Plant Circular RNA Database

Detail information of PGSC0003DMG400026820_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400026820_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000944
					
						Alias
						chr07:49556671|49560239
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr7: 49556672-49560239  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							PGSC0003DMG400026820						
					
						Parent gene annotation
						
							Aminotransferase family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							PGSC0003DMG400026820_circ_igg.1 PGSC0003DMG400026820_circ_igg.2 PGSC0003DMG400026820_circ_igg.3 						
					
						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-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
						PGSC0003DMT400068953:1
PGSC0003DMT400068955:1
PGSC0003DMT400068957:6

General Information
CircRNA Name	PGSC0003DMG400026820_circ_g.1
ID in PlantcircBase	stu_circ_000944
Alias	chr07:49556671\|49560239
Organism	Solanum tuberosum
Position	chr7: 49556672-49560239 JBrowse»
Reference genome	3.0.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	PGSC0003DMG400026820
Parent gene annotation	Aminotransferase family protein
Parent gene strand	+
Alternative splicing	PGSC0003DMG400026820_circ_igg.1 PGSC0003DMG400026820_circ_igg.2 PGSC0003DMG400026820_circ_igg.3
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-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	PGSC0003DMT400068953:1 PGSC0003DMT400068955:1 PGSC0003DMT400068957:6

			
						 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  
						
							TTGTAGGTTCAACTTCATTTGAATCTTCTAGAAGACATCGAAGATGACCTGGACTTTTGCGCAA
AGCTGGCTAGGGAAGAATCTATGATAATTTTACCAGtgttgccgtgggactcaagaattggctc
aggataacctttgcatgtgagccatcatatttggaagatggcttccagagactaaatgctttct
accaaagg

									
								

					

