Plant Circular RNA Database

Detail information of PGSC0003DMG401029444_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG401029444_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000501
					
						Alias
						chr04:3262780|3266762
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr4: 3262781-3266762  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG401029444						
					
						Parent gene annotation
						
							Conserved gene of unknown function
							
						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  
						
							CT-CA							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
						PGSC0003DMT400075699:1
PGSC0003DMT400075694:1
PGSC0003DMT400075698:1
PGSC0003DMT400075701:4
PGSC0003DMT400075702:6
PGSC0003DMT400075695:1
PGSC0003DMT400075696:1
PGSC0003DMT400075700:4

General Information
CircRNA Name	PGSC0003DMG401029444_circ_g.1
ID in PlantcircBase	stu_circ_000501
Alias	chr04:3262780\|3266762
Organism	Solanum tuberosum
Position	chr4: 3262781-3266762 JBrowse»
Reference genome	3.0.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG401029444
Parent gene annotation	Conserved gene of unknown function
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	CT-CA 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	PGSC0003DMT400075699:1 PGSC0003DMT400075694:1 PGSC0003DMT400075698:1 PGSC0003DMT400075701:4 PGSC0003DMT400075702:6 PGSC0003DMT400075695:1 PGSC0003DMT400075696:1 PGSC0003DMT400075700:4

			
						 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  
						
							CAATCTGTATGCATTTTCTGATCTCCATTTCCGAGCTCGTGTTCAATATGAATGGATCGATAAA
AGTTGATAAATCTTGTTCTTTCCATAACATCCATGCtatcccaaaaggctcaaagaggatgtct
cagtccaagaatttgtactttttcgaccacttatgatctctaagactagaactccaaagctgaa
aacatcgg

									
								

					

