Plant Circular RNA Database

Detail information of PGSC0003DMG402032161_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG402032161_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000013
					
						Alias
						chr01:1043880|1046571
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr1: 1043881-1046571  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG402032161						
					
						Parent gene annotation
						
							Iaa-amino acid hydrolase 4
							
						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
						PGSC0003DMT400081929:2
PGSC0003DMT400081932:1
PGSC0003DMT400081930:1
PGSC0003DMT400081928:1
PGSC0003DMT400081931:3

General Information
CircRNA Name	PGSC0003DMG402032161_circ_g.1
ID in PlantcircBase	stu_circ_000013
Alias	chr01:1043880\|1046571
Organism	Solanum tuberosum
Position	chr1: 1043881-1046571 JBrowse»
Reference genome	3.0.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG402032161
Parent gene annotation	Iaa-amino acid hydrolase 4
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	PGSC0003DMT400081929:2 PGSC0003DMT400081932:1 PGSC0003DMT400081930:1 PGSC0003DMT400081928:1 PGSC0003DMT400081931:3

			
						 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  
						
							GCAATCTAGCTGCTCCAAGCAACATGGTGACATGAGCGTCATGGCCGCAGGCATGCATTTTGCC
ATTGATCTTGCTTTTGTACTCTGAATCTACCAATTCtgcatagggagagcatccatttcagctc
tcaaaccaaaccatggttgatgacccgacccgacagttccaaccagacccgttttcgctactgg
tgatacat

									
								

					

						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
						
							TGCATAGGGAGAGCATCCATTTCAGCTCTCAAACCAAACCATGGTTGATGACCCGACCCGACAG
TTCCAACCAGACCCGTTTTCGCTACTGGTGATACATACTCAATCCCCAGCAAATCCAGTTCATC
TCGAATGAATTGACTCGTTTTGTGTTCTTCAAAAGCCAATTCTGGGTACTCATGGATTCTCCTC
CGAACCCTTTTTAACCAATCGAAAAACTCCGGCTGCTTCGCCGATTCAAGAAGTTCCTGAGTTA
GCAACTTAGTTTCAGATCTCAAAAGGGTCTCTTTTACAGCCCATGAATTGTATGAAAAACTTGT
TAATACCAATAGAATGTACATACAGAGGAAGAAGATCAAGTTTGTGCTAAATGGACCCATCAAT
GGCACACCAAAATGTGATGTGTTGACTCTTGAAGCTCATTTTGTCGAAAACATCAATGACAACT
AAATAATAATAAGAAATTACACTAAAATATTAACTACTTGCATTTCCTCGACTTATAATTAATA
TGCCTATGTATGTGTTCTTTAGTTTGAATATTCAGTTGTCTTAAATTGGCAAAGGTTAATGGAC
