Plant Circular RNA Database

Detail information of PGSC0003DMG400005200_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400005200_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000091
					
						Alias
						chr01:63197450|63200812
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr1: 63197451-63200812  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400005200						
					
						Parent gene annotation
						
							Cyclase/dehydrase
							
						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-CC							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
						PGSC0003DMT400013328:1
PGSC0003DMT400013323:2
PGSC0003DMT400013331:3
PGSC0003DMT400013324:3
PGSC0003DMT400013325:1

General Information
CircRNA Name	PGSC0003DMG400005200_circ_g.1
ID in PlantcircBase	stu_circ_000091
Alias	chr01:63197450\|63200812
Organism	Solanum tuberosum
Position	chr1: 63197451-63200812 JBrowse»
Reference genome	3.0.38
Type	ei-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400005200
Parent gene annotation	Cyclase/dehydrase
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-CC 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	PGSC0003DMT400013328:1 PGSC0003DMT400013323:2 PGSC0003DMT400013331:3 PGSC0003DMT400013324:3 PGSC0003DMT400013325:1

			
						 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  
						
							AGTTGAAGTCAAAAGGAAAGGACAAAATTATGTTTCAAGTAAAATTCTCACTTCTATGATGCAG
GATGATGGGCCTTTGGGGAAAAATCGCACAGCTCCCtgtggggaagtccctcctgatatctcca
gtggatcttctggtttggcgtaggctgtaaaacagaataaaaactgagtttaggatcaaataaa
cataatga

									
								

					

