Plant Circular RNA Database

Detail information of PGSC0003DMG400025108_circ_ag.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400025108_circ_ag.1
					
						ID in PlantcircBase
						stu_circ_000680
					
						Alias
						chr05:1688543|1699389
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr5: 1688544-1690959  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
						
							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  
						
							TA-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	PGSC0003DMG400025108_circ_ag.1
ID in PlantcircBase	stu_circ_000680
Alias	chr05:1688543\|1699389
Organism	Solanum tuberosum
Position	chr5: 1688544-1690959 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	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	TA-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  
						
							TGTTTAAATATATATGTTGCTGGACAATTGTATGTTTGGATATTCTAAAATTGCTTACTCCATG
ATAGATCTTCAATGGAGTTAAGCTAGTAATAAATAAagaagatagaaaagtccctcaaggaagt
ttaccatatcgtccatcacaaaaagaaccaatatgcaagaagaatataattggcaaatgtattg
ccaataag

									
								

					

						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
						
							AGAAGATAGAAAAGTCCCTCAAGGAAGTTTACCATATCGTCCATCACAAAAAGAACCAATATGC
AAGAAGAATATAATTGGCAAATGTATTGCCAATAAGAAACCGCCACGTATTGAAAAACCCTGCA
AGAGTTTAACCAACTGTCATAAAATGAAACCATAAAAAAGAGGTAGTGTACTAAAAATAAAATA
TGAGTATGTGTGTTTTTTAACCGTAGTTTTGAAGCAATAGAAAAATTATCTTCGTGTAATCTAT
AAGTTATGAATTTGAATAGTAATTAAAATTAGTCATTAATATTTGTATTAGCGTAAGTGCTATG
GGTGTGGACGTGTGGTCATTCTCCAAGTCCTGCTCATATGAGATGTTTTATGTAGTGGACTATT
TTTTTCTATATGTATGAGTTTAATTTATTACCAGTACTATTGTGTTGTATTTTCTTTTGGGATT
TCTCAATGATGTACCACTATACTCAGTGACGGAGCCAGAATTTTTAATAAGGGGATTCAATATC
TGAGAAGTAAACACACGAACTAGTGGAAGGGGATTCGACATCTATTATACATACCTAAAAAATA
ATTTTAACCATATATAAATACTATTTTTTTCCGCCGAGGAGGTTCGGATGAAACCCAAGTATAT