TTATCATAGGTCACGAGTTCAAGCCCTGCGTCAAGGAACCAAGTTCAGAATTTAAACGGAGAAT
CGAAGGATGTGGTTAGCCCAGAAGTGGCTCCACATGGACTTTTTGTTCATTAAAATCAAAATAT
ATTTCATTTACAAATGGGATGATTCTTCAATCTCCAAAAATGTATAATTCTACTATGTCTGAAC
ATGTGTATCAAAATAAGAAATGGCAACAGCAGCATGGAGGGCTGCACCTATTGGAAGAACATCT
TCATCAAGAGTGAAGTAAGGGGAGTGTAAACCTTTAACACCAGTCGCGGTGGCCGTTTCATTTT
GTGATCCGATGATAAAAAAAGCAGCAGGCATCTTCTGGGAATAGAAGCTGAAGTCCTCTGCACC
CATTGTAATTGAGGCATACTGCACGTTTTGCTCACCGAGCAAGACTTCTCCAACTTTCTTAGCA
TGCTCGTACATTGTGGGGTCGTTTACAGTTGGTGGATATGGCCTCAGTAAGTCCTCCGCGAAAT
CAACAGTGGCTGAACACTGATGTACACTTGCTTGTGTCTCGATGATCTACGAGTAGTGTTAATC
ATCTAAATCAATGCTTATTATGAGTAATGCTGAAGATTTCTGGAAAATTAAAGCACAAGTTTTT
GCAAAATGGTATGTTTAACTTCTATGACCTGATATTACAGATGAGGTTTATCAAACCTACAGTT
GATAAAGAAGTTCAAGGAAGATTCAACGATCATCTAAGACTTTGAGGGGAGTAATTGATTTATC
GCCTTTTCGTCGAACTTCCAAATCTGATTATTCTGAAAGTACTTGTGATTTTCGATTTGGAGAA
CACTTGTGCCTATATTGGAGTAGTAATTTGTACTTGGCCAAGGTTCTAAATATGTTCCAAGGAA
AAACTAGTTTTTTTAGCTTCTGAAAAACGACTTCTGCTATTACTCATGAAACATTTAATTTCTT
CCTAAAATCTTGGTCAAACACCTCAACTTTCTAAAATAAGTACTTTTGGCTTCCCAAAAGCTTG
GTTAGATAGGCTATTAGTAGCAGCGAAACTCTAGTGCATACCTCTTTGATCCTTTGCTTAAGAT
AGGAATGACCCTCAAACGTCATGAACCGGAACGTTCCACCAAATTTCACACTTTCAGGGATTAC
ATTTCCAGCCTCACCACCATCTACAAATGCAACAGAGACAACCTGCATGTAATTGCGCATAAGC
AGAAACATAATTTAGATCCTGCTTCATGGAATCCAGCATTCTGAACGGAGAAGTAAAATCATAA
TGCTCAAAAACACATTTAAAGTATCCCAATTTTTTTAGTTTCCTACCTGAACTATCACGGTATC
ACCAACTATTAATCAAAACACCACCTCAACTATCAGCTGTTCCCTTTTCCTACTTGAAATATCA
CCATCGTTCAGGTAGGAAAAGAGAGCAATTGATAGTTGAGGGGTGCTTTGATAAATAGTTGATG
ACAGTTCAGGTTGAAACTCGAAAAACCGGGATACTTTAAGCATGTTTTTGACCCTTCACTCTTG
TTTTAACTGTTTGGAATCAGAGCGAGACATACCCTAGACTCGAGAGGATCAGTTTCTCGGGAAA
CAAGTTGCTGGAGTGCAAGAACTGCCATAGAAACAGCAAGAATAGGATCCTTAGTTCTATGTGG
TGTTGCTGCATGTCCACCTTTCCCTTGCCATTATTGCTGTAAACCTTCCTGCACCAGCCATAAT
AGGACCAGGTCTTGAACCAATAATACCAGTGGGAATAAATGGCCAGACATGCATGCCAAATATT
GCTTTAACCCCATCTAATGCTCCTTCTTCTATCATATAGGAGGCTCCAGCATAGCCTTCTTCTG
CAGGCTGGAAGACTAGCTTAACCGTGCCCTACAGTTCAGAGCGCAAAATACCCATATCAACTTA
TTGAATTTAGACGAAGACCAAAAGTGGTAAGTTCATATCAAAAGACAAAACAATAACGAGTTTT
CCTACCTTCAACTTGTCCCTTCTATTTTGAAGCAATCTAGCTGCTCCAAGCAACATGGTGACAT
GAGCGTCATGGCCGCAGGCATGCATTTTGCCATTGATCTTGCTTTTGTACTCTGAATCTACCAA
TTC
						
