Plant Circular RNA Database

Detail information of AT3G54890_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G54890_circ_g.6
					
						ID in PlantcircBase
						ath_circ_027553
					
						Alias
						At_ciR984, Ath_circ_FC2384, Ath_circ_FC2385
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20339940-20340418  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ, CIRI-full
					
						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.5 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
						6/2
					
						Tissues
						leaf/seedlings
					
						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
						AT3G54890.2:3
AT3G54890.4:2
AT3G54890.1:2
AT3G54890.3:3

General Information
CircRNA Name	AT3G54890_circ_g.6
ID in PlantcircBase	ath_circ_027553
Alias	At_ciR984, Ath_circ_FC2384, Ath_circ_FC2385
Organism	Arabidpsis thaliana
Position	chr3: 20339940-20340418 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ, CIRI-full
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.5 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	6/2
Tissues	leaf/seedlings
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	AT3G54890.2:3 AT3G54890.4:2 AT3G54890.1:2 AT3G54890.3:3

			
						 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  
						
							AGCGAGCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGA
ACTTCTCCAAGTCCAAGTGGGTCAAACCCAAAGTCAcgttcttgatctctttaactttcaattc
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: 290
Transcript exons: 20339940-20339967,20340070-20340228,20340316-20340418
CGTTCTTGATCTCTTTAACTTTCAATTCAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGT
GGGCAAAGTACCCCACGGGACTGGGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCC
CATTCCTGAGCCTTAACCCAGTTTCCATATCCTAATGCTTCTGGTACCAAAATCCCAGGAACAG
CGAGCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAAC
TTCTCCAAGTCCAAGTGGGTCAAACCCAAAGTCA
Transcript length: 325
Transcript exons: 20339940-20340014,20340082-20340228,20340316-20340418
CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGTTTC
CCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCCATA
TCCTAATGCTTCTGGTACCAAAATCCCAGGAACAGCGAGCATAGCCCATCTACAGTGGATGAGC
TCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTCTCCAAGTCCAAGTGGGTCAAACCCAA
AGTCA
Transcript length: 392
Transcript exons: 20339940-20340228,20340316-20340418
CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA
ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT
TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC
ATATCCTAATGCTTCTGGTACCAAAATCCCAGGAACAGCGAGCATAGCCCATCTACAGTGGATG
AGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTCTCCAAGTCCAAGTGGGTCAAACC
CAAAGTCA
						
					

						Genomic sequence
						
							CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG
GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA
ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT
TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC
ATATCCTAATGCTTCTGGTACCAAAATCCCAGGCTACAACACCACCCACCAAGTCCATTAGATT
AAACTTAACAAGACTAAACCCTTATGATAAGACAAAGATTGGATATTGAAACTTACAACAGCGA
GCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTC
TCCAAGTCCAAGTGGGTCAAACCCAAAGTCA
						
					

			
		

Sequences
Splice junction sequence	AGCGAGCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGA ACTTCTCCAAGTCCAAGTGGGTCAAACCCAAAGTCAcgttcttgatctctttaactttcaattc 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: 290 Transcript exons: 20339940-20339967,20340070-20340228,20340316-20340418 CGTTCTTGATCTCTTTAACTTTCAATTCAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGT GGGCAAAGTACCCCACGGGACTGGGTTTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCC CATTCCTGAGCCTTAACCCAGTTTCCATATCCTAATGCTTCTGGTACCAAAATCCCAGGAACAG CGAGCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAAC TTCTCCAAGTCCAAGTGGGTCAAACCCAAAGTCA Transcript length: 325 Transcript exons: 20339940-20340014,20340082-20340228,20340316-20340418 CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGTTTC CCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCCATA TCCTAATGCTTCTGGTACCAAAATCCCAGGAACAGCGAGCATAGCCCATCTACAGTGGATGAGC TCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTCTCCAAGTCCAAGTGGGTCAAACCCAA AGTCA Transcript length: 392 Transcript exons: 20339940-20340228,20340316-20340418 CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC ATATCCTAATGCTTCTGGTACCAAAATCCCAGGAACAGCGAGCATAGCCCATCTACAGTGGATG AGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTCTCCAAGTCCAAGTGGGTCAAACC CAAAGTCA
Genomic sequence	CGTTCTTGATCTCTTTAACTTTCAATTCCTCGAGCTTCTTGGGGTCCTTCGAGTATCCAAGAGG GTCAAATGCGCCTCCCGGGTACTTCTTCTTCTCAGGGTCTTTCTCCATACTTCTCTGGTGCTCA ACAAATGCAATGGCTAAGAACTCAATGGCCAAGATTGTGGGCAAAGTACCCCACGGGACTGGGT TTCCCAAGTAAGTGGCTTGACCCCCTGGTAGTGCTGCCCATTCCTGAGCCTTAACCCAGTTTCC ATATCCTAATGCTTCTGGTACCAAAATCCCAGGCTACAACACCACCCACCAAGTCCATTAGATT AAACTTAACAAGACTAAACCCTTATGATAAGACAAAGATTGGATATTGAAACTTACAACAGCGA GCATAGCCCATCTACAGTGGATGAGCTCTGACTCTTTGTATCTCTCAAGGTTCGCTGGAACTTC TCCAAGTCCAAGTGGGTCAAACCCAAAGTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.343066045

Conservation Information
Conserved circRNAs	NA
PMCS	0.343066045

			
						 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
						Ye et al., 2015;Pan et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G54890_circ_g.6

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