Plant Circular RNA Database

Detail information of PGSC0003DMG400006523_circ_ig.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400006523_circ_ig.1
					
						ID in PlantcircBase
						stu_circ_000504
					
						Alias
						chr04:4345377|4348417
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr4: 4345378-4348419  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							PGSC0003DMG400006524_circ_ig.1 PGSC0003DMG400006523_circ_ig.2 PGSC0003DMG400006523_circ_ig.3 						
					
						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  
						
							GA-GT							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	PGSC0003DMG400006523_circ_ig.1
ID in PlantcircBase	stu_circ_000504
Alias	chr04:4345377\|4348417
Organism	Solanum tuberosum
Position	chr4: 4345378-4348419 JBrowse»
Reference genome	3.0.38
Type	ig-circRNA
Identification method	CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	PGSC0003DMG400006524_circ_ig.1 PGSC0003DMG400006523_circ_ig.2 PGSC0003DMG400006523_circ_ig.3
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	GA-GT 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  
						
							ATTAAATATTCTTGAATATGCAGGAAAATCTGTAATTAGCAAGATGAACAAACTTGGAGAAAGG
ATGGACTGTCTTGCACAAGGCATCCGCGAGCATGGTgagccttagcccgaagctaacggaaact
gtgaagggaaaattgagcctcggagcgaaaattcttcaagttggagaagatattcaagcagaag
tgtagtgt

									
								

					

						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
						
							GAGCCTTAGCCCGAAGCTAACGGAAACTGTGAAGGGAAAATTGAGCCTCGGAGCGAAAATTCTT
CAAGTTGGAGAAGATATTCAAGCAGAAGTGTAGTGTTAGAAATGATGAAAAGTTATTAAAGGTT
TCTCAATCCTATTTTATCAACTACAGCTGGTCTAATAGCAGGCCTTCTCTTCATCTCTACCGAT
AAGATTGCTTTCTGCAGTGAGATTAATAAAGCTCATATCTCCAACAAGAAAGTTGCTTAGAATC
TACTACAAGGTACCACTCTGTTCCATTTTTCCTTCAACTCTTAATTTTCTAGCCACGTAAAGCA
TAATCTAATAGGCCGGTTCACAATTGCAGGTATCGATCCCAATAAGTAAGATAATGAAAGCAAA
AGAAAGTGAAAATAGGGAAAAGCCACCACAGAAGATGATTTTGAGTTCTGGTTTATGGGATTCC
TTAAGTATATACAAGTACTTACAGAAGAAGATAATTTTTTCTTTTTTTATTTTCATTTTGTTTC
CTAATAAGCCCATTCATCAATGTAATATGTTGATTCAAAAATGAATGTACAGATCTTTTCGAAC
TTGTAATTAGCTCCATTGCTCAAAGGAGGCTTTAGGCTTTGAGCTGTAGCTGTCAACACAAATG
TATAAACTTATTGTAAAACTAATGCAGTCAGCAGGCTAATTCACCTTCTGGGACTTGACATAGT
CATCACTTCCTCGAGAGACACATTTAAAATATTATGCTAAGGTTCAAACAAAGGGAGCTCCCCT
TGATTTTCCTTTTCACCTGGAGAAACATTTAGGCAAAATTTGCATAATTAATACCAAGTCTAGC