						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
						
							TGTGGGGAAGTCCCTCCTGATATCTCCAGTGGATCTTCTGGTTTGGCGTAGGCTGTAAAACAGA
ATAAAAACTGAGTTTAGGATCAAATAAACATAATGAGCGAATTGCTTAACTAAAGGGGTATTTT
ACCTGCATATTTCGAGCAAGCCCTGAATATTCAATGTTCTGCCCGAAAGCTTTATACTTCAATG
ACCATCTTGATAAGTTAGGTTTATCCTCCAAAATCAGGCAAGAGAGTCTAACATCAAGTTCCCT
TAGAATGAGATTCAGAAGGTAAGATGACCTGTGTAATGGATGTCTAAAATAATCAAGAACTAGA
ATGTAGACCCCTAATTGTTAATACATCTGCATTCAACTTCAATTGTTTTTGGTGAGTGGTTTCT
TTATATCCAAAGTGCAAATCAAAAATCTGACAATGATACTCATTAAGTGAAGCTCGCATTGAGA
CAGATGAAGAGATAGTCAAGATGACAAAGAGAAGTAATTCAGGATGCAGGACACCAGCATACTT
ACTACCCAGCAATATGGGGAAAATACTTAATAACATCCTGGGAAGAAATTGTAAAGAGAGAAGA
TAATATTTCCTCCGTTCAATTTATATGACACTCTTCCCATTTTAGAAGTTCCTAAAATGTGTAA
CATCATTCCCCTAATAATATTCAAGAATTTTGATTCGTTTCACTTAATTTAGATTTGTTCTAGC
AGGATAATGTCTATAACTATATTACTTTTAACACTTCCATTCATTACTGTTAATATTTCCTTTC
TCGACTACTAGTTCACTACTGGTACTTAAAATTTGCATCCAATCAAACAAGGTCATATAAAATG
AGCAATGGAGTAATACTTGAAATGCATCATTCCGGATAAAACAGCCAATAACACCATACTTAAA
CAAACAGTCGTGCAGTCTTAATAGTTTAATTGCAAAGACAAGGTTATTTAATTGAGTACATTTG
AAATGACTCTTCGGCTAAGCTTAAATGCAGAGATAACATGGCATTGCGTACCTTTACAGTTGAA
ATAAAAGGCATCCATTCAGGAATGGCCTCACTATCAGAATAACACTTATAAGCAACTGAAATGG
GCATATCTACTTTCATTTTGATCCTGAGTTCATCATAAATCGAAATTTCTCACAGTTAGATTGC
AAATAGTAATCCAAAATAGAACTCAACCACCACATATTTGTCAAGTAAATCACAAAATCGAACA
AAAATCTCAGCTCTAAACAAGTATTTGAATACAAAAGAAGATGGCAACTTACGTGCAATCTTGC
CATTCCATGACAGGAGAGAGCGGTCTAATCCTGATGGGAGAAGGATAAGAGATCCTCCGGAAGG
ATCTAGAGATGCTGCAGTTGAATCGGTATGCGCTGATGAAGGAGGAAGAGGATGCGCTAATTGA
CTTTCTTCTTCTTCCATTAAGTGAAACAATGAGCTGATGATTGTGATTGAGATTTGAGTATGTG
GGAGGCGGAAGCAGAAGTTTCAGCGGCGGATATGGTAGTTGAAACAGGTACGACGGCGGTTGCA
GACATTTGGACGAAAAGATAGGCATGCATGCCATATGGCAATTAGGCCACTGGATTTCTGATTT
GGACCACCACGGATTCCATGTTTTTTTATTTATTACCAGTAGTATAACGGCCATACGGGAATAA
TTTTAAAAATAATATTATGGTCGAATATGTATTGTACTTTTGTTTATATGGAGAAAATCATTTA
ATTTATTGTACTCCTTTGAACCCTATTTACTTGTCTATCTTTTTAAAATAATAATTGACATAAC
GAGTTTATCATTTTATTCTAATTGGTCCCTCCATTTACTTTTACTTGTCATTTATTCCTAAAAT
ATATTTTAATTTTTACTTGTCACTTTTGACCTATCGAAAAAAGACTATTTTTTCGTGTTTTACC
ATCAATATTAAATACTTATTTTCCAAATTATTTTTCAAAATATTATTTAATAAATGTTAGTTTG
GTAAAATACATATATCATTATATATCATTAATTATTTTTTTTAATGGGGTCCCAAATCAAACTA
TGACAACTAACAAGTAAAAGTGAAGGGAGGGAGTAATTGATAGAATTCCAAATTTAATTTATTC
ATTAAAGAAGTTTTATCTTTTTCAAAAACATTAACTTTCTAAATAAATTGAGTTTATAATAAGT
AAAAAAAATTGTCTTTTCTTGATTTGTCAAAAATGACAAGTTAAAAGCCAAAATTGGACAATTA
AAAAAAGTGATATTAATGAATGAGATGAGTGAGATGTTTCAATTCATGAGTTTTTGTTGCATAT
TTTTTATGGTGATTAGTAAAACAAGTTTTTCAACACTTTTTAACACATCTTGAATATTCGAATA
GTACATTTGTAATTTTCATGTTCATATAATAACGAAAGCAAAACTTCCATTGATGAGCATAATG
CTATATAAAGGCAGCAGCACAGTCGAAGTTGCCCAATCAAAGAAAATACTGGCGTCTCTTTATC
GATGTGAGGAAGGGTTTTTTGAACAACCTATTGAGTTCAGTGCACTGCAATACGATATGAATGG
GGAGCAATCAAGACTAGAAGTCTGCAATTATACTCGAGCAATAAACAGTGAATGACCATGCAGC
TAGATGATCTGTAAGACCATGATAAGAATTAAAACTGCTTGCTCCTAGCTGACAAGCCATACAT
TGCAGCTAGATGATTATTGCATGATATAGGACCAATGGATGTTACTGGCATGAATTAGTTTATA
CATCATTTAGGTGTGCCAGCTGAGTAACTCTTAGCAAATGTTGCAAAGCGTTCCAACCCTTGTG
TCAGCAGGTTTTCAGTAAATGGTTTCAATGCCTAGACAATATTTGAAAAGGTGAAAAAATATAT
TATAAAGTGAAGCTTGAAAATCAGAGTTTCTGCTATTATAAGAAATCTGCAATCTCGTTGTTTG
AAAAAGATTTTATGCCCAAGCATGTGAATTCCAGTTTCTAATATAGGAGTTAAGAGTGCTTACT
GATGCCACTGGAACCAACAGTTGAGGCACTTCATATGAAAATGTTAGCTGAAATGAGGAGAAGC
ACTAGTCAATTTTGAGCAGTCAAAAACCAAAACGATATAGCAATTTCTGTCAACACATTCTCAA
TTGTATGATTGCCTATAAGAAACTAGGAGAAGGAAAGGTGCAAACAATTTTTACCCCTACCTGC
ATAGGATCGTCCAAGATTATCCCAGAAGTATTTGTTGTAACAATTAATGTTGAATAGAGATAAG
TTGAAGTCAAAAGGAAAGGACAAAATTATGTTTCAAGTAAAATTCTCACTTCTATGATGCAGGA
TGATGGGCCTTTGGGGAAAAATCGCACAGCTCCC
						
