCTTGGATTTCT AACTAACCAAAACTTTGTTCCCTCCACAAGCTAAATTATCTTTGTCGATAGTGTCAAAAGAAAA TGAAATGGATTAGGAATTAATCTGATTTGGATTAGCCGATATGTCTTTTGCCAAATATTGTTGC ATGAAAAAAAGAATTATACTTATGACAAATGGATCTAACTCAACTGTAAAAGCTAACTCATGAG AAAAAGATTATCAAGTCCATATAAGTAGACCTTCAATCAATTTTCCAACCAATTTTAATACCCC TTCGTGCTCAAGCCGTCCAGCTTTAGCGTGTACTAAGAGTCCAAACAGAAATGGACTTGGCCCT GATACTATATAAAAATATGACATATCGACTAACTCAATTTCAAAAGTTAGCTTATGAGAAAGGA TTATATAAGTTCATATAAGCAAGCCACCAATTCATTTTCCAATCTAAAATCCCCATACAAAGTC GAATAGCATCACTCCTTTTGTAGTGTTTGGAAGACTCAGAAATATTCCAAAAAGGTATTCATAT GGCATTTTACATTATTTTCTATTTTTGTTTTTTTTTTCCCTTTGAAATAATGGAAGCAAATTTA AAGTTACTTTGGGGAATTAGGTGTTTAAAAAATAGAGCATATTTTAAGAAATCTTCTTTGATTA ATAAGTTGGTTTTTTTTTAAAGATTATATCAATTTCAATATTTGCTTTTCTAATATGTGTTTGA TACGACATAAATTGTCATAAAAAAATTATTAATCTCCAATTATCACTTGTTCCTCCTAAGTAAA AAAGTAACATATTTCGTTCTTGATTTGTTCACGTGTTACATGTGAGTTGAACGCACGTCATGAT TTATGTCCGTTATAACAGAAAAAACGTTGTTCAATTGGGAGGACATACAACATGGTTCATGCCT TACTGTAACAAGAACACTTTTATTCGATTTGAAAATGAACTGATAACTTGTTATTCAAGTAAAA AGAATCGAGCATAGATATATTACGTATCAAAATTTGAATCAAAATACGTGCACGATTAACCTTC CAAAATTTGTCAAATATAAAAAGAATATATAAAAAATAACATAAAATGCCAATGATTGGCCACT ATTGGAGCATACTTTCAAATCAAGGGAAATATTCGCAACCTACATTTTTAAAGTATCTCAACTA ATTCTATCATATTTTTTGTTAAATCAACACATTAATTAATGTCGTTTTACTACTCTAAATGAGC AAAAAAAAAATCATTTTGCTATAAGTGATAGTGCAACTATTGTTTACACCACCAGTACAATTTA ATTCACTCATTATTTTATCATGTTGTAGATTAACATTAAAAATAAATAAATACTTAAAACTATT TTATGAGTAGACTTAATTTATAATATTTTTCAAACTCTACGACCAAAAATATTTGTACAATGTC TTTAATCCTCATAGATTTTGAAGTTGAAATTTAGAAAAATATTAGAAAAAAATAGTTTTTATTT TCAAAATGATGGTATTTAAAAGTTAAAGTTGTGTTTGGCCATGAATATAAATTGAAATTGTTTT TGAATTTTTTAGAGTACATGACTTTTTGGTATTCTTCAAATTTTGAGTTTTATTGTCAAATTTT GAATTTTATGTGTTTCGGAGTTTAACGATTATGACCAACACCGTCTTAAAATTATTAAAAGATT AGATTTTCTAAATAAATTAAATTTTATGATCAAATAAATATTTAAAGATGAATTTTTAAAATTA ACGTCAAACAAATAATCTTCAAAAACATATTACTATTGATTATTCTATTTTTTTTAACAGAAAA TAAAAAGGAAGAGAAAAAAAATCAAAGTTAGAACATTCACCGTAAACGCCGCCAGGGTCAGGTT TGACAACTAGACTCGGACGTATTACAAAAGCTATAGGTTCGGAACATCCAGCTGTATACAGCCT GTTATTTTTAGTATTTCATTTTTTCATTATATTTTTGTATATTTCACATTTAAACATTATAAAT CTCAATTATAATTTCCAATTCTGGGTTTGGTTTATTCGCTGGCGACAGCCTGTTTCCAACAAAG CTCTCCTACCACACTACCCCCACACCCCCCTCTATCTTCTCCCCCATTTTCCCTCACTCTTCTC TTCCATCAATCCTCTCTCTCTCTCTCTCTTTTTTTTCTTCTGTACTTAGGGTTTTTTTCTTCTT CTCCCGATTCTCACTGGATACAAGAAGATTCAGAATTTGCGCTTTTCAGATCAAGATTCTCCGT CTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.139949777

Conservation Information
Conserved circRNAs	NA
PMCS	0.139949777

			
						 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 PGSC0003DMG400024874_circ_ag.4

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