CCAAGTTCTGCTTGAGAATCTCTCTGTAAAAATATAATACCTTTGTCAATTCAAAATGTTTATT
GGAAACAGTCACCCTACCTCACACAAGGTAGGAGTAAGGTCTGCGTACACCCCAACCTCCCCAG
ACCCCACAGGTGGAATCACACCGGGTATGTTAACGTTGTTGTTGTAATTCATCAGAATATATAA
GAGGGCGTTGATCAATTCAATTACGCCATTGGAAAAGCACTTAGCATCTAACCCTTAGCACCAA
TTGAAACTCAAGGAGATTTCCATCTTCAGCTAAAGTATTCGGCTGAACATTGGAACAGTAACGA
GAAAAATACTCCACTACTCTACATGCATGAACTTAACATGCTTAAGCCTCTTTCATCCATCCCC
TTCATATCATCTCCATAGCATATTCACACTGCTCATAAGTTATAAAGAGCGTCTTATAAACCGT
TTGGTACTGTCAAATATCTCCAATTGCTTCAATAGTTCAAATCTCAAGTCGGGAATGAAGTTTT
GGCTGAATAGGAAATCCAACTGAAAATCTAAGATTTGAGAGTTAGATCATGTGTTATTATATTA
GGTGTAGCTTCAATCAAGTTAAAATGACTTACCTTGAGGAAGGGAAGAAATGAGGGAGATACAT
CTTCTTGCACAGAGAATCTAGAGAAGTGAAAAAAAATTATAGTTGTGTATCTGAGATACCTGTG
TTGCAACCGCAGGCCTTGTGCAGCAATCGCAACACTAAAGATTTGATAACCAAGGAAGAAAGTT
GTGATTGCGGTCCTTGTACCCGTGTAAAGAAGATCAAGTTGTCCCTTGCGAAAATCTTGATGCA
CTATCTCCCTTCAACCCTTTGGGTGAATGCAGCAAAATAAAAGGAAGGAATATCCATAGACCGA
CCCCATCATCTCCACCGTGTAGGAACTACGAGATCACCCAAAGACACTTTCGGCATCCAGGGGT
CACGGACCGACCATAGAACCGATTTAAATAAGTGGAACGCATTAACTGACCACTCTTAGGTTGG
GCAGTCAGGGTCGGAGAAGGGTAATGACTCATTCATAAAACCAGTGTTCTTAAGACCAAAGAGT
TGGGTGGAAAGGCAGAAGAAGATGTCATTCATTTGATTGAGAAATAAAAAGGAATACCAGAAAC
TCTCAATGTCAATGTCGACCAAACAGCCTTCACCGTTGGTTAGCACTATAAGCACAATGAATTC
CTTTACACCTCAAGATAAGATGACAAAAAAGGCAAGATAAGATGATAAAAAGGGCAAGATAAGG
TAACTGCCTTATAAGAGAAGCTAATATAATCTAGAACTGTTGGCCCTATGTAACAGATTGAAAT
ATTTGAATGGATCCTCTTTTTCCTTTGCCTGATTTATTAAGCAACAAATCAACGTTCATGGATG
ACTCATTCATGACCCACAACCACTACTTAACTTTAATGTCATATATAAATCCGTGTCATTATCT
TGTCAACCTTTGTCATACAAGACTAATAATTTTACTATGCACCAACAGCCTTCTCTTACTTTTA
CTCAACTTGTAAAAGCAGCTTACATCATAAAGAAAATCTTTCAACTCAAAAGTTGACAACACCA
CATGTGCACACAAATCTTGATAATAAACTAAGACAGCATGAGATAGTTTACTGTAATTAAAAAG
ACAGATAAAAGAAGACATTTTAAATATTCTATTTTGCTGACCCATAGCTGACTCATGCAACAGT
TAGTAGTTAAAAGATTCATCAACTTTGCCCAAACTGCTGTATATATATAGTGCTGCAAGGAATG
TTATTAAACCATTAACCATAATAATATCTCAGTTACCTTCACAATATAGCAACTCCCTCCAAAA
TCAGAAGTCACAATGAAGAACTTACTCGGTAGAAATGAGGTGGGTGTTACCATGAGTTCAGCAG
TATACTCATTTGAACGGCAGCCAAAAAGACTACTGTCTCTATCTGCTTGCCAAGACCATCTTCC
ATCTGCAACTTCAAAACACTTGCCTAAAATAAAGCAAAGTGAGTATTTTTCCCTCGAAGAATAA
TCGACGTGTTCTTGTATTAGTTATAAAGAGTATTAATGACCCTCTAAGAAGAGATCATTAAAAT
TAAATATTCTTGAATATGCAGGAAAATCTGTAATTAGCAAGATGAACAAACTTGGAGAAAGGAT
GGACTGTCTTGCACAAGGCATCCGCGAGCATGGT
						
