Plant Circular RNA Database

Detail information of AT3G54890_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G54890_circ_g.5
					
						ID in PlantcircBase
						ath_circ_027552
					
						Alias
						At_ciR633, AT3G54890_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20339940-20340228  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT3G54890						
					
						Parent gene annotation
						
							Chlorophyll a-b binding protein, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G54890_circ_g.1 AT3G54890_circ_g.2 AT3G54890_circ_g.3 AT3G54890_circ_g.4 AT3G54890_circ_g.6 AT3G54890_circ_g.7 AT3G54890_circ_g.8 AT3G54890_circ_g.9 AT3G54890_circ_g.10 AT3G54890_circ_g.11 AT3G54890_circ_g.12 AT3G54890_circ_g.13 AT3G54890_circ_g.14 AT3G54890_circ_g.15 						
					
						Support reads
						32
					
						Tissues
						leaf
					
						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
						AT3G54890.3:2
AT3G54890.2:2
AT3G54890.1:1
AT3G54890.4:1

General Information
CircRNA Name	AT3G54890_circ_g.5
ID in PlantcircBase	ath_circ_027552
Alias	At_ciR633, AT3G54890_C1
Organism	Arabidpsis thaliana
Position	chr3: 20339940-20340228 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ, CIRI-full, CIRI2
Parent gene	AT3G54890
Parent gene annotation	Chlorophyll a-b binding protein, chloroplastic
Parent gene strand	-
Alternative splicing	AT3G54890_circ_g.1 AT3G54890_circ_g.2 AT3G54890_circ_g.3 AT3G54890_circ_g.4 AT3G54890_circ_g.6 AT3G54890_circ_g.7 AT3G54890_circ_g.8 AT3G54890_circ_g.9 AT3G54890_circ_g.10 AT3G54890_circ_g.11 AT3G54890_circ_g.12 AT3G54890_circ_g.13 AT3G54890_circ_g.14 AT3G54890_circ_g.15
Support reads	32
Tissues	leaf
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	AT3G54890.3:2 AT3G54890.2:2 AT3G54890.1:1 AT3G54890.4:1

			
						 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  
						
							GGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTT
TCCATATCCTAATGCTTCTGGTACCAAAATCCCAGGcgttcttgatctctttaactttcaattc
ctcgagcttcttggggtccttcgagtatccaagagggtcaaatgcgcctcccgggtacttcttc
ttctcagg

						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: 187
Transcript exons: 20339940-20339967,20340070-20340228
CGTTCTTGATCTCTTTAACTTTCAATTCAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGT
GGGCAAAGTACCCCACGGGACTGGGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCC
CATTCCTGAGCCTTAACCCAGTTTCCATATCCTAATGCTTCTGGTACCAAAATCCCAGG
Transcript length: 222
Transcript exons: 20339940-20340014,20340082-20340228
CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGTTTC
CCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCCATA
TCCTAATGCTTCTGGTACCAAAATCCCAGG
Transcript length: 289
Transcript exons: 20339940-20340228
CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA
ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT
TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC
ATATCCTAATGCTTCTGGTACCAAAATCCCAGG
						
						Genomic sequence
						
							CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA
ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT
TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC
ATATCCTAATGCTTCTGGTACCAAAATCCCAGG

Sequences
Splice junction sequence	GGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTT TCCATATCCTAATGCTTCTGGTACCAAAATCCCAGGcgttcttgatctctttaactttcaattc ctcgagcttcttggggtccttcgagtatccaagagggtcaaatgcgcctcccgggtacttcttc ttctcagg
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: 187 Transcript exons: 20339940-20339967,20340070-20340228 CGTTCTTGATCTCTTTAACTTTCAATTCAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGT GGGCAAAGTACCCCACGGGACTGGGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCC CATTCCTGAGCCTTAACCCAGTTTCCATATCCTAATGCTTCTGGTACCAAAATCCCAGG Transcript length: 222 Transcript exons: 20339940-20340014,20340082-20340228 CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGTTTC CCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCCATA TCCTAATGCTTCTGGTACCAAAATCCCAGG Transcript length: 289 Transcript exons: 20339940-20340228 CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC ATATCCTAATGCTTCTGGTACCAAAATCCCAGG
Genomic sequence	CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC ATATCCTAATGCTTCTGGTACCAAAATCCCAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.501340704

Conservation Information
Conserved circRNAs	NA
PMCS	0.501340704

			
						 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
						response to drought stress

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	response to drought stress

			
						 Other Information
					
						References
						Ye et al., 2015;Zhang et al., 2019

circRNA

Detail information of AT3G54890_circ_g.5

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