GTTGCCTCCGCCCTGACTATACTCGATGCTTTGTATCAATAAGATGTATGAAATATCATTAATA
CATATATGGATGAAGTATACTTTATATTAAATAAAAATAAAAATATGCTTATATTATACATATA
ATATATACAGAATACATACAACTACAATATATAAACAATGTATACTTCAATCATAATAATAAAC
TAATTAGCCGAAGGATATATTTACGTAAGTTCCTTAAACGCTAGCCCAAGAATCCAAGTCACTA
CGATAATAAAATAATTTTTAGCGGTAATAAATACATTAACAAAGAGTGTTAAAACATTTACCAG
CATTAATTAATTGTTATTAGATCCAATATTGCGATGAACTTTAGAAACATTTATAAAAAGTGTT
AATTACTTTTGAAAAGTAATGATAATTAAGCAATTGTCATACATATATTCCACCAAACGAGTCT
TAAATGTTAGCCAAAAGACTCCAAGTCAAGCACCAAAAAGAAAAAATTAAAGTGAAATTTATTT
TATTTTTCTACATTAAAGGGTCCACACGTTTATGAATGTTCCATTGAGAAATATTATAAAAGGA
CTAGAATATAAGCTTATTGATTCATATAATATAACATAAATCACCTCATATAAGAGAATTAATT
CCCCTTTGATCTCCATGAATCACAAAGCATTATTTTTAGCTTGTTTTGTCATAATCCTCTGTCT
ATCTTCAACAACCTCTAGGAGATTGCCAGGTGTAGTATTAATCCCTTTATTGTAATGTAATGTA
AGGGCGGAGCTAGATAAGGTCGAGACTCGAGAGGGTTCGTCCAAATCCTCTTCAGTAAAAAAAA
TTACATTGTTTATATATATATATATATATATATATATATATCTTTTAATTTGATCAATCGGCTT
AAATTTATGCTCTCCAATTTTGAATGTGCATACATAGACACTTAAACTTGTGTAAAATTGTACT
CATAAACACATATATCCTACATGATAATTCATGTGAGATACACTCCCATTGACACACGTAAGAG
CTAAATTTGTATAAGTTTAAGTGTCTACTTGTGCACACCCAAAACTGAACGGCAATATATCAGC
TGAAAATTGAAATCAAGTTAGAGAACATGTTTATGTATTATGCTTTTTAGAATTTGAAAGTATA
AACCATATTTAGAAAAAGTGTATTCAAATTCTAAATATGTTTTATAAAATATAATCAAACACAA
CTCAACATAAAAAAAAATGTATTTGTTTTTCATAGTTAGCCAATTCAAACAAGTGTTTCAATTT
TTATAGTACTTTTTTCGAATTTAAATATTACTTGTATATGTATAATTTAATTCCTCTCTGAATA
TAGGTTATAGATGTGGTGGCTATAAATATGGAGAAGAATCGTGTTCACCACGTAGATCACTCTT
TGTAGTTCGTATGAGACCAGTAATCGCACCTCGAAAGCCAATATCACCACCTGGTAAAAATTTT
ACGTAAAATCTGTTATTTTATCTGTCTCAATTTTAAAAAGTTTTTTAAAATAAAAAATATATTT
ATTTACGTATTATGTCTAAAAATTATTTACGCTAACAATATTTACACCCTTTCATCTTTACATG
TTTGCAGATAATGGATCTTGAGAAGAGTTTGAGTAACAAAAAAAAAATATTAAGCAAGAATTTT
ATATTGTATTTATGTTTAAATATATATGTTGCTGGACAATTGTATGTTTGGATATTCTAAAATT
GCTTACTCCATGATAGATCTTCAATGGAGTTAAGCTAGTAATAAATAA
						