					

			
		

Sequences
Splice junction sequence	ATTAAATATTCTTGAATATGCAGGAAAATCTGTAATTAGCAAGATGAACAAACTTGGAGAAAGG ATGGACTGTCTTGCACAAGGCATCCGCGAGCATGGTgagccttagcccgaagctaacggaaact gtgaagggaaaattgagcctcggagcgaaaattcttcaagttggagaagatattcaagcagaag tgtagtgt
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	GAGCCTTAGCCCGAAGCTAACGGAAACTGTGAAGGGAAAATTGAGCCTCGGAGCGAAAATTCTT CAAGTTGGAGAAGATATTCAAGCAGAAGTGTAGTGTTAGAAATGATGAAAAGTTATTAAAGGTT TCTCAATCCTATTTTATCAACTACAGCTGGTCTAATAGCAGGCCTTCTCTTCATCTCTACCGAT AAGATTGCTTTCTGCAGTGAGATTAATAAAGCTCATATCTCCAACAAGAAAGTTGCTTAGAATC TACTACAAGGTACCACTCTGTTCCATTTTTCCTTCAACTCTTAATTTTCTAGCCACGTAAAGCA TAATCTAATAGGCCGGTTCACAATTGCAGGTATCGATCCCAATAAGTAAGATAATGAAAGCAAA AGAAAGTGAAAATAGGGAAAAGCCACCACAGAAGATGATTTTGAGTTCTGGTTTATGGGATTCC TTAAGTATATACAAGTACTTACAGAAGAAGATAATTTTTTCTTTTTTTATTTTCATTTTGTTTC CTAATAAGCCCATTCATCAATGTAATATGTTGATTCAAAAATGAATGTACAGATCTTTTCGAAC TTGTAATTAGCTCCATTGCTCAAAGGAGGCTTTAGGCTTTGAGCTGTAGCTGTCAACACAAATG TATAAACTTATTGTAAAACTAATGCAGTCAGCAGGCTAATTCACCTTCTGGGACTTGACATAGT CATCACTTCCTCGAGAGACACATTTAAAATATTATGCTAAGGTTCAAACAAAGGGAGCTCCCCT TGATTTTCCTTTTCACCTGGAGAAACATTTAGGCAAAATTTGCATAATTAATACCAAGTCTAGC CCAAGTTCTGCTTGAGAATCTCTCTGTAAAAATATAATACCTTTGTCAATTCAAAATGTTTATT GGAAACAGTCACCCTACCTCACACAAGGTAGGAGTAAGGTCTGCGTACACCCCAACCTCCCCAG ACCCCACAGGTGGAATCACACCGGGTATGTTAACGTTGTTGTTGTAATTCATCAGAATATATAA GAGGGCGTTGATCAATTCAATTACGCCATTGGAAAAGCACTTAGCATCTAACCCTTAGCACCAA TTGAAACTCAAGGAGATTTCCATCTTCAGCTAAAGTATTCGGCTGAACATTGGAACAGTAACGA GAAAAATACTCCACTACTCTACATGCATGAACTTAACATGCTTAAGCCTCTTTCATCCATCCCC TTCATATCATCTCCATAGCATATTCACACTGCTCATAAGTTATAAAGAGCGTCTTATAAACCGT TTGGTACTGTCAAATATCTCCAATTGCTTCAATAGTTCAAATCTCAAGTCGGGAATGAAGTTTT GGCTGAATAGGAAATCCAACTGAAAATCTAAGATTTGAGAGTTAGATCATGTGTTATTATATTA GGTGTAGCTTCAATCAAGTTAAAATGACTTACCTTGAGGAAGGGAAGAAATGAGGGAGATACAT CTTCTTGCACAGAGAATCTAGAGAAGTGAAAAAAAATTATAGTTGTGTATCTGAGATACCTGTG TTGCAACCGCAGGCCTTGTGCAGCAATCGCAACACTAAAGATTTGATAACCAAGGAAGAAAGTT GTGATTGCGGTCCTTGTACCCGTGTAAAGAAGATCAAGTTGTCCCTTGCGAAAATCTTGATGCA CTATCTCCCTTCAACCCTTTGGGTGAATGCAGCAAAATAAAAGGAAGGAATATCCATAGACCGA CCCCATCATCTCCACCGTGTAGGAACTACGAGATCACCCAAAGACACTTTCGGCATCCAGGGGT CACGGACCGACCATAGAACCGATTTAAATAAGTGGAACGCATTAACTGACCACTCTTAGGTTGG GCAGTCAGGGTCGGAGAAGGGTAATGACTCATTCATAAAACCAGTGTTCTTAAGACCAAAGAGT TGGGTGGAAAGGCAGAAGAAGATGTCATTCATTTGATTGAGAAATAAAAAGGAATACCAGAAAC TCTCAATGTCAATGTCGACCAAACAGCCTTCACCGTTGGTTAGCACTATAAGCACAATGAATTC CTTTACACCTCAAGATAAGATGACAAAAAAGGCAAGATAAGATGATAAAAAGGGCAAGATAAGG TAACTGCCTTATAAGAGAAGCTAATATAATCTAGAACTGTTGGCCCTATGTAACAGATTGAAAT ATTTGAATGGATCCTCTTTTTCCTTTGCCTGATTTATTAAGCAACAAATCAACGTTCATGGATG ACTCATTCATGACCCACAACCACTACTTAACTTTAATGTCATATATAAATCCGTGTCATTATCT TGTCAACCTTTGTCATACAAGACTAATAATTTTACTATGCACCAACAGCCTTCTCTTACTTTTA CTCAACTTGTAAAAGCAGCTTACATCATAAAGAAAATCTTTCAACTCAAAAGTTGACAACACCA CATGTGCACACAAATCTTGATAATAAACTAAGACAGCATGAGATAGTTTACTGTAATTAAAAAG ACAGATAAAAGAAGACATTTTAAATATTCTATTTTGCTGACCCATAGCTGACTCATGCAACAGT TAGTAGTTAAAAGATTCATCAACTTTGCCCAAACTGCTGTATATATATAGTGCTGCAAGGAATG TTATTAAACCATTAACCATAATAATATCTCAGTTACCTTCACAATATAGCAACTCCCTCCAAAA TCAGAAGTCACAATGAAGAACTTACTCGGTAGAAATGAGGTGGGTGTTACCATGAGTTCAGCAG TATACTCATTTGAACGGCAGCCAAAAAGACTACTGTCTCTATCTGCTTGCCAAGACCATCTTCC ATCTGCAACTTCAAAACACTTGCCTAAAATAAAGCAAAGTGAGTATTTTTCCCTCGAAGAATAA TCGACGTGTTCTTGTATTAGTTATAAAGAGTATTAATGACCCTCTAAGAAGAGATCATTAAAAT TAAATATTCTTGAATATGCAGGAAAATCTGTAATTAGCAAGATGAACAAACTTGGAGAAAGGAT GGACTGTCTTGCACAAGGCATCCGCGAGCATGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.158418502

Conservation Information
Conserved circRNAs	NA
PMCS	0.158418502

			
						 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 PGSC0003DMG400006523_circ_ig.1

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