Plant Circular RNA Database

Detail information of PGSC0003DMG400016115_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400016115_circ_g.1
					
						ID in PlantcircBase
						stu_circ_001510
					
						Alias
						chr11:2034488|2036872
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr11: 2034489-2036872  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400016115						
					
						Parent gene annotation
						
							Cinnamyl alcohol dehydrogenase
							
						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-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
						PGSC0003DMT400041577:1
PGSC0003DMT400041578:3
PGSC0003DMT400041576:3
PGSC0003DMT400041579:3

General Information
CircRNA Name	PGSC0003DMG400016115_circ_g.1
ID in PlantcircBase	stu_circ_001510
Alias	chr11:2034488\|2036872
Organism	Solanum tuberosum
Position	chr11: 2034489-2036872 JBrowse»
Reference genome	3.0.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400016115
Parent gene annotation	Cinnamyl alcohol dehydrogenase
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-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	PGSC0003DMT400041577:1 PGSC0003DMT400041578:3 PGSC0003DMT400041576:3 PGSC0003DMT400041579:3

			
						 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  
						
							AGGATGTCAAATTGAAGGTTCTTTACTGTGGTATCTGTCATTCTGATATTCATCAGCTGAAGAA
TGAATGGGGATCTTCTCTATACCCTCCAGTCCCCGGcatgagattgtgggtgaagtaactgagg
ttggtagcaaggtggagaaattcaaacttggagataaagctggtgtggggtgtctagttggatc
atgtcgat

									
								

					

						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
						
							CATGAGATTGTGGGTGAAGTAACTGAGGTTGGTAGCAAGGTGGAGAAATTCAAACTTGGAGATA
AAGCTGGTGTGGGGTGTCTAGTTGGATCATGTCGATCTTGCGAAAACTGTAACAACGATATCGA
GAACTATTGTTCTAAGGGAATAGCCACCTATAGTGCAATGTACCATGATGGAACACCAACGTAC
GGAGGCTACTCGGACATAATCATTGTTGATGAACATTTCGTTGTTCGTGTCCCAGAAAACATGC
CCCTAGCTGCTGCAGCTCCTCTGCTTTGTGCTGGAATTACAACTTACAGCCCGTTGAGGTACTT
TGGACTTGATAAACCGGGGCTTCACGTTGGTGTAGTAGGTCTTGGTGGACTTGGTCATGTTGGT