					

			
		

Sequences
Splice junction sequence	AGTTGAAGTCAAAAGGAAAGGACAAAATTATGTTTCAAGTAAAATTCTCACTTCTATGATGCAG GATGATGGGCCTTTGGGGAAAAATCGCACAGCTCCCtgtggggaagtccctcctgatatctcca gtggatcttctggtttggcgtaggctgtaaaacagaataaaaactgagtttaggatcaaataaa cataatga
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	TGTGGGGAAGTCCCTCCTGATATCTCCAGTGGATCTTCTGGTTTGGCGTAGGCTGTAAAACAGA ATAAAAACTGAGTTTAGGATCAAATAAACATAATGAGCGAATTGCTTAACTAAAGGGGTATTTT ACCTGCATATTTCGAGCAAGCCCTGAATATTCAATGTTCTGCCCGAAAGCTTTATACTTCAATG ACCATCTTGATAAGTTAGGTTTATCCTCCAAAATCAGGCAAGAGAGTCTAACATCAAGTTCCCT TAGAATGAGATTCAGAAGGTAAGATGACCTGTGTAATGGATGTCTAAAATAATCAAGAACTAGA ATGTAGACCCCTAATTGTTAATACATCTGCATTCAACTTCAATTGTTTTTGGTGAGTGGTTTCT TTATATCCAAAGTGCAAATCAAAAATCTGACAATGATACTCATTAAGTGAAGCTCGCATTGAGA CAGATGAAGAGATAGTCAAGATGACAAAGAGAAGTAATTCAGGATGCAGGACACCAGCATACTT ACTACCCAGCAATATGGGGAAAATACTTAATAACATCCTGGGAAGAAATTGTAAAGAGAGAAGA TAATATTTCCTCCGTTCAATTTATATGACACTCTTCCCATTTTAGAAGTTCCTAAAATGTGTAA CATCATTCCCCTAATAATATTCAAGAATTTTGATTCGTTTCACTTAATTTAGATTTGTTCTAGC AGGATAATGTCTATAACTATATTACTTTTAACACTTCCATTCATTACTGTTAATATTTCCTTTC TCGACTACTAGTTCACTACTGGTACTTAAAATTTGCATCCAATCAAACAAGGTCATATAAAATG AGCAATGGAGTAATACTTGAAATGCATCATTCCGGATAAAACAGCCAATAACACCATACTTAAA CAAACAGTCGTGCAGTCTTAATAGTTTAATTGCAAAGACAAGGTTATTTAATTGAGTACATTTG AAATGACTCTTCGGCTAAGCTTAAATGCAGAGATAACATGGCATTGCGTACCTTTACAGTTGAA ATAAAAGGCATCCATTCAGGAATGGCCTCACTATCAGAATAACACTTATAAGCAACTGAAATGG GCATATCTACTTTCATTTTGATCCTGAGTTCATCATAAATCGAAATTTCTCACAGTTAGATTGC AAATAGTAATCCAAAATAGAACTCAACCACCACATATTTGTCAAGTAAATCACAAAATCGAACA AAAATCTCAGCTCTAAACAAGTATTTGAATACAAAAGAAGATGGCAACTTACGTGCAATCTTGC CATTCCATGACAGGAGAGAGCGGTCTAATCCTGATGGGAGAAGGATAAGAGATCCTCCGGAAGG ATCTAGAGATGCTGCAGTTGAATCGGTATGCGCTGATGAAGGAGGAAGAGGATGCGCTAATTGA CTTTCTTCTTCTTCCATTAAGTGAAACAATGAGCTGATGATTGTGATTGAGATTTGAGTATGTG GGAGGCGGAAGCAGAAGTTTCAGCGGCGGATATGGTAGTTGAAACAGGTACGACGGCGGTTGCA GACATTTGGACGAAAAGATAGGCATGCATGCCATATGGCAATTAGGCCACTGGATTTCTGATTT GGACCACCACGGATTCCATGTTTTTTTATTTATTACCAGTAGTATAACGGCCATACGGGAATAA