					

			
		

Sequences
Splice junction sequence	TGTTTAAATATATATGTTGCTGGACAATTGTATGTTTGGATATTCTAAAATTGCTTACTCCATG ATAGATCTTCAATGGAGTTAAGCTAGTAATAAATAAagaagatagaaaagtccctcaaggaagt ttaccatatcgtccatcacaaaaagaaccaatatgcaagaagaatataattggcaaatgtattg ccaataag
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	AGAAGATAGAAAAGTCCCTCAAGGAAGTTTACCATATCGTCCATCACAAAAAGAACCAATATGC AAGAAGAATATAATTGGCAAATGTATTGCCAATAAGAAACCGCCACGTATTGAAAAACCCTGCA AGAGTTTAACCAACTGTCATAAAATGAAACCATAAAAAAGAGGTAGTGTACTAAAAATAAAATA TGAGTATGTGTGTTTTTTAACCGTAGTTTTGAAGCAATAGAAAAATTATCTTCGTGTAATCTAT AAGTTATGAATTTGAATAGTAATTAAAATTAGTCATTAATATTTGTATTAGCGTAAGTGCTATG GGTGTGGACGTGTGGTCATTCTCCAAGTCCTGCTCATATGAGATGTTTTATGTAGTGGACTATT TTTTTCTATATGTATGAGTTTAATTTATTACCAGTACTATTGTGTTGTATTTTCTTTTGGGATT TCTCAATGATGTACCACTATACTCAGTGACGGAGCCAGAATTTTTAATAAGGGGATTCAATATC TGAGAAGTAAACACACGAACTAGTGGAAGGGGATTCGACATCTATTATACATACCTAAAAAATA ATTTTAACCATATATAAATACTATTTTTTTCCGCCGAGGAGGTTCGGATGAAACCCAAGTATAT GTTGCCTCCGCCCTGACTATACTCGATGCTTTGTATCAATAAGATGTATGAAATATCATTAATA CATATATGGATGAAGTATACTTTATATTAAATAAAAATAAAAATATGCTTATATTATACATATA ATATATACAGAATACATACAACTACAATATATAAACAATGTATACTTCAATCATAATAATAAAC TAATTAGCCGAAGGATATATTTACGTAAGTTCCTTAAACGCTAGCCCAAGAATCCAAGTCACTA CGATAATAAAATAATTTTTAGCGGTAATAAATACATTAACAAAGAGTGTTAAAACATTTACCAG CATTAATTAATTGTTATTAGATCCAATATTGCGATGAACTTTAGAAACATTTATAAAAAGTGTT AATTACTTTTGAAAAGTAATGATAATTAAGCAATTGTCATACATATATTCCACCAAACGAGTCT TAAATGTTAGCCAAAAGACTCCAAGTCAAGCACCAAAAAGAAAAAATTAAAGTGAAATTTATTT TATTTTTCTACATTAAAGGGTCCACACGTTTATGAATGTTCCATTGAGAAATATTATAAAAGGA CTAGAATATAAGCTTATTGATTCATATAATATAACATAAATCACCTCATATAAGAGAATTAATT CCCCTTTGATCTCCATGAATCACAAAGCATTATTTTTAGCTTGTTTTGTCATAATCCTCTGTCT ATCTTCAACAACCTCTAGGAGATTGCCAGGTGTAGTATTAATCCCTTTATTGTAATGTAATGTA AGGGCGGAGCTAGATAAGGTCGAGACTCGAGAGGGTTCGTCCAAATCCTCTTCAGTAAAAAAAA TTACATTGTTTATATATATATATATATATATATATATATATCTTTTAATTTGATCAATCGGCTT AAATTTATGCTCTCCAATTTTGAATGTGCATACATAGACACTTAAACTTGTGTAAAATTGTACT CATAAACACATATATCCTACATGATAATTCATGTGAGATACACTCCCATTGACACACGTAAGAG CTAAATTTGTATAAGTTTAAGTGTCTACTTGTGCACACCCAAAACTGAACGGCAATATATCAGC TGAAAATTGAAATCAAGTTAGAGAACATGTTTATGTATTATGCTTTTTAGAATTTGAAAGTATA AACCATATTTAGAAAAAGTGTATTCAAATTCTAAATATGTTTTATAAAATATAATCAAACACAA CTCAACATAAAAAAAAATGTATTTGTTTTTCATAGTTAGCCAATTCAAACAAGTGTTTCAATTT TTATAGTACTTTTTTCGAATTTAAATATTACTTGTATATGTATAATTTAATTCCTCTCTGAATA TAGGTTATAGATGTGGTGGCTATAAATATGGAGAAGAATCGTGTTCACCACGTAGATCACTCTT TGTAGTTCGTATGAGACCAGTAATCGCACCTCGAAAGCCAATATCACCACCTGGTAAAAATTTT ACGTAAAATCTGTTATTTTATCTGTCTCAATTTTAAAAAGTTTTTTAAAATAAAAAATATATTT ATTTACGTATTATGTCTAAAAATTATTTACGCTAACAATATTTACACCCTTTCATCTTTACATG TTTGCAGATAATGGATCTTGAGAAGAGTTTGAGTAACAAAAAAAAAATATTAAGCAAGAATTTT ATATTGTATTTATGTTTAAATATATATGTTGCTGGACAATTGTATGTTTGGATATTCTAAAATT GCTTACTCCATGATAGATCTTCAATGGAGTTAAGCTAGTAATAAATAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.106047137

Conservation Information
Conserved circRNAs	NA
PMCS	0.106047137

			
						 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 PGSC0003DMG400025108_circ_ag.1

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