						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
						
							TATCCCAAAAGGCTCAAAGAGGATGTCTCAGTCCAAGAATTTGTACTTTTTCGACCACTTATGA
TCTCTAAGACTAGAACTCCAAAGCTGAAAACATCGGATTTCTCTGAGAATCTTCCTTCCATTGC
ATATTCGGGTGCCATGTATCCACTGTAAATATGTCAGTACGATTCGAGTAGTTAAATTATGCAA
AGTTATGGTATTGTATATAGATAAATGATCACTTACTAAGTACCAACTACTCTCATTGTGTCTG
CTTGATCTTGATCAGATCCGAAAATCCTAGCCATGCCAAAATCTGAAATCTTTGGATTGAAGTT
ATTATCGAGCAAGATGTTACTTGGCTTTAGATCTCTATGAATTATCTTCAATCTTGAATCTCTG
TGTAGATAAAGGAGTCCTCGACCAACTCCTTCGATTATAATGGAACGTTTTGTCCAATCCAAAA
TGTCTCGATGTGCTTCATCTAGATGTTTGTCAAATATGAATGGAGAATTTAAACAAAAGGATCA
GAAGAAATGTGGAGTAATGTTGCTCAGAATGCTGATGTACTCATGTTGGATCCTCCAAAAATGC
AGTACTTTTGGGGGATCTAGCAAGCATCCATCAACATTATTGAAGAGTCCGAGCAACATAGATG
TGGAGTAATGCAGATGAGAAGTAACAAGGACTAACCAAAGAGAAACACATCTAAGCTTTTCTTT
GGCATATATTCATAAATCAGCATCTTCTCCTCTTTATCGACACAGCATCCACAGAGTCTAACAA
GGTTTCTATGTTGGACTTTCGAGATCACCAACACTTCATTCATGAACTCCTCCAGCCCTTGTTT
CGAGGCTTTTGAGAGCCTCTTGACAGCTATTTCTTTCCCATCTTCCAATTTCCCCTACAAGGAA
TCACCAATATCAGTAACTTGAATTATGGGAAGTGATCGAGAGAGATGAAACTCGTACCTTGTAA
ACTGGACCAAAACCGCCCTGACCAAGCTTATTATCCTCATTGAATTGGGATGTTGCATTTGCAA
TCGTATCGAGGCTGAAGACTGGTAATTCTTCCATATTAACTGGACTTTTGTTACCAAGTAAAGC
TACCTCCTCTCTTTTCACTCCTAATATCAGCAGGAATACAAGTTAACTATAGCGAACAAAGTGC
TTCTTAATGTGTAATACAAAAACTTATTAGCATGTTTACCTCTACGTCTGATCACCATTGTATA
GCAAAGGAACAGACAAACACAGAGTGTAAGAGAACCAACAATTACTGGAATTACGATTTTCTTT
ATGTCTTTACCATGATCTGCAGAAAACACTAAAGGTGAACAAATATCAGTTCTTTACAGAATAC
ATGGAATTCAATTAAGTCGAACATATCTCAAAGGCATAATACATAAATGTGTCTTTTGATTTGG
CCTTTGCTGACATCCATGCCATCTAACTTTGAGTGTTCATGAGAGCATAGATGTGAGTTGAGGC
CAAGTAAAAGGGCACATTTATGTATTACGCCTATCTGAAATGACTGACAATGAGTTTTTTATTC
AGTACCAGAATACATACCAAGCTCTGAATTTGCCACGTGAATATAGAGATCTTTCCCCGAGCTT
TGGAACTGCTGAATGTCAATCATTTCACTCCACGACATACAGCCGATACCTGAATCAAATGCAT
ACCCTATGCAGGAACAATTCCCCAAGCATTGGCTTCTACATAAGTCTTCTGAAGTAGATGACCT
TTCAGCAAAATCAGGCAATTTCATCAACTCCATCTTTAGAAATCCGTCTTCTTTACTTGAATTC
GCGGTGTTATTCTTAACTTCACATTGCAAAGCACTCCTCCTAACACAACCACTAGTCCAATTCC
CCTTTTCCCATTCTTCCCTATGCTTTGGCTCGAAACCTTTCAGACAAGAACAGACCGGCGACTC
CAAATGATTGCAGCTCCCAAATGGACCACACGTTCCATAAACTTCACAATTGTTACTGGGAGCT
