Plant Circular RNA Database

Detail information of AT4G05050_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT4G05050_circ_g.9
					
						ID in PlantcircBase
						ath_circ_029759
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 2588984-2589294  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup
					
						Parent gene
						
							AT4G05050						
					
						Parent gene annotation
						
							Polyubiquitin
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G05050_circ_g.1 AT4G05050_circ_g.2 4_circ_ag.3 AT4G05050_circ_g.4 AT4G05050_circ_g.5 AT4G05050_circ_g.6 AT4G05050_circ_g.7 AT4G05050_circ_g.8 AT4G05050_circ_g.10 AT4G05060_circ_g.1 AT4G05060_circ_g.2 AT4G05060_circ_g.3 AT4G05060_circ_g.4 AT4G05060_circ_g.5 4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 4_circ_ag.10 4_circ_ag.11 AT4G05150_circ_g.1 AT4G05160_circ_g.1 AT4G05160_circ_g.2 AT4G05160_circ_g.3 AT4G05160_circ_g.4 AT4G05170_circ_g.1 AT4G05180_circ_g.1 AT4G05190_circ_g.1 AT4G05190_circ_g.2 AT4G05190_circ_g.3 AT4G05190_circ_g.4 AT4G05190_circ_g.5 AT4G05190_circ_g.6 AT4G05190_circ_g.7 AT4G05190_circ_g.8 AT4G05190_circ_g.9 AT4G05320_circ_g.1 AT4G05320_circ_g.2 AT4G05320_circ_g.3 AT4G05320_circ_g.4 AT4G05320_circ_g.5 AT4G05320_circ_g.6 AT4G05320_circ_g.7 AT4G05320_circ_g.8 AT4G05320_circ_g.9 AT4G05320_circ_g.10 AT4G05320_circ_g.11 AT4G05320_circ_g.12 AT4G05320_circ_g.13 AT4G05320_circ_g.14 AT4G05320_circ_g.15 AT4G05320_circ_g.16 AT4G05320_circ_g.17 AT4G05320_circ_g.18 AT4G05320_circ_g.19 AT4G05320_circ_g.20 AT4G05320_circ_g.21 AT4G05320_circ_g.22 AT4G05320_circ_g.23 AT4G05320_circ_g.24 AT4G05320_circ_g.25 AT4G05320_circ_g.26 AT4G05320_circ_g.27 AT4G05320_circ_g.28 AT4G05320_circ_g.29 AT4G05320_circ_g.30 AT4G05320_circ_g.31 AT4G05320_circ_g.32 AT4G05320_circ_g.33 AT4G05320_circ_g.34 AT4G05320_circ_g.35 AT4G05320_circ_g.36 AT4G05320_circ_g.37 AT4G05320_circ_g.38 AT4G05320_circ_g.39 AT4G05320_circ_g.40 AT4G05320_circ_g.41 AT4G05320_circ_g.42 AT4G05320_circ_g.43 AT4G05320_circ_g.44 AT4G05320_circ_g.45 						
					
						Support reads
						3
					
						Tissues
						seedlings
					
						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  
						
							CT-AT							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
						AT4G05050.3:1
AT4G05050.2:1
AT4G05050.4:1