GTTAAGTTTGCCAAGGCTTTAGGGGTAAAGGTGACGGTTATTAGTACGTCTCAAAGTAAACAGA
AGGAAGCTATTGAACGTCTCGGTGCTGATTCGTTTTTGATTAGCTCTGATCCGGATCAGCTACA
GGTAACTAAAATGAAAAACAAATGTGTATTGTCATAGAATAACGTCTCGTAGACTTGTAGTACT
AAACTATGGTTCTTGTATTCATAGGCTGCTATGGGCACAATGGATGGCATTCTTGATACAGTTG
CTGCTACTCACCCTGTCCTACCGTTGATCGGCCTATTGAAGACTAATGGGAAACTTATCATGCT
CGGTGGAGTGACAAAACCTCTCGACCTACCCGTCTTTCCATTACTTATGGGTGAGTACATTACT
CTTGCTATCTAGATTTTGACATGACCATACAAGGAATGTGTTTTAGTTCTTAGTTATAGTGTAA
ATAAGTCGAGAATCGTGTATTATGATAGGGAGGAAGCTCGTAGCTGGAAGTGGGATCGGAGGGA
TGAAAGAAACGCAAGAAATGATTGATTTTGCTGCAAAACACAATATAACAGCAGATATTGAAGT
CATTCCAATGGATTATGTCAATACTGCAATGGAACGTCTCGCTAAAGCTGATGTCAAGTATCGT
TTTGTCATTGACGTTGCTAAGACCCTCAAACCAGATGAGTAGACGACTATGAGTTCTTCTTCAT
GTAATTCTAGTATTTCATGATGTTTTGGGCGTTAAACGATGACTTTTGATTTCTTCTTGTGGAA
CATTACTAAAGAAAATGCATACATAATAAAGTTTGAGTGGCTTCTCAAATGTTGGAAACCAATT
GCAGTCTTTTATCTTCAATGATAAGTTCTGGTAATGAAGCAAGTTTCAGTTTTTCATACGCGGT
GAAAAGTATTAGGTGATTTCTTATTATAGAACATTTTCTCGGAACAAGTTACCTTGTACATTGT
GCTAGTGAGAGATAGTATATACCTGATGGATTAGTCGAGGTGCGAGAAAATTGGTCAAGATGCC
ATCGTCATCAAAAAAAAAAACATAGCAGGAGTATGGAGACAATGATATATGAGTTTTGCCACTT
TTGATACTTCAGAAAGATGAGTAAACTACAAGAAAAATCACAACTTCTTGATCTCATTCCCTTG
AACTAAAAATGAGGGTGTATATTTTATTTGTCAGTTTCAATGTCAACCATTGTTTGATGACCAA
CCAAGATTACGAGAGGGTACCTCCATCTTTAATCAGAGATTTCAAATTTCAGTATTCAAACAAG
TACTGAACAAAGAGCGGAAACTAAACAAAAATGTTTTGTTAGTCGCATAATTCTCAAGTCAATT
ATGAAGGCCAAATATGTTTTGTTTAAGGTCCATTCAAAAGAACACTTTTTAAAACTGACCAGTC
CATATTGACAACTCTAGTAGTAAACAAAGCAAATTTTTTAAAGAATTTAATTCCCTAAAAATTG
ACTAAATGCAATTTGTACCATACTTAAAACACCATAATAATATAGAGTTAATCACTTAACACTT
TAGTAAAAAAAAAAATCAAGAATGCACCCTGTTGAGGCTTTTGGTTGGGCTGCTAGAGACACTT
CTGGATTCCTTTCCCCATTCAACTTCTTTAGAAGGTATACATCCTTTTTATCATGTTTTTTTCC
TTAATAATAATGATGTTCATGACTATCAGAAACGTCTCTACGTACTTGTGGGACTACACTGGAT
ATGTTGTAGTTGTTGTTCACACTATAGTTGACTTCAACCACAACGTCCATCTAAACAATCAAAT
GTTTGGAATGGTCCCTCTTCTAGGACAAGATTTTGTTTGTGATCATCTTGATTAATGTTTGTAT
TCTTTCGGTTTTCAAATGATGTGGTTGCAGGGCAACGGGCGATAAGGATGTCAAATTGAAGGTT
CTTTACTGTGGTATCTGTCATTCTGATATTCATCAGCTGAAGAATGAATGGGGATCTTCTCTAT
ACCCTCCAGTCCCCGG
						