GACCATATTATCTTCCAGTTTGTCTCAGTCACATTCCAATATGATTGAACCAAGTTCCCTCTCC
AATCCAAGACTAATATCCTTAAAAAATTATCACGAATAGGTCCAGTAAAATATACAGTACCTTC
GCGATCATTCACTACATTAAATCCATCAGATACCACAGCATACATATTCTGCACTCCTATAAAG
ATCTGTCCATTCCATTGACCAGTTCGCCAATAGGGACGGTTTCCTTTCCATATATACACTTGAG
GAATGACTCCAGAGTTCATTCTTAAAGAAAAGTCTCCGATATTAGGATCCGAAGGACTTCTCCA
AGATCTTGCTTCTACCATCTCCCCTGTCCTTGTATTTTCACTTATTCTCATTCTAGGAATAGTT
GAATCAGAAGGATGTTCAAAACTCTGCCATATAGTGCTCATATTGTCCCGATGATCAACGAGAA
CAAAGTTCCCAGAATCTTGGAGAAGGCCAATTGAGTTTACCTGAGAAGTTGAAACATTTGATGA
CCAAAGAATCTCCTCCTCTCCATTCGTTATAACGACATTTCCATCACGAGATATCTTTACAACA
CCAGAAGAATCTCTTAAAGGTTTGTCCCTATTAGCCACCCAAATGACAGTTGTTACAGAAAAAT
TGTACCAAATACCAACATACCTATTAGTACTGTTTTGAGGACTGAAAAATCCTAACTTGAATAC
GCCTCCTGGAGACGATAAAATTCCAGGATCTCTCAGAGATTGAATGCTGGTAATGTTATCCACT
TCACTGCATAATCCTGTATCGATAAAACGAAGAATAACAAGAATTATATGAACAAAATATTGCA
AATTTCTTCTTCTGCTGCTGCTGTTGCTCATCTTTTTGGTTTTCTAAGACTTTTCTTATTACCA
CACTATATGAACAAAAGCACAATATGTTGTCAAAGTCTAATATCACAAGCAGCCAAATAGGATT
TTTAATTTGTTGACCCTATAGAAATATCACAAACCACATATCATTCTCTATCCGAGACTTTTAG
GCCAATGCAAAAATTGACACTTAAAAACGAATAATGTAAAATGTAGAGTTTAACTTCTATACGC
TGACAATATAAGTCTTTTCTCCCATCACTATCATTGTGTAGTATGTTCCTGAAATAACATTGTG
AATTGACAAGTTTTAACTTGTTGAAATAACACATTTCTTTTCCTTAAATTATTAAATGCTCATT
GAAAAAAGAAGAAGAAAATAAAATAAAATGAGTATTGATGTAAAGATATGACATCTAAGCTTAA
TTCAACCTTAGACCAGAAATATAATGATTGATATATTTAAACTATTTCGAAAAAGTAAAATGAG
TGAAAATCCAAAAGCCACGTTAGTGTGAGAATTGAGTGGGGACCTTGACAATAAGCTAGCATCT
CAACGTCAACATGCTTGTCAACTATAAGTGGTAATAATGCACATAGTGTAATGAAAAATGTATT
GTTGCACAAATTGACATTAAACCTAAATGCCTTTTCATTTTATTCCAAATACATCCCATAATAT
ATTCTGTGATTGGCAAACACATATTACACTTGTGGATTATGATATTTGATTCAACACGAATATT
TAACATGTAATCGAAAAATGAATGACAAAGATATCATACAAATTGAGACAAATGGATAATTTTG
CATATCTTAAAAATAATAATTTCATATACTCATGTCATCTACCAGTTATGTTTGTGATACTGAT
ATTGTTCAAAGTACAATTAGTTACATTGCACATTTTGAAGATACAATCATGTCTTTCAGTAAAA
GCAGGTTGTGATGGTGCAGGAAGACTTGTAGTTTCACTGGTAAGCATAGCAAGAACAGATGAAA
TACTTGGTCTGTCTTCAGCAAATTCTTGAACACATAGTAAACCAATCTGTATGCATTTTCTGAT
CTCCATTTCCGAGCTCGTGTTCAATATGAATGGATCGATAAAAGTTGATAAATCTTGTTCTTTC
CATAACATCCATGC
						
