Plant Circular RNA Database

Detail information of PGSC0003DMG400000157_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400000157_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000125
					
						Alias
						chr01:71943913|71945851
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr1: 71943914-71945851  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400000157						
					
						Parent gene annotation
						
							Remorin 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							No-No							"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-GG							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
						PGSC0003DMT400000462:2

General Information
CircRNA Name	PGSC0003DMG400000157_circ_g.1
ID in PlantcircBase	stu_circ_000125
Alias	chr01:71943913\|71945851
Organism	Solanum tuberosum
Position	chr1: 71943914-71945851 JBrowse»
Reference genome	3.0.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400000157
Parent gene annotation	Remorin 2
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	stem
Exon boundary	No-No "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-GG 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	PGSC0003DMT400000462:2

			
						 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  
						
							TTGAAATTTAAGGAATAATTACTTGTTGGAGGAAGAGTAGCAAGAGCTTTAGAGTCATCAGTTT
TAGCCATGGCAGGAGGAGGTGGTAATTCTGGTTGAGgatccctttgaacttttctttgtagaag
agtcaggctctgccaaatcagtaaatgagaatacatcatcagtcgcggaatatttccctcgaga
cacaagca

									
								

					

						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
						
							GATCCCTTTGAACTTTTCTTTGTAGAAGAGTCAGGCTCTGCCAAATCAGTAAATGAGAATACAT
CATCAGTCGCGGAATATTTCCCTCGAGACACAAGCAGTTCATATATGTGCTTTCTCTACAACTT
TTCAATCAGAAATTAGTTACAAAAATCACAGAACTTCAAGAATGTGATCAGCCAAGTTAACACC
AATGATGCCCCCAAGGCCTAGCTCGAGTGGCAAAAGGTGGAGGATTTGCGGCTTAAGTCGCAAG
TTCAAGCCCCACACTACTCAAAGCGAAGTCCGATATTTAAGTGGAGAAGGGTAGAGGGGCGGGA
CTATTATCCACCGAGTTTAGAAGGCTGTGATTGGTCCAAAGGGCGGGTCACAAACGGATTTCTC
GATTATCAAAAAAAAGAAAAAGTTAACACCAATGATCTGTTTGAAATGCATCAAATTTTCATCA
TAACAATACTAGGAGATACTATTATCAACTTTCTATTTAAATGAAGGTTAGTGTCCGAGTCCGT
TTGTGTGCACCTCGATTATTCCATGTGGTACCTGCTATCCTACAAGTGCGGGTACCAAGTGACT
CTACAGTAGGTATCACCTACCCGCCTTCACTACAATCATTATCTACCAATGATTCCCAGAGTAC
TAATTCTTTTGATTAAGGTAAACCAGAGTGGCCATCCACTAATTCTATTGATTAAAGTTTAAAC
CAGACTGGCCATCCACTAATTAAGCAAGGCATCTAATCATATTGATTTATTTTTGCCAAAAAGT
AAAGGAGAGATATTGGACCTATTAATGATCTTTAAAAAACAGTATACCAAGTCTTTCCAATAAT
TCAACAGTTGTTAGGAGTATAAAGGCATCAAAATTAGTTGAGTCCAGCCAGATATGAACAATAA
TAGAATTAGATGCCTCAACTGAAAATAGATCGATTAATAATGACAAATAAAACACAACTCCATC
TTCAAGAATTTTAAATGAAGTGAAACAATACTTGCAATAATTTGTTGTATATGGGATCAAATCT
ATGATATTATGTGACTATCTATTTTGAGATATTACACTTTTACAAAAAAATTGATTGCATGTTT
GAGGTAAATTAGTTGAGTTACATGATTTTTCTAGTTTTTACATATTGCGAGGTATAAACCATAT
GTAATAAAAAGTACATTCGAATTCAACTTTTTAAAATTCCAAATGAAGTGAATATTTTTATTTA
TATACAGGCTATAACTCAATCATTTAATCATGATTAATTAATGTATATTTTTATATCGATATAT
TACCTAACCAACCATGTTTAACTGATTTTTGTCGGCTGAATAATTAACCTAAATCAGAATCTGG
CAGTAAAAAAGTTTATCTTTGGATGCTTTCTTTGTGATATTCAGATATTCAACAGATCCTATCA
AACTTCTCCAAGCATAATAAAAAGAATTAAGTTAATATAAAGGTTTAAAACCAAAAATTTAGAA
GAATCTTAGACATTCAGTTGGTTGGCTACCTACTTGAATTTTTACCTTCATATTGGTGAAAAAT
CTCGGTAGTTCAATTAGTTGGCTACCTACTTAGACTTTTACCTTGATATTGGTGAAGGTTGATT
AGAAGAATCACAGTAGTTCAACTGGTTGGCTACCTACTTAAACTTTTACCTTATTGATAAGGGT
TCGATTCTCCACCCCATTTCCAATATAGTGTTTTAGACCAACGATTTAACAATGAATAAACGAA
ATAAAAGATATCAATAGGGATATATATATATATAGGTCATACCAATATTTAACAGGCACAAATT
GGAGTTTTAGAATTTGACGATAATTAAAACAGAGATATATAGAGGTTTGAAATTTAAGGAATAA
TTACTTGTTGGAGGAAGAGTAGCAAGAGCTTTAGAGTCATCAGTTTTAGCCATGGCAGGAGGAG
GTGGTAATTCTGGTTGAG
						