					

			
		

Sequences
Splice junction sequence	AGGATGTCAAATTGAAGGTTCTTTACTGTGGTATCTGTCATTCTGATATTCATCAGCTGAAGAA TGAATGGGGATCTTCTCTATACCCTCCAGTCCCCGGcatgagattgtgggtgaagtaactgagg ttggtagcaaggtggagaaattcaaacttggagataaagctggtgtggggtgtctagttggatc atgtcgat
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	CATGAGATTGTGGGTGAAGTAACTGAGGTTGGTAGCAAGGTGGAGAAATTCAAACTTGGAGATA AAGCTGGTGTGGGGTGTCTAGTTGGATCATGTCGATCTTGCGAAAACTGTAACAACGATATCGA GAACTATTGTTCTAAGGGAATAGCCACCTATAGTGCAATGTACCATGATGGAACACCAACGTAC GGAGGCTACTCGGACATAATCATTGTTGATGAACATTTCGTTGTTCGTGTCCCAGAAAACATGC CCCTAGCTGCTGCAGCTCCTCTGCTTTGTGCTGGAATTACAACTTACAGCCCGTTGAGGTACTT TGGACTTGATAAACCGGGGCTTCACGTTGGTGTAGTAGGTCTTGGTGGACTTGGTCATGTTGGT GTTAAGTTTGCCAAGGCTTTAGGGGTAAAGGTGACGGTTATTAGTACGTCTCAAAGTAAACAGA AGGAAGCTATTGAACGTCTCGGTGCTGATTCGTTTTTGATTAGCTCTGATCCGGATCAGCTACA GGTAACTAAAATGAAAAACAAATGTGTATTGTCATAGAATAACGTCTCGTAGACTTGTAGTACT AAACTATGGTTCTTGTATTCATAGGCTGCTATGGGCACAATGGATGGCATTCTTGATACAGTTG CTGCTACTCACCCTGTCCTACCGTTGATCGGCCTATTGAAGACTAATGGGAAACTTATCATGCT CGGTGGAGTGACAAAACCTCTCGACCTACCCGTCTTTCCATTACTTATGGGTGAGTACATTACT CTTGCTATCTAGATTTTGACATGACCATACAAGGAATGTGTTTTAGTTCTTAGTTATAGTGTAA ATAAGTCGAGAATCGTGTATTATGATAGGGAGGAAGCTCGTAGCTGGAAGTGGGATCGGAGGGA TGAAAGAAACGCAAGAAATGATTGATTTTGCTGCAAAACACAATATAACAGCAGATATTGAAGT CATTCCAATGGATTATGTCAATACTGCAATGGAACGTCTCGCTAAAGCTGATGTCAAGTATCGT TTTGTCATTGACGTTGCTAAGACCCTCAAACCAGATGAGTAGACGACTATGAGTTCTTCTTCAT GTAATTCTAGTATTTCATGATGTTTTGGGCGTTAAACGATGACTTTTGATTTCTTCTTGTGGAA CATTACTAAAGAAAATGCATACATAATAAAGTTTGAGTGGCTTCTCAAATGTTGGAAACCAATT GCAGTCTTTTATCTTCAATGATAAGTTCTGGTAATGAAGCAAGTTTCAGTTTTTCATACGCGGT GAAAAGTATTAGGTGATTTCTTATTATAGAACATTTTCTCGGAACAAGTTACCTTGTACATTGT GCTAGTGAGAGATAGTATATACCTGATGGATTAGTCGAGGTGCGAGAAAATTGGTCAAGATGCC ATCGTCATCAAAAAAAAAAACATAGCAGGAGTATGGAGACAATGATATATGAGTTTTGCCACTT TTGATACTTCAGAAAGATGAGTAAACTACAAGAAAAATCACAACTTCTTGATCTCATTCCCTTG AACTAAAAATGAGGGTGTATATTTTATTTGTCAGTTTCAATGTCAACCATTGTTTGATGACCAA CCAAGATTACGAGAGGGTACCTCCATCTTTAATCAGAGATTTCAAATTTCAGTATTCAAACAAG TACTGAACAAAGAGCGGAAACTAAACAAAAATGTTTTGTTAGTCGCATAATTCTCAAGTCAATT ATGAAGGCCAAATATGTTTTGTTTAAGGTCCATTCAAAAGAACACTTTTTAAAACTGACCAGTC CATATTGACAACTCTAGTAGTAAACAAAGCAAATTTTTTAAAGAATTTAATTCCCTAAAAATTG ACTAAATGCAATTTGTACCATACTTAAAACACCATAATAATATAGAGTTAATCACTTAACACTT TAGTAAAAAAAAAAATCAAGAATGCACCCTGTTGAGGCTTTTGGTTGGGCTGCTAGAGACACTT CTGGATTCCTTTCCCCATTCAACTTCTTTAGAAGGTATACATCCTTTTTATCATGTTTTTTTCC TTAATAATAATGATGTTCATGACTATCAGAAACGTCTCTACGTACTTGTGGGACTACACTGGAT ATGTTGTAGTTGTTGTTCACACTATAGTTGACTTCAACCACAACGTCCATCTAAACAATCAAAT GTTTGGAATGGTCCCTCTTCTAGGACAAGATTTTGTTTGTGATCATCTTGATTAATGTTTGTAT TCTTTCGGTTTTCAAATGATGTGGTTGCAGGGCAACGGGCGATAAGGATGTCAAATTGAAGGTT CTTTACTGTGGTATCTGTCATTCTGATATTCATCAGCTGAAGAATGAATGGGGATCTTCTCTAT ACCCTCCAGTCCCCGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12985819

Conservation Information
Conserved circRNAs	NA
PMCS	0.12985819

			
						 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 PGSC0003DMG400016115_circ_g.1

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