					

			
		

Sequences
Splice junction sequence	CAATCTGTATGCATTTTCTGATCTCCATTTCCGAGCTCGTGTTCAATATGAATGGATCGATAAA AGTTGATAAATCTTGTTCTTTCCATAACATCCATGCtatcccaaaaggctcaaagaggatgtct cagtccaagaatttgtactttttcgaccacttatgatctctaagactagaactccaaagctgaa aacatcgg
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	TATCCCAAAAGGCTCAAAGAGGATGTCTCAGTCCAAGAATTTGTACTTTTTCGACCACTTATGA TCTCTAAGACTAGAACTCCAAAGCTGAAAACATCGGATTTCTCTGAGAATCTTCCTTCCATTGC ATATTCGGGTGCCATGTATCCACTGTAAATATGTCAGTACGATTCGAGTAGTTAAATTATGCAA AGTTATGGTATTGTATATAGATAAATGATCACTTACTAAGTACCAACTACTCTCATTGTGTCTG CTTGATCTTGATCAGATCCGAAAATCCTAGCCATGCCAAAATCTGAAATCTTTGGATTGAAGTT ATTATCGAGCAAGATGTTACTTGGCTTTAGATCTCTATGAATTATCTTCAATCTTGAATCTCTG TGTAGATAAAGGAGTCCTCGACCAACTCCTTCGATTATAATGGAACGTTTTGTCCAATCCAAAA TGTCTCGATGTGCTTCATCTAGATGTTTGTCAAATATGAATGGAGAATTTAAACAAAAGGATCA GAAGAAATGTGGAGTAATGTTGCTCAGAATGCTGATGTACTCATGTTGGATCCTCCAAAAATGC AGTACTTTTGGGGGATCTAGCAAGCATCCATCAACATTATTGAAGAGTCCGAGCAACATAGATG TGGAGTAATGCAGATGAGAAGTAACAAGGACTAACCAAAGAGAAACACATCTAAGCTTTTCTTT GGCATATATTCATAAATCAGCATCTTCTCCTCTTTATCGACACAGCATCCACAGAGTCTAACAA GGTTTCTATGTTGGACTTTCGAGATCACCAACACTTCATTCATGAACTCCTCCAGCCCTTGTTT CGAGGCTTTTGAGAGCCTCTTGACAGCTATTTCTTTCCCATCTTCCAATTTCCCCTACAAGGAA TCACCAATATCAGTAACTTGAATTATGGGAAGTGATCGAGAGAGATGAAACTCGTACCTTGTAA ACTGGACCAAAACCGCCCTGACCAAGCTTATTATCCTCATTGAATTGGGATGTTGCATTTGCAA TCGTATCGAGGCTGAAGACTGGTAATTCTTCCATATTAACTGGACTTTTGTTACCAAGTAAAGC TACCTCCTCTCTTTTCACTCCTAATATCAGCAGGAATACAAGTTAACTATAGCGAACAAAGTGC TTCTTAATGTGTAATACAAAAACTTATTAGCATGTTTACCTCTACGTCTGATCACCATTGTATA GCAAAGGAACAGACAAACACAGAGTGTAAGAGAACCAACAATTACTGGAATTACGATTTTCTTT ATGTCTTTACCATGATCTGCAGAAAACACTAAAGGTGAACAAATATCAGTTCTTTACAGAATAC ATGGAATTCAATTAAGTCGAACATATCTCAAAGGCATAATACATAAATGTGTCTTTTGATTTGG CCTTTGCTGACATCCATGCCATCTAACTTTGAGTGTTCATGAGAGCATAGATGTGAGTTGAGGC CAAGTAAAAGGGCACATTTATGTATTACGCCTATCTGAAATGACTGACAATGAGTTTTTTATTC AGTACCAGAATACATACCAAGCTCTGAATTTGCCACGTGAATATAGAGATCTTTCCCCGAGCTT TGGAACTGCTGAATGTCAATCATTTCACTCCACGACATACAGCCGATACCTGAATCAAATGCAT ACCCTATGCAGGAACAATTCCCCAAGCATTGGCTTCTACATAAGTCTTCTGAAGTAGATGACCT TTCAGCAAAATCAGGCAATTTCATCAACTCCATCTTTAGAAATCCGTCTTCTTTACTTGAATTC GCGGTGTTATTCTTAACTTCACATTGCAAAGCACTCCTCCTAACACAACCACTAGTCCAATTCC CCTTTTCCCATTCTTCCCTATGCTTTGGCTCGAAACCTTTCAGACAAGAACAGACCGGCGACTC CAAATGATTGCAGCTCCCAAATGGACCACACGTTCCATAAACTTCACAATTGTTACTGGGAGCT