Plant Circular RNA Database

Detail information of AT5G20520_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G20520_circ_g.3
					
						ID in PlantcircBase
						ath_circ_039509
					
						Alias
						Chr5:6944510|6945169
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6944510-6945169  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT5G20520						
					
						Parent gene annotation
						
							WAV2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G20520_circ_g.1 AT5G20520_circ_g.2 AT5G20520_circ_g.4 						
					
						Support reads
						3
					
						Tissues
						seedling
					
						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  
						
							TT-TA							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
						AT5G20520.1:1

General Information
CircRNA Name	AT5G20520_circ_g.3
ID in PlantcircBase	ath_circ_039509
Alias	Chr5:6944510\|6945169
Organism	Arabidpsis thaliana
Position	chr5: 6944510-6945169 JBrowse»
Reference genome	TAIR10.38
Type	ei-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT5G20520
Parent gene annotation	WAV2
Parent gene strand	-
Alternative splicing	AT5G20520_circ_g.1 AT5G20520_circ_g.2 AT5G20520_circ_g.4
Support reads	3
Tissues	seedling
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	TT-TA 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	AT5G20520.1:1

			
						 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  
						
							CTGGCGGCTGGTACTTGGCCTATACTGTCTCTCTTCTAATAAAATATACATTTTCCCTACTCAT
GAAATGCTACCAATAGCAATATGTACTAATAGTACCtaaggcgtgtggatatcaaatgaaatac
tggaagtagagacaacaagaacaaaaataatagcttaatcaaggcatctacaaatttcatttac
caagaaat

						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
						
							TAAGGCGTGTGGATATCAAATGAAATACTGGAAGTAGAGACAACAAGAACAAAAATAATAGCTT
AATCAAGGCATCTACAAATTTCATTTACCAAGAAATTTTCTGAGAAGGATAAGGTTCTTGTGCA
TATAATAGTAAATATCAGTGGGGGTGATAAAAGGAGGCCTATAACAAAGCTCAAACGAATACCC
CTATCAACCAGGTTCTTTTATTGCCAGATGACTAAAACTTTAACACAAAAAATAATTATATTCA
GATAGTACAAACCGCGTAGATTGTTACTGATGATAAGTGACTAGAATCTAAATAAAGAGGTACT
CTAGAAATTTTTATACAATTGGACTCCAGGTCATCTGCCAAAGACCATGAGTTATAATAATTTG
CAACAGTAACCAGAATCTCATTAATATACTGATAAGAAGCCATCCAAACCAAGCCCCTAGAGGA
GAGAGGAAGGTGCCCTTAGGCGTTATAATTTATAAGGCATTTGTTAGTCTCATTCGTAACCATG
TGGGACTCTCAATAATACTTCTCCCTTTAAACAGTAACATCCACAGAGCTGGCGGCTGGTACTT
GGCCTATACTGTCTCTCTTCTAATAAAATATACATTTTCCCTACTCATGAAATGCTACCAATAG
CAATATGTACTAATAGTACC

Sequences
Splice junction sequence	CTGGCGGCTGGTACTTGGCCTATACTGTCTCTCTTCTAATAAAATATACATTTTCCCTACTCAT GAAATGCTACCAATAGCAATATGTACTAATAGTACCtaaggcgtgtggatatcaaatgaaatac tggaagtagagacaacaagaacaaaaataatagcttaatcaaggcatctacaaatttcatttac caagaaat
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	TAAGGCGTGTGGATATCAAATGAAATACTGGAAGTAGAGACAACAAGAACAAAAATAATAGCTT AATCAAGGCATCTACAAATTTCATTTACCAAGAAATTTTCTGAGAAGGATAAGGTTCTTGTGCA TATAATAGTAAATATCAGTGGGGGTGATAAAAGGAGGCCTATAACAAAGCTCAAACGAATACCC CTATCAACCAGGTTCTTTTATTGCCAGATGACTAAAACTTTAACACAAAAAATAATTATATTCA GATAGTACAAACCGCGTAGATTGTTACTGATGATAAGTGACTAGAATCTAAATAAAGAGGTACT CTAGAAATTTTTATACAATTGGACTCCAGGTCATCTGCCAAAGACCATGAGTTATAATAATTTG CAACAGTAACCAGAATCTCATTAATATACTGATAAGAAGCCATCCAAACCAAGCCCCTAGAGGA GAGAGGAAGGTGCCCTTAGGCGTTATAATTTATAAGGCATTTGTTAGTCTCATTCGTAACCATG TGGGACTCTCAATAATACTTCTCCCTTTAAACAGTAACATCCACAGAGCTGGCGGCTGGTACTT GGCCTATACTGTCTCTCTTCTAATAAAATATACATTTTCCCTACTCATGAAATGCTACCAATAG CAATATGTACTAATAGTACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110984949

Conservation Information
Conserved circRNAs	NA
PMCS	0.110984949

			
						 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
						responsive to methyl jasmonate

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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT5G20520_circ_g.3

Address

Any questions?

Supported by