						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
						
							TGTTGCCGTGGGACTCAAGAATTGGCTCAGGATAACCTTTGCATGTGAGCCATCATATTTGGAA
GATGGCTTCCAGAGACTAAATGCTTTCTACCAAAGGCATGCCAAAAAACAATAAGCTACTGTCT
GAGAAACAACCTTGATATCTGTTACGGTCCCCTGATATGTATCTTGTTATGAGACACGTTGCAA
GATGAAATCAGATGTTTCTTCCTATGACCTATGATCCTGGTTTGTCAAGAGACAACCTACAATC
TTGAGTTAGAGTACTCAAAAACTCAAACGATTTCCTGCTCATCTTTCCATTGAATTCAAATAAC
TTTAAAAACAATATTGGCGGATATCTCTGCTTTACAGATTGGCAATTGCTTCAACTACTCGTTG
ACCCTCGGTGCTACAATAGCTCATGCATAAGTTGGCTAGATTTTCAACAATTTCCTCGAGTCAT
CAGAGGAATGTAATATGTTATTCTGAATGGTATCCACTTCAGGATTATCACAGACAATATCATT
CTGGGGAATATCTTCCGAACTCCTGCTACTGAATATCAATAATGCACCATTGCTAGTGAATGTG
GTTGTAAGATAACCTTTAACTAGCTAAGCTAGAACAAGTGTTTGTGAAATGTGCAGATTGTTTA
ATATCGTTGAGCACAATTGGTTGCTCACCGCGTAAACTTTATTCTTACTAAGTAAGGACCATCT
TCGGTCTTACAATTTTTATACTCAATTTCTTTTGCATTCATACGCTAGTAACTTCTTTTGTTGC
TCTATTATTTCTCACTTAATACATTTCAAATTTGATACTTACTTGGGAACTCATAACTCAAATG
AACCAGTTGCCTGATGACGGAGGATTAATTAACTAACTTACTTCATTCTAGAAGTTCTAAATTT
TCCATTCTTTGCCTTGTAACTATATTTCTATAAATTCACCTCCTAATTCTCTACAACCTCTTGG
AATGTTCTATATTTTTTATTAGGGCAAAGATGTCTATAATTCAAAGTCTAGAAAAAAAAACTAG
TTTCTGTGTTTGGTATATGAAAGAAAAATATATTTTTCAATTTTTTCATATTTGATTGACTTAA
ATATTTTTCAAATGAACTTATTTTTTCCTCTAACTTAAAGAAAAAATGTCGGGAATGTGATAGA
GGTTCGGGTTCGTGTCAAAGAGTGGTGGTTCGAATATGATATTATAATATTTGTCCAGATTATA
TCTAAATATTTTTCTCTTAAAAAATAAATAAATTATTTTCCCTTTGGAATACATACACCCCTAT
TTATTGTTAAGAGGGCAAAAATCACTTGTACTGTGCCTCGTGAGATACACGAGCTTATCTTTCT
GTTTCTACCTCCTTTGCTTCTTCAACTCCATATCTGCGAATTCATAGTCATGGAGAACGGTACT
ACTACAACAAGGAAAATATGGAACTTTAAGGAGACTGAGAAGTTAGAAAGTGCACCGAATCTCA
CCATAAGAATTGTCCTTGACAAGTTGACGTCTTGCCTCAACACTGCTGATACCCGACCGGTTAT
CCCTCTCTGCCTTGCCGATCCTTCTGCTTTCCCCTGTTTCCGGACTACACCAATCGCCGAAGAT
GCTATTGTTGATGCTGTTCGCTCTGCCAAATTTAACTGTTATTCGCCCACTGTCGGCATCCTTC
CTGCTAGAAGGTAGCATATTATTTGCCTTGCTTACTCAAAATTTTAGTCGAACAATGTTAATTT
TAATGTTTTAATTGATTTTGTAAAGATTTTGAAATCTGTAATCGTTCTAAGTTTTTGATTTTTG
ATAGCACTTGGTTTAGGTGTCTCTGGCACTGATTGCATAGTAGTGTTTCTCATTTGGAGGTGTT
TGATTAAATGTGTACCTCAGTCAGTGTAATCTGTTTAATTGTGAAGAGACAGATTCAAAATTTT
GAGTTTATGGGTTTTGGATTCTAGAAACTATAGCTTACTGAGTTCGGAGTAAGTTATGTATACA
TATTGGATTTCTCAACTTAAATTTAGGGAAGGGGAAAAAGCTAGTGGTTCTGTCAAACTCGTAA
CCAAGGCTCTAGTTCCCCAGCTTTATTTAGTGTAAAGTTAATGTTGGAGACATGTTTCATGATC
GTCAAATTCATTTAATTTTGTTCTCTGAAAAGGGCGGTAGCAGAATACCTTTCTCAAGATCTCC
CATACAAGTTGTCCCCGGATGATATTTACTTGACAAGTGGATGTATTCAAGCAATTGAAGTACT
TTTGAGTGCTCTTGCGCGTCCAAACGCAAATATTCTACTTCCCACTCCTGGATTCCTTTTTTAT
GAAGCTAGGGCTGCATTTACCCATATCGAAATGCGCCACTTTAATCTTCTCCCGGACAAGGAGT
GGGAGGTGGACCTTAATGCGGTTGAGTCTTTGGCCGATGAAAATACCATGGCTATAGTTATTAT
TAATCCTGGGAATCCTTGTGGCAATGTCTACACAGACCATCACTTGAAGAAGGTATGTGTGTGT
ACTTCCTTTTTTGTTGTAGTATATTGATATCCTAAGTCATTATTATGAATATAAAGAGGTGGTT
TAATTTCTATCAGGTGGCAGAGACGGCAAGAAAACTTGGAATTTTAGTTATTTCTGATGAAGTT
TATGCTCATCTCACTTTTGGAAGTAGACCATTTGTGCCTATGGGAGTCTTTGGATCGATTGCCC
CTGTTATTACTCTCGGATCCATATCAAAGATGTGGATTGTCCCTGGTTGGCGACTTGGTTGGCT
TGTTACAAATGATCCAAATGGTATACTAAAAGAGCATGGGGTACTTACCTTTTAAAGATGGCCA
TTTTCTACTGCTTCCACACATATTATAGGGGACTATATAAGTATAATATGATATCTTAGATTAT
TTTACAAACAAACAATGTCTATCCGTCGTCACTTTGTGTATTGTTATTTGCAGGTCATAGATTC
CATCACGGGATATCTCAATATATCTTCTGACCCTGCGACTTTTATTCAGGTTTGCTCTTTATAG
TTCTCTCTTCTGCTTGCGTTCTTTTGGAAATGTAACACTTGTTGTTCCATTTTGCCACACATTT
GGTAGAGTTGCTAAAGGATTGGAATTTATTTTGGTCTAACAGCTTGTTGTATTATGTAAACATG
TTTCACATAAGCTAATGGAATAGTTATTTGAAAATTTAGTAGTATAGGTGTAATTTTCCTCGTC
GCTTACTGAGGTATCTGGTTTCTTTTTGTTCTTACTTTGACAGGGGGCAATTCCTCAGATCCTT
AAGAATACAAAAGACGATTTCTTCTCTAAAATAGTAAATATGCTAAGAGAAGATGCAGATTTCT
GTTATGAAAGAATCAAGGATATTCCTTGCATCACTTGCCCAAGTAAACCTCAAGGATCTATGTT
TGTGATGGTATGAGAAAAATGGAAGCTTAATTAGTTAGAAGATGTTATCAATAGTCTAATATAG
GTCTTTTTCCTCTTGTAGGTTCAACTTCATTTGAATCTTCTAGAAGACATCGAAGATGACCTGG
ACTTTTGCGCAAAGCTGGCTAGGGAAGAATCTATGATAATTTTACCAG
						