GACCATATTATCTTCCAGTTTGTCTCAGTCACATTCCAATATGATTGAACCAAGTTCCCTCTCC AATCCAAGACTAATATCCTTAAAAAATTATCACGAATAGGTCCAGTAAAATATACAGTACCTTC GCGATCATTCACTACATTAAATCCATCAGATACCACAGCATACATATTCTGCACTCCTATAAAG ATCTGTCCATTCCATTGACCAGTTCGCCAATAGGGACGGTTTCCTTTCCATATATACACTTGAG GAATGACTCCAGAGTTCATTCTTAAAGAAAAGTCTCCGATATTAGGATCCGAAGGACTTCTCCA AGATCTTGCTTCTACCATCTCCCCTGTCCTTGTATTTTCACTTATTCTCATTCTAGGAATAGTT GAATCAGAAGGATGTTCAAAACTCTGCCATATAGTGCTCATATTGTCCCGATGATCAACGAGAA CAAAGTTCCCAGAATCTTGGAGAAGGCCAATTGAGTTTACCTGAGAAGTTGAAACATTTGATGA CCAAAGAATCTCCTCCTCTCCATTCGTTATAACGACATTTCCATCACGAGATATCTTTACAACA CCAGAAGAATCTCTTAAAGGTTTGTCCCTATTAGCCACCCAAATGACAGTTGTTACAGAAAAAT TGTACCAAATACCAACATACCTATTAGTACTGTTTTGAGGACTGAAAAATCCTAACTTGAATAC GCCTCCTGGAGACGATAAAATTCCAGGATCTCTCAGAGATTGAATGCTGGTAATGTTATCCACT TCACTGCATAATCCTGTATCGATAAAACGAAGAATAACAAGAATTATATGAACAAAATATTGCA AATTTCTTCTTCTGCTGCTGCTGTTGCTCATCTTTTTGGTTTTCTAAGACTTTTCTTATTACCA CACTATATGAACAAAAGCACAATATGTTGTCAAAGTCTAATATCACAAGCAGCCAAATAGGATT TTTAATTTGTTGACCCTATAGAAATATCACAAACCACATATCATTCTCTATCCGAGACTTTTAG GCCAATGCAAAAATTGACACTTAAAAACGAATAATGTAAAATGTAGAGTTTAACTTCTATACGC TGACAATATAAGTCTTTTCTCCCATCACTATCATTGTGTAGTATGTTCCTGAAATAACATTGTG AATTGACAAGTTTTAACTTGTTGAAATAACACATTTCTTTTCCTTAAATTATTAAATGCTCATT GAAAAAAGAAGAAGAAAATAAAATAAAATGAGTATTGATGTAAAGATATGACATCTAAGCTTAA TTCAACCTTAGACCAGAAATATAATGATTGATATATTTAAACTATTTCGAAAAAGTAAAATGAG TGAAAATCCAAAAGCCACGTTAGTGTGAGAATTGAGTGGGGACCTTGACAATAAGCTAGCATCT CAACGTCAACATGCTTGTCAACTATAAGTGGTAATAATGCACATAGTGTAATGAAAAATGTATT GTTGCACAAATTGACATTAAACCTAAATGCCTTTTCATTTTATTCCAAATACATCCCATAATAT ATTCTGTGATTGGCAAACACATATTACACTTGTGGATTATGATATTTGATTCAACACGAATATT TAACATGTAATCGAAAAATGAATGACAAAGATATCATACAAATTGAGACAAATGGATAATTTTG CATATCTTAAAAATAATAATTTCATATACTCATGTCATCTACCAGTTATGTTTGTGATACTGAT ATTGTTCAAAGTACAATTAGTTACATTGCACATTTTGAAGATACAATCATGTCTTTCAGTAAAA GCAGGTTGTGATGGTGCAGGAAGACTTGTAGTTTCACTGGTAAGCATAGCAAGAACAGATGAAA TACTTGGTCTGTCTTCAGCAAATTCTTGAACACATAGTAAACCAATCTGTATGCATTTTCTGAT CTCCATTTCCGAGCTCGTGTTCAATATGAATGGATCGATAAAAGTTGATAAATCTTGTTCTTTC CATAACATCCATGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.164048068

Conservation Information
Conserved circRNAs	NA
PMCS	0.164048068

			
						 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 PGSC0003DMG401029444_circ_g.1

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