					

			
		

Sequences
Splice junction sequence	GCAATCTAGCTGCTCCAAGCAACATGGTGACATGAGCGTCATGGCCGCAGGCATGCATTTTGCC ATTGATCTTGCTTTTGTACTCTGAATCTACCAATTCtgcatagggagagcatccatttcagctc tcaaaccaaaccatggttgatgacccgacccgacagttccaaccagacccgttttcgctactgg tgatacat
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	TGCATAGGGAGAGCATCCATTTCAGCTCTCAAACCAAACCATGGTTGATGACCCGACCCGACAG TTCCAACCAGACCCGTTTTCGCTACTGGTGATACATACTCAATCCCCAGCAAATCCAGTTCATC TCGAATGAATTGACTCGTTTTGTGTTCTTCAAAAGCCAATTCTGGGTACTCATGGATTCTCCTC CGAACCCTTTTTAACCAATCGAAAAACTCCGGCTGCTTCGCCGATTCAAGAAGTTCCTGAGTTA GCAACTTAGTTTCAGATCTCAAAAGGGTCTCTTTTACAGCCCATGAATTGTATGAAAAACTTGT TAATACCAATAGAATGTACATACAGAGGAAGAAGATCAAGTTTGTGCTAAATGGACCCATCAAT GGCACACCAAAATGTGATGTGTTGACTCTTGAAGCTCATTTTGTCGAAAACATCAATGACAACT AAATAATAATAAGAAATTACACTAAAATATTAACTACTTGCATTTCCTCGACTTATAATTAATA TGCCTATGTATGTGTTCTTTAGTTTGAATATTCAGTTGTCTTAAATTGGCAAAGGTTAATGGAC TTATCATAGGTCACGAGTTCAAGCCCTGCGTCAAGGAACCAAGTTCAGAATTTAAACGGAGAAT CGAAGGATGTGGTTAGCCCAGAAGTGGCTCCACATGGACTTTTTGTTCATTAAAATCAAAATAT ATTTCATTTACAAATGGGATGATTCTTCAATCTCCAAAAATGTATAATTCTACTATGTCTGAAC ATGTGTATCAAAATAAGAAATGGCAACAGCAGCATGGAGGGCTGCACCTATTGGAAGAACATCT TCATCAAGAGTGAAGTAAGGGGAGTGTAAACCTTTAACACCAGTCGCGGTGGCCGTTTCATTTT GTGATCCGATGATAAAAAAAGCAGCAGGCATCTTCTGGGAATAGAAGCTGAAGTCCTCTGCACC CATTGTAATTGAGGCATACTGCACGTTTTGCTCACCGAGCAAGACTTCTCCAACTTTCTTAGCA TGCTCGTACATTGTGGGGTCGTTTACAGTTGGTGGATATGGCCTCAGTAAGTCCTCCGCGAAAT CAACAGTGGCTGAACACTGATGTACACTTGCTTGTGTCTCGATGATCTACGAGTAGTGTTAATC ATCTAAATCAATGCTTATTATGAGTAATGCTGAAGATTTCTGGAAAATTAAAGCACAAGTTTTT GCAAAATGGTATGTTTAACTTCTATGACCTGATATTACAGATGAGGTTTATCAAACCTACAGTT GATAAAGAAGTTCAAGGAAGATTCAACGATCATCTAAGACTTTGAGGGGAGTAATTGATTTATC GCCTTTTCGTCGAACTTCCAAATCTGATTATTCTGAAAGTACTTGTGATTTTCGATTTGGAGAA CACTTGTGCCTATATTGGAGTAGTAATTTGTACTTGGCCAAGGTTCTAAATATGTTCCAAGGAA AAACTAGTTTTTTTAGCTTCTGAAAAACGACTTCTGCTATTACTCATGAAACATTTAATTTCTT CCTAAAATCTTGGTCAAACACCTCAACTTTCTAAAATAAGTACTTTTGGCTTCCCAAAAGCTTG GTTAGATAGGCTATTAGTAGCAGCGAAACTCTAGTGCATACCTCTTTGATCCTTTGCTTAAGAT AGGAATGACCCTCAAACGTCATGAACCGGAACGTTCCACCAAATTTCACACTTTCAGGGATTAC ATTTCCAGCCTCACCACCATCTACAAATGCAACAGAGACAACCTGCATGTAATTGCGCATAAGC AGAAACATAATTTAGATCCTGCTTCATGGAATCCAGCATTCTGAACGGAGAAGTAAAATCATAA TGCTCAAAAACACATTTAAAGTATCCCAATTTTTTTAGTTTCCTACCTGAACTATCACGGTATC ACCAACTATTAATCAAAACACCACCTCAACTATCAGCTGTTCCCTTTTCCTACTTGAAATATCA CCATCGTTCAGGTAGGAAAAGAGAGCAATTGATAGTTGAGGGGTGCTTTGATAAATAGTTGATG ACAGTTCAGGTTGAAACTCGAAAAACCGGGATACTTTAAGCATGTTTTTGACCCTTCACTCTTG TTTTAACTGTTTGGAATCAGAGCGAGACATACCCTAGACTCGAGAGGATCAGTTTCTCGGGAAA CAAGTTGCTGGAGTGCAAGAACTGCCATAGAAACAGCAAGAATAGGATCCTTAGTTCTATGTGG TGTTGCTGCATGTCCACCTTTCCCTTGCCATTATTGCTGTAAACCTTCCTGCACCAGCCATAAT AGGACCAGGTCTTGAACCAATAATACCAGTGGGAATAAATGGCCAGACATGCATGCCAAATATT GCTTTAACCCCATCTAATGCTCCTTCTTCTATCATATAGGAGGCTCCAGCATAGCCTTCTTCTG CAGGCTGGAAGACTAGCTTAACCGTGCCCTACAGTTCAGAGCGCAAAATACCCATATCAACTTA TTGAATTTAGACGAAGACCAAAAGTGGTAAGTTCATATCAAAAGACAAAACAATAACGAGTTTT CCTACCTTCAACTTGTCCCTTCTATTTTGAAGCAATCTAGCTGCTCCAAGCAACATGGTGACAT GAGCGTCATGGCCGCAGGCATGCATTTTGCCATTGATCTTGCTTTTGTACTCTGAATCTACCAA TTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.107463229

Conservation Information
Conserved circRNAs	NA
PMCS	0.107463229

			
						 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 PGSC0003DMG402032161_circ_g.1

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