					

			
		

Sequences
Splice junction sequence	TTGTAGGTTCAACTTCATTTGAATCTTCTAGAAGACATCGAAGATGACCTGGACTTTTGCGCAA AGCTGGCTAGGGAAGAATCTATGATAATTTTACCAGtgttgccgtgggactcaagaattggctc aggataacctttgcatgtgagccatcatatttggaagatggcttccagagactaaatgctttct accaaagg
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	TGTTGCCGTGGGACTCAAGAATTGGCTCAGGATAACCTTTGCATGTGAGCCATCATATTTGGAA GATGGCTTCCAGAGACTAAATGCTTTCTACCAAAGGCATGCCAAAAAACAATAAGCTACTGTCT GAGAAACAACCTTGATATCTGTTACGGTCCCCTGATATGTATCTTGTTATGAGACACGTTGCAA GATGAAATCAGATGTTTCTTCCTATGACCTATGATCCTGGTTTGTCAAGAGACAACCTACAATC TTGAGTTAGAGTACTCAAAAACTCAAACGATTTCCTGCTCATCTTTCCATTGAATTCAAATAAC TTTAAAAACAATATTGGCGGATATCTCTGCTTTACAGATTGGCAATTGCTTCAACTACTCGTTG ACCCTCGGTGCTACAATAGCTCATGCATAAGTTGGCTAGATTTTCAACAATTTCCTCGAGTCAT CAGAGGAATGTAATATGTTATTCTGAATGGTATCCACTTCAGGATTATCACAGACAATATCATT CTGGGGAATATCTTCCGAACTCCTGCTACTGAATATCAATAATGCACCATTGCTAGTGAATGTG GTTGTAAGATAACCTTTAACTAGCTAAGCTAGAACAAGTGTTTGTGAAATGTGCAGATTGTTTA ATATCGTTGAGCACAATTGGTTGCTCACCGCGTAAACTTTATTCTTACTAAGTAAGGACCATCT TCGGTCTTACAATTTTTATACTCAATTTCTTTTGCATTCATACGCTAGTAACTTCTTTTGTTGC TCTATTATTTCTCACTTAATACATTTCAAATTTGATACTTACTTGGGAACTCATAACTCAAATG AACCAGTTGCCTGATGACGGAGGATTAATTAACTAACTTACTTCATTCTAGAAGTTCTAAATTT TCCATTCTTTGCCTTGTAACTATATTTCTATAAATTCACCTCCTAATTCTCTACAACCTCTTGG AATGTTCTATATTTTTTATTAGGGCAAAGATGTCTATAATTCAAAGTCTAGAAAAAAAAACTAG TTTCTGTGTTTGGTATATGAAAGAAAAATATATTTTTCAATTTTTTCATATTTGATTGACTTAA ATATTTTTCAAATGAACTTATTTTTTCCTCTAACTTAAAGAAAAAATGTCGGGAATGTGATAGA GGTTCGGGTTCGTGTCAAAGAGTGGTGGTTCGAATATGATATTATAATATTTGTCCAGATTATA TCTAAATATTTTTCTCTTAAAAAATAAATAAATTATTTTCCCTTTGGAATACATACACCCCTAT TTATTGTTAAGAGGGCAAAAATCACTTGTACTGTGCCTCGTGAGATACACGAGCTTATCTTTCT GTTTCTACCTCCTTTGCTTCTTCAACTCCATATCTGCGAATTCATAGTCATGGAGAACGGTACT ACTACAACAAGGAAAATATGGAACTTTAAGGAGACTGAGAAGTTAGAAAGTGCACCGAATCTCA CCATAAGAATTGTCCTTGACAAGTTGACGTCTTGCCTCAACACTGCTGATACCCGACCGGTTAT CCCTCTCTGCCTTGCCGATCCTTCTGCTTTCCCCTGTTTCCGGACTACACCAATCGCCGAAGAT GCTATTGTTGATGCTGTTCGCTCTGCCAAATTTAACTGTTATTCGCCCACTGTCGGCATCCTTC CTGCTAGAAGGTAGCATATTATTTGCCTTGCTTACTCAAAATTTTAGTCGAACAATGTTAATTT