Plant Circular RNA Database

Detail information of AT1G07350_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT1G07350_circ_g.7
					
						ID in PlantcircBase
						ath_circ_001142
					
						Alias
						At_ciR3989
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2259003-2259586  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT1G07350						
					
						Parent gene annotation
						
							Serine/arginine-rich splicing factor SR45a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G07350_circ_g.6 AT1G07350_circ_g.8 						
					
						Support reads
						6/1
					
						Tissues
						leaf/whole_plant
					
						Exon boundary  
						
							Yes-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-AC							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
						AT1G07350.1:3
AT1G07350.6:3
AT1G07350.3:3
AT1G07350.4:3
AT1G07350.5:3
AT1G07350.2:3

General Information
CircRNA Name	AT1G07350_circ_g.7
ID in PlantcircBase	ath_circ_001142
Alias	At_ciR3989
Organism	Arabidpsis thaliana
Position	chr1: 2259003-2259586 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	AT1G07350
Parent gene annotation	Serine/arginine-rich splicing factor SR45a
Parent gene strand	-
Alternative splicing	AT1G07350_circ_g.6 AT1G07350_circ_g.8
Support reads	6/1
Tissues	leaf/whole_plant
Exon boundary	Yes-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-AC 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	AT1G07350.1:3 AT1G07350.6:3 AT1G07350.3:3 AT1G07350.4:3 AT1G07350.5:3 AT1G07350.2:3

			
						 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  
						
							TCGTCGGGCTTCTAGACAATGACCTTGACACAGACCTTCCACGACGCTTGTCATAAGGAGATAG
TGAAGGAGAGTATCTTGACCTTCTTGAGTAAGACATcttctcaacagtgatgacgcggccctgc
agaacagagtgatctagagatctgatgcaacggttagcatcaccaacacttttcatagagataa
aaccaaat

						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: 360
Transcript exons: 2259003-2259152,2259277-2259385,2259486-2259586
CTTCTCAACAGTGATGACGCGGCCCTGCAGAACAGAGTGATCTAGAGATCTGATGCAACGGTTA
GCATCACCAACACTTTTCATAGAGATAAAACCAAATCCGCGAGATTCTCTAGTCCATGGGTCCA
GGACAAGGTGAACATCAGTTACCTTTCCTTCTTTAGCGAAATGATCCTCCAGATCTCTTTCAGT
AACCCGGTGAGACAATCCAGTTACATATAAACTGTTACCAGGATTCTCAGCATCGCTTGAGACA
CTCCTCGTCGGGCTTCTAGACAATGACCTTGACACAGACCTTCCACGACGCTTGTCATAAGGAG
ATAGTGAAGGAGAGTATCTTGACCTTCTTGAGTAAGACAT
						
						Genomic sequence
						
							CTTCTCAACAGTGATGACGCGGCCCTGCAGAACAGAGTGATCTAGAGATCTGATGCAACGGTTA
GCATCACCAACACTTTTCATAGAGATAAAACCAAATCCGCGAGATTCTCTAGTCCATGGGTCCA
GGACAAGGTGAACATCAGTTACCTAGAAATATCAAAAGCTCACAAATGTTAAAACTCATGAACA
AACAAATTTCTCTTTAAACATTATACACTAGTGAGCTACTCGAAACTGAATTGTGTTCAAAATT
AAAGATAACATCCACAACCTTTCCTTCTTTAGCGAAATGATCCTCCAGATCTCTTTCAGTAACC
CGGTGAGACAATCCAGTTACATATAAACTGTTACCAGGATTCTCAGCATCGCTTGAGACACTCC
TAATGTAACAAAAGCGATTTAAAACAATCAGACATTAGCGCATTCAAAAGCAGCAAACATCAAG
TCACGACAACTCAAACCTAAGAATAAGACAAATACCTCGTCGGGCTTCTAGACAATGACCTTGA
CACAGACCTTCCACGACGCTTGTCATAAGGAGATAGTGAAGGAGAGTATCTTGACCTTCTTGAG
TAAGACAT