TTTTAAAAATAATATTATGGTCGAATATGTATTGTACTTTTGTTTATATGGAGAAAATCATTTA ATTTATTGTACTCCTTTGAACCCTATTTACTTGTCTATCTTTTTAAAATAATAATTGACATAAC GAGTTTATCATTTTATTCTAATTGGTCCCTCCATTTACTTTTACTTGTCATTTATTCCTAAAAT ATATTTTAATTTTTACTTGTCACTTTTGACCTATCGAAAAAAGACTATTTTTTCGTGTTTTACC ATCAATATTAAATACTTATTTTCCAAATTATTTTTCAAAATATTATTTAATAAATGTTAGTTTG GTAAAATACATATATCATTATATATCATTAATTATTTTTTTTAATGGGGTCCCAAATCAAACTA TGACAACTAACAAGTAAAAGTGAAGGGAGGGAGTAATTGATAGAATTCCAAATTTAATTTATTC ATTAAAGAAGTTTTATCTTTTTCAAAAACATTAACTTTCTAAATAAATTGAGTTTATAATAAGT AAAAAAAATTGTCTTTTCTTGATTTGTCAAAAATGACAAGTTAAAAGCCAAAATTGGACAATTA AAAAAAGTGATATTAATGAATGAGATGAGTGAGATGTTTCAATTCATGAGTTTTTGTTGCATAT TTTTTATGGTGATTAGTAAAACAAGTTTTTCAACACTTTTTAACACATCTTGAATATTCGAATA GTACATTTGTAATTTTCATGTTCATATAATAACGAAAGCAAAACTTCCATTGATGAGCATAATG CTATATAAAGGCAGCAGCACAGTCGAAGTTGCCCAATCAAAGAAAATACTGGCGTCTCTTTATC GATGTGAGGAAGGGTTTTTTGAACAACCTATTGAGTTCAGTGCACTGCAATACGATATGAATGG GGAGCAATCAAGACTAGAAGTCTGCAATTATACTCGAGCAATAAACAGTGAATGACCATGCAGC TAGATGATCTGTAAGACCATGATAAGAATTAAAACTGCTTGCTCCTAGCTGACAAGCCATACAT TGCAGCTAGATGATTATTGCATGATATAGGACCAATGGATGTTACTGGCATGAATTAGTTTATA CATCATTTAGGTGTGCCAGCTGAGTAACTCTTAGCAAATGTTGCAAAGCGTTCCAACCCTTGTG TCAGCAGGTTTTCAGTAAATGGTTTCAATGCCTAGACAATATTTGAAAAGGTGAAAAAATATAT TATAAAGTGAAGCTTGAAAATCAGAGTTTCTGCTATTATAAGAAATCTGCAATCTCGTTGTTTG AAAAAGATTTTATGCCCAAGCATGTGAATTCCAGTTTCTAATATAGGAGTTAAGAGTGCTTACT GATGCCACTGGAACCAACAGTTGAGGCACTTCATATGAAAATGTTAGCTGAAATGAGGAGAAGC ACTAGTCAATTTTGAGCAGTCAAAAACCAAAACGATATAGCAATTTCTGTCAACACATTCTCAA TTGTATGATTGCCTATAAGAAACTAGGAGAAGGAAAGGTGCAAACAATTTTTACCCCTACCTGC ATAGGATCGTCCAAGATTATCCCAGAAGTATTTGTTGTAACAATTAATGTTGAATAGAGATAAG TTGAAGTCAAAAGGAAAGGACAAAATTATGTTTCAAGTAAAATTCTCACTTCTATGATGCAGGA TGATGGGCCTTTGGGGAAAAATCGCACAGCTCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123436625

Conservation Information
Conserved circRNAs	NA
PMCS	0.123436625

			
						 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 PGSC0003DMG400005200_circ_g.1

Address

Any questions?

Supported by