TAATGTTTTAATTGATTTTGTAAAGATTTTGAAATCTGTAATCGTTCTAAGTTTTTGATTTTTG ATAGCACTTGGTTTAGGTGTCTCTGGCACTGATTGCATAGTAGTGTTTCTCATTTGGAGGTGTT TGATTAAATGTGTACCTCAGTCAGTGTAATCTGTTTAATTGTGAAGAGACAGATTCAAAATTTT GAGTTTATGGGTTTTGGATTCTAGAAACTATAGCTTACTGAGTTCGGAGTAAGTTATGTATACA TATTGGATTTCTCAACTTAAATTTAGGGAAGGGGAAAAAGCTAGTGGTTCTGTCAAACTCGTAA CCAAGGCTCTAGTTCCCCAGCTTTATTTAGTGTAAAGTTAATGTTGGAGACATGTTTCATGATC GTCAAATTCATTTAATTTTGTTCTCTGAAAAGGGCGGTAGCAGAATACCTTTCTCAAGATCTCC CATACAAGTTGTCCCCGGATGATATTTACTTGACAAGTGGATGTATTCAAGCAATTGAAGTACT TTTGAGTGCTCTTGCGCGTCCAAACGCAAATATTCTACTTCCCACTCCTGGATTCCTTTTTTAT GAAGCTAGGGCTGCATTTACCCATATCGAAATGCGCCACTTTAATCTTCTCCCGGACAAGGAGT GGGAGGTGGACCTTAATGCGGTTGAGTCTTTGGCCGATGAAAATACCATGGCTATAGTTATTAT TAATCCTGGGAATCCTTGTGGCAATGTCTACACAGACCATCACTTGAAGAAGGTATGTGTGTGT ACTTCCTTTTTTGTTGTAGTATATTGATATCCTAAGTCATTATTATGAATATAAAGAGGTGGTT TAATTTCTATCAGGTGGCAGAGACGGCAAGAAAACTTGGAATTTTAGTTATTTCTGATGAAGTT TATGCTCATCTCACTTTTGGAAGTAGACCATTTGTGCCTATGGGAGTCTTTGGATCGATTGCCC CTGTTATTACTCTCGGATCCATATCAAAGATGTGGATTGTCCCTGGTTGGCGACTTGGTTGGCT TGTTACAAATGATCCAAATGGTATACTAAAAGAGCATGGGGTACTTACCTTTTAAAGATGGCCA TTTTCTACTGCTTCCACACATATTATAGGGGACTATATAAGTATAATATGATATCTTAGATTAT TTTACAAACAAACAATGTCTATCCGTCGTCACTTTGTGTATTGTTATTTGCAGGTCATAGATTC CATCACGGGATATCTCAATATATCTTCTGACCCTGCGACTTTTATTCAGGTTTGCTCTTTATAG TTCTCTCTTCTGCTTGCGTTCTTTTGGAAATGTAACACTTGTTGTTCCATTTTGCCACACATTT GGTAGAGTTGCTAAAGGATTGGAATTTATTTTGGTCTAACAGCTTGTTGTATTATGTAAACATG TTTCACATAAGCTAATGGAATAGTTATTTGAAAATTTAGTAGTATAGGTGTAATTTTCCTCGTC GCTTACTGAGGTATCTGGTTTCTTTTTGTTCTTACTTTGACAGGGGGCAATTCCTCAGATCCTT AAGAATACAAAAGACGATTTCTTCTCTAAAATAGTAAATATGCTAAGAGAAGATGCAGATTTCT GTTATGAAAGAATCAAGGATATTCCTTGCATCACTTGCCCAAGTAAACCTCAAGGATCTATGTT TGTGATGGTATGAGAAAAATGGAAGCTTAATTAGTTAGAAGATGTTATCAATAGTCTAATATAG GTCTTTTTCCTCTTGTAGGTTCAACTTCATTTGAATCTTCTAGAAGACATCGAAGATGACCTGG ACTTTTGCGCAAAGCTGGCTAGGGAAGAATCTATGATAATTTTACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.111184793

Conservation Information
Conserved circRNAs	NA
PMCS	0.111184793

			
						 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 PGSC0003DMG400026820_circ_g.1

Address

Any questions?

Supported by