Plant Circular RNA Database

Detail information of PGSC0003DMG400003718_circ_g.1

			
						 General Information
					
						CircRNA Name
						PGSC0003DMG400003718_circ_g.1
					
						ID in PlantcircBase
						stu_circ_000665
					
						Alias
						chr04:70547904|70548049
					
						Organism
						
							Solanum tuberosum						
					
						Position
						
							chr4: 70547905-70548051  JBrowse»						
					
						Reference genome
						
							3.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRI2, circseq_cup
					
						Parent gene
						
							PGSC0003DMG400003718						
					
						Parent gene annotation
						
							Cell growth defect factor 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  
						
							CA-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
						PGSC0003DMT400009533:1

General Information
CircRNA Name	PGSC0003DMG400003718_circ_g.1
ID in PlantcircBase	stu_circ_000665
Alias	chr04:70547904\|70548049
Organism	Solanum tuberosum
Position	chr4: 70547905-70548051 JBrowse»
Reference genome	3.0.38
Type	ui-circRNA
Identification method	CIRI2, circseq_cup
Parent gene	PGSC0003DMG400003718
Parent gene annotation	Cell growth defect factor 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	CA-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	PGSC0003DMT400009533:1

			
						 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  
						
							ATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCCCTTGCAGCCATCTCTGCCAAATTCTTCAC
CTCCCAGGTaatagttttgaactatctgatgatttggcaagagttcaagtgagatctacagttc
aattcatcaatggagggct

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 146
Transcript exons: 70547905-70548051
AATAGTTTTGAACTATCTGATGATTTGGCAAGAGTTCAAGTGAGATCTACAGTTCAATTCATCA
ATGGAGGGCTATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCTCTTGCAGCCATCTCTGCCA
AATTCTTCACCTCCCAGA
						
						Genomic sequence
						
							AATAGTTTTGAACTATCTGATGATTTGGCAAGAGTTCAAGTGAGATCTACAGTTCAATTCATCA
ATGGAGGGCTATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCCCTTGCAGCCATCTCTGCCA
AATTCTTCACCTCCCAGGT

Sequences
Splice junction sequence	ATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCCCTTGCAGCCATCTCTGCCAAATTCTTCAC CTCCCAGGTaatagttttgaactatctgatgatttggcaagagttcaagtgagatctacagttc aattcatcaatggagggct
Assembled circRNA sequence	Yes 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	Transcript length: 146 Transcript exons: 70547905-70548051 AATAGTTTTGAACTATCTGATGATTTGGCAAGAGTTCAAGTGAGATCTACAGTTCAATTCATCA ATGGAGGGCTATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCTCTTGCAGCCATCTCTGCCA AATTCTTCACCTCCCAGA
Genomic sequence	AATAGTTTTGAACTATCTGATGATTTGGCAAGAGTTCAAGTGAGATCTACAGTTCAATTCATCA ATGGAGGGCTATGTGTGGGCTATCGCCGCTGGACTCAACGCTGCCCTTGCAGCCATCTCTGCCA AATTCTTCACCTCCCAGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.181404308

Conservation Information
Conserved circRNAs	NA
PMCS	0.181404308

			
						 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 PGSC0003DMG400003718_circ_g.1

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