General Information
CircRNA Name	AT4G05050_circ_g.9
ID in PlantcircBase	ath_circ_029759
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 2588984-2589294 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, circseq_cup
Parent gene	AT4G05050
Parent gene annotation	Polyubiquitin
Parent gene strand	-
Alternative splicing	AT4G05050_circ_g.1 AT4G05050_circ_g.2 4_circ_ag.3 AT4G05050_circ_g.4 AT4G05050_circ_g.5 AT4G05050_circ_g.6 AT4G05050_circ_g.7 AT4G05050_circ_g.8 AT4G05050_circ_g.10 AT4G05060_circ_g.1 AT4G05060_circ_g.2 AT4G05060_circ_g.3 AT4G05060_circ_g.4 AT4G05060_circ_g.5 4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 4_circ_ag.10 4_circ_ag.11 AT4G05150_circ_g.1 AT4G05160_circ_g.1 AT4G05160_circ_g.2 AT4G05160_circ_g.3 AT4G05160_circ_g.4 AT4G05170_circ_g.1 AT4G05180_circ_g.1 AT4G05190_circ_g.1 AT4G05190_circ_g.2 AT4G05190_circ_g.3 AT4G05190_circ_g.4 AT4G05190_circ_g.5 AT4G05190_circ_g.6 AT4G05190_circ_g.7 AT4G05190_circ_g.8 AT4G05190_circ_g.9 AT4G05320_circ_g.1 AT4G05320_circ_g.2 AT4G05320_circ_g.3 AT4G05320_circ_g.4 AT4G05320_circ_g.5 AT4G05320_circ_g.6 AT4G05320_circ_g.7 AT4G05320_circ_g.8 AT4G05320_circ_g.9 AT4G05320_circ_g.10 AT4G05320_circ_g.11 AT4G05320_circ_g.12 AT4G05320_circ_g.13 AT4G05320_circ_g.14 AT4G05320_circ_g.15 AT4G05320_circ_g.16 AT4G05320_circ_g.17 AT4G05320_circ_g.18 AT4G05320_circ_g.19 AT4G05320_circ_g.20 AT4G05320_circ_g.21 AT4G05320_circ_g.22 AT4G05320_circ_g.23 AT4G05320_circ_g.24 AT4G05320_circ_g.25 AT4G05320_circ_g.26 AT4G05320_circ_g.27 AT4G05320_circ_g.28 AT4G05320_circ_g.29 AT4G05320_circ_g.30 AT4G05320_circ_g.31 AT4G05320_circ_g.32 AT4G05320_circ_g.33 AT4G05320_circ_g.34 AT4G05320_circ_g.35 AT4G05320_circ_g.36 AT4G05320_circ_g.37 AT4G05320_circ_g.38 AT4G05320_circ_g.39 AT4G05320_circ_g.40 AT4G05320_circ_g.41 AT4G05320_circ_g.42 AT4G05320_circ_g.43 AT4G05320_circ_g.44 AT4G05320_circ_g.45
Support reads	3
Tissues	seedlings
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	CT-AT 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	AT4G05050.3:1 AT4G05050.2:1 AT4G05050.4:1

			
						 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  
						
							CTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTAAATTGCGATCGAACGAAAC
AAATCGAAGAAATACAATAAGAACTCAGAAATCTACtaatcgacaaattcgatcgcacaaacaa
gaaactaacaccaaatctagataaaaatcacagatcaaagcgtaaataatcgagaacacacaaa
ttctttca

						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: 311
Transcript exons: 2588984-2589294
TAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC
AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA
CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG
ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA
AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC
Transcript length: 622
Transcript exons: 2588984-2589294
AAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC
AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA
CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG
ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA
AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTACTAATCGACA
AATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATCAAAGCGTAA
ATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAACAAGAAAAT
AAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACGATGAAACTA
TGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTAAATTGCGAT
CGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC
						
						Genomic sequence
						
							TAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC
AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA
CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG
ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA
AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC

Sequences
Splice junction sequence	CTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTAAATTGCGATCGAACGAAAC AAATCGAAGAAATACAATAAGAACTCAGAAATCTACtaatcgacaaattcgatcgcacaaacaa gaaactaacaccaaatctagataaaaatcacagatcaaagcgtaaataatcgagaacacacaaa ttctttca
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: 311 Transcript exons: 2588984-2589294 TAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC Transcript length: 622 Transcript exons: 2588984-2589294 AAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTACTAATCGACA AATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATCAAAGCGTAA ATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAACAAGAAAAT AAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACGATGAAACTA TGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTAAATTGCGAT CGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC
Genomic sequence	TAATCGACAAATTCGATCGCACAAACAAGAAACTAACACCAAATCTAGATAAAAATCACAGATC AAAGCGTAAATAATCGAGAACACACAAATTCTTTCAACAAATCGGATCAAATACAAGGAAACAA CAAGAAAATAAACAGATCTGCGAAAAATACGAACCCTAATCGAGAAATAAGAAGAGATCTAACG ATGAAACTATGTAATTTGCCTCCGATCAGAGATTAACGAGATCAAAATCAAAGAACAGAGCCTA AATTGCGATCGAACGAAACAAATCGAAGAAATACAATAAGAACTCAGAAATCTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.43929087

Conservation Information
Conserved circRNAs	NA
PMCS	0.43929087

			
						 Functional Information
					
						Coding potential
						N
					
						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	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Pan et al., 2017

circRNA

Detail information of AT4G05050_circ_g.9

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