Sequences
Splice junction sequence	TCGTCGGGCTTCTAGACAATGACCTTGACACAGACCTTCCACGACGCTTGTCATAAGGAGATAG TGAAGGAGAGTATCTTGACCTTCTTGAGTAAGACATcttctcaacagtgatgacgcggccctgc agaacagagtgatctagagatctgatgcaacggttagcatcaccaacacttttcatagagataa aaccaaat
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: 360 Transcript exons: 2259003-2259152,2259277-2259385,2259486-2259586 CTTCTCAACAGTGATGACGCGGCCCTGCAGAACAGAGTGATCTAGAGATCTGATGCAACGGTTA GCATCACCAACACTTTTCATAGAGATAAAACCAAATCCGCGAGATTCTCTAGTCCATGGGTCCA GGACAAGGTGAACATCAGTTACCTTTCCTTCTTTAGCGAAATGATCCTCCAGATCTCTTTCAGT AACCCGGTGAGACAATCCAGTTACATATAAACTGTTACCAGGATTCTCAGCATCGCTTGAGACA CTCCTCGTCGGGCTTCTAGACAATGACCTTGACACAGACCTTCCACGACGCTTGTCATAAGGAG ATAGTGAAGGAGAGTATCTTGACCTTCTTGAGTAAGACAT
Genomic sequence	CTTCTCAACAGTGATGACGCGGCCCTGCAGAACAGAGTGATCTAGAGATCTGATGCAACGGTTA GCATCACCAACACTTTTCATAGAGATAAAACCAAATCCGCGAGATTCTCTAGTCCATGGGTCCA GGACAAGGTGAACATCAGTTACCTAGAAATATCAAAAGCTCACAAATGTTAAAACTCATGAACA AACAAATTTCTCTTTAAACATTATACACTAGTGAGCTACTCGAAACTGAATTGTGTTCAAAATT AAAGATAACATCCACAACCTTTCCTTCTTTAGCGAAATGATCCTCCAGATCTCTTTCAGTAACC CGGTGAGACAATCCAGTTACATATAAACTGTTACCAGGATTCTCAGCATCGCTTGAGACACTCC TAATGTAACAAAAGCGATTTAAAACAATCAGACATTAGCGCATTCAAAAGCAGCAAACATCAAG TCACGACAACTCAAACCTAAGAATAAGACAAATACCTCGTCGGGCTTCTAGACAATGACCTTGA CACAGACCTTCCACGACGCTTGTCATAAGGAGATAGTGAAGGAGAGTATCTTGACCTTCTTGAG TAAGACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.184251358

Conservation Information
Conserved circRNAs	NA
PMCS	0.184251358

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2259587-2259005(-)
						
						Potential amino acid sequence
						
							MSYSRRSRYSPSLSPYDKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDH
FAKEGKVTDVHLVLDPWTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSR
YSPSLSPYDKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVT
DVHLVLDPWTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSRYSPSLSPY
DKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVTDVHLVLDP
WTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSRYSPSLSPYDKRRGRSV
SRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVTDVHLVLDPWTRESRGF
GFISMKSVGDANRCIRSLDHSVLQGRVITVEK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2259587-2259005(-)
Potential amino acid sequence	MSYSRRSRYSPSLSPYDKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDH FAKEGKVTDVHLVLDPWTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSR YSPSLSPYDKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVT DVHLVLDPWTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSRYSPSLSPY DKRRGRSVSRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVTDVHLVLDP WTRESRGFGFISMKSVGDANRCIRSLDHSVLQGRVITVEKMSYSRRSRYSPSLSPYDKRRGRSV SRSLSRSPTRSVSSDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVTDVHLVLDPWTRESRGF GFISMKSVGDANRCIRSLDHSVLQGRVITVEK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT1G07350_circ_g.7

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