Plant Circular RNA Database

Detail information of AT1G54460_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G54460_circ_g.4
					
						ID in PlantcircBase
						ath_circ_007384
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20342109-20342374  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G54460						
					
						Parent gene annotation
						
							Protein WVD2-like 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G54460_circ_g.1 AT1G54460_circ_g.2 AT1G54460_circ_g.3 						
					
						Support reads
						2
					
						Tissues
						root, inflorescences
					
						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
						AT1G54460.1:2

General Information
CircRNA Name	AT1G54460_circ_g.4
ID in PlantcircBase	ath_circ_007384
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 20342109-20342374 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT1G54460
Parent gene annotation	Protein WVD2-like 2
Parent gene strand	-
Alternative splicing	AT1G54460_circ_g.1 AT1G54460_circ_g.2 AT1G54460_circ_g.3
Support reads	2
Tissues	root, inflorescences
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	AT1G54460.1:2

			
						 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  
						
							TATCACATAAAGGATACGAGGAAGCAACAGAAAAACTATCTTCTTCATCATGGTGCATCTTATG
ATCTGGTATCCTCCTAGTTGGTAAAGGAGAGTTTAGctctcttcgtctctccagtcgcgatgtg
ctactaaatgttggagcaactccaatcgttatcttgggtttaaaacttcttatggatgtagctg
atctatat

						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: 177
Transcript exons: 20342109-20342202,20342292-20342374
CTCTCTTCGTCTCTCCAGTCGCGATGTGCTACTAAATGTTGGAGCAACTCCAATCGTTATCTTG
GGTTTAAAACTTCTTATGGATGTAGCTGATGAGGAAGCAACAGAAAAACTATCTTCTTCATCAT
GGTGCATCTTATGATCTGGTATCCTCCTAGTTGGTAAAGGAGAGTTTAG
						
						Genomic sequence
						
							CTCTCTTCGTCTCTCCAGTCGCGATGTGCTACTAAATGTTGGAGCAACTCCAATCGTTATCTTG
GGTTTAAAACTTCTTATGGATGTAGCTGATCTATATATGGCTAAGGATAAAAGTCCTTTAGTGG
TTAGATATTAAAAATCAATGTTTCTGTTTTCGTTTAACTATCACATAAAGGATACGAGGAAGCA
ACAGAAAAACTATCTTCTTCATCATGGTGCATCTTATGATCTGGTATCCTCCTAGTTGGTAAAG
GAGAGTTTAG

Sequences
Splice junction sequence	TATCACATAAAGGATACGAGGAAGCAACAGAAAAACTATCTTCTTCATCATGGTGCATCTTATG ATCTGGTATCCTCCTAGTTGGTAAAGGAGAGTTTAGctctcttcgtctctccagtcgcgatgtg ctactaaatgttggagcaactccaatcgttatcttgggtttaaaacttcttatggatgtagctg atctatat
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: 177 Transcript exons: 20342109-20342202,20342292-20342374 CTCTCTTCGTCTCTCCAGTCGCGATGTGCTACTAAATGTTGGAGCAACTCCAATCGTTATCTTG GGTTTAAAACTTCTTATGGATGTAGCTGATGAGGAAGCAACAGAAAAACTATCTTCTTCATCAT GGTGCATCTTATGATCTGGTATCCTCCTAGTTGGTAAAGGAGAGTTTAG
Genomic sequence	CTCTCTTCGTCTCTCCAGTCGCGATGTGCTACTAAATGTTGGAGCAACTCCAATCGTTATCTTG GGTTTAAAACTTCTTATGGATGTAGCTGATCTATATATGGCTAAGGATAAAAGTCCTTTAGTGG TTAGATATTAAAAATCAATGTTTCTGTTTTCGTTTAACTATCACATAAAGGATACGAGGAAGCA ACAGAAAAACTATCTTCTTCATCATGGTGCATCTTATGATCTGGTATCCTCCTAGTTGGTAAAG GAGAGTTTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.397742967

Conservation Information
Conserved circRNAs	NA
PMCS	0.397742967

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20342333-20342111(-)
						
						Potential amino acid sequence
						
							MHHDEEDSFSVASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDE
EDSFSVASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDEEDSFS
VASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDEEDSFSVASSS
ATSIRSFKPKITIGVAPTFSSTSRLERRRE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20342333-20342111(-)
Potential amino acid sequence	MHHDEEDSFSVASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDE EDSFSVASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDEEDSFS VASSSATSIRSFKPKITIGVAPTFSSTSRLERRRELNSPLPTRRIPDHKMHHDEEDSFSVASSS ATSIRSFKPKITIGVAPTFSSTSRLERRRE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G54460_circ_g.4

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