					

			
		

Sequences
Splice junction sequence	TTGAAATTTAAGGAATAATTACTTGTTGGAGGAAGAGTAGCAAGAGCTTTAGAGTCATCAGTTT TAGCCATGGCAGGAGGAGGTGGTAATTCTGGTTGAGgatccctttgaacttttctttgtagaag agtcaggctctgccaaatcagtaaatgagaatacatcatcagtcgcggaatatttccctcgaga cacaagca
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	GATCCCTTTGAACTTTTCTTTGTAGAAGAGTCAGGCTCTGCCAAATCAGTAAATGAGAATACAT CATCAGTCGCGGAATATTTCCCTCGAGACACAAGCAGTTCATATATGTGCTTTCTCTACAACTT TTCAATCAGAAATTAGTTACAAAAATCACAGAACTTCAAGAATGTGATCAGCCAAGTTAACACC AATGATGCCCCCAAGGCCTAGCTCGAGTGGCAAAAGGTGGAGGATTTGCGGCTTAAGTCGCAAG TTCAAGCCCCACACTACTCAAAGCGAAGTCCGATATTTAAGTGGAGAAGGGTAGAGGGGCGGGA CTATTATCCACCGAGTTTAGAAGGCTGTGATTGGTCCAAAGGGCGGGTCACAAACGGATTTCTC GATTATCAAAAAAAAGAAAAAGTTAACACCAATGATCTGTTTGAAATGCATCAAATTTTCATCA TAACAATACTAGGAGATACTATTATCAACTTTCTATTTAAATGAAGGTTAGTGTCCGAGTCCGT TTGTGTGCACCTCGATTATTCCATGTGGTACCTGCTATCCTACAAGTGCGGGTACCAAGTGACT CTACAGTAGGTATCACCTACCCGCCTTCACTACAATCATTATCTACCAATGATTCCCAGAGTAC TAATTCTTTTGATTAAGGTAAACCAGAGTGGCCATCCACTAATTCTATTGATTAAAGTTTAAAC CAGACTGGCCATCCACTAATTAAGCAAGGCATCTAATCATATTGATTTATTTTTGCCAAAAAGT AAAGGAGAGATATTGGACCTATTAATGATCTTTAAAAAACAGTATACCAAGTCTTTCCAATAAT TCAACAGTTGTTAGGAGTATAAAGGCATCAAAATTAGTTGAGTCCAGCCAGATATGAACAATAA TAGAATTAGATGCCTCAACTGAAAATAGATCGATTAATAATGACAAATAAAACACAACTCCATC TTCAAGAATTTTAAATGAAGTGAAACAATACTTGCAATAATTTGTTGTATATGGGATCAAATCT ATGATATTATGTGACTATCTATTTTGAGATATTACACTTTTACAAAAAAATTGATTGCATGTTT GAGGTAAATTAGTTGAGTTACATGATTTTTCTAGTTTTTACATATTGCGAGGTATAAACCATAT GTAATAAAAAGTACATTCGAATTCAACTTTTTAAAATTCCAAATGAAGTGAATATTTTTATTTA TATACAGGCTATAACTCAATCATTTAATCATGATTAATTAATGTATATTTTTATATCGATATAT TACCTAACCAACCATGTTTAACTGATTTTTGTCGGCTGAATAATTAACCTAAATCAGAATCTGG CAGTAAAAAAGTTTATCTTTGGATGCTTTCTTTGTGATATTCAGATATTCAACAGATCCTATCA AACTTCTCCAAGCATAATAAAAAGAATTAAGTTAATATAAAGGTTTAAAACCAAAAATTTAGAA GAATCTTAGACATTCAGTTGGTTGGCTACCTACTTGAATTTTTACCTTCATATTGGTGAAAAAT CTCGGTAGTTCAATTAGTTGGCTACCTACTTAGACTTTTACCTTGATATTGGTGAAGGTTGATT AGAAGAATCACAGTAGTTCAACTGGTTGGCTACCTACTTAAACTTTTACCTTATTGATAAGGGT TCGATTCTCCACCCCATTTCCAATATAGTGTTTTAGACCAACGATTTAACAATGAATAAACGAA ATAAAAGATATCAATAGGGATATATATATATATAGGTCATACCAATATTTAACAGGCACAAATT GGAGTTTTAGAATTTGACGATAATTAAAACAGAGATATATAGAGGTTTGAAATTTAAGGAATAA TTACTTGTTGGAGGAAGAGTAGCAAGAGCTTTAGAGTCATCAGTTTTAGCCATGGCAGGAGGAG GTGGTAATTCTGGTTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.15171213

Conservation Information
Conserved circRNAs	NA
PMCS	0.15171213

			
						 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 PGSC0003DMG400000157_circ_g.1

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