Plant Circular RNA Database

Detail information of AT3G55440_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G55440_circ_g.3
					
						ID in PlantcircBase
						ath_circ_027642
					
						Alias
						At_ciR4182
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20554160-20555305  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT3G55440						
					
						Parent gene annotation
						
							Triosephosphate isomerase, cytosolic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G55440_circ_g.2 AT3G55440_circ_g.4 AT3G55440_circ_g.5 AT3G55440_circ_g.6 AT3G55440_circ_g.7 AT3G55440_circ_g.8 AT3G55440_circ_g.9 AT3G55440_circ_g.10 AT3G55440_circ_g.11 AT3G55440_circ_g.12 AT3G55440_circ_g.13 AT3G55440_circ_g.14 AT3G55440_circ_g.15 3_circ_ag.16 AT3G55440_circ_g.17 AT3G55440_circ_g.18 AT3G55440_circ_g.19 AT3G55450_circ_g.1 AT3G55450_circ_g.2 AT3G55450_circ_g.3 AT3G55460_circ_g.1 AT3G55460_circ_g.2 AT3G55460_circ_g.3 AT3G55460_circ_g.4 AT3G55460_circ_g.5 AT3G55460_circ_g.6 AT3G55460_circ_g.7 AT3G55470_circ_g.1 AT3G55470_circ_g.2 AT3G55480_circ_g.1 AT3G55480_circ_g.2 AT3G55480_circ_g.3 AT3G55480_circ_g.4 ENSRNA049493723_circ_g.1 AT3G55490_circ_g.1 AT3G55510_circ_g.1 AT3G55510_circ_g.2 AT3G55530_circ_g.1 AT3G55530_circ_g.2 AT3G55530_circ_g.3 AT3G55580_circ_g.1 AT3G55580_circ_g.2 AT3G55600_circ_g.1 AT3G55610_circ_g.1 AT3G55610_circ_g.2 AT3G55610_circ_g.3 AT3G55610_circ_g.4 AT3G55610_circ_g.5 AT3G55610_circ_g.6 AT3G55610_circ_g.7 AT3G55610_circ_g.8 AT3G55610_circ_g.9 AT3G55610_circ_g.10 AT3G55610_circ_g.11 AT3G55610_circ_g.12 AT3G55610_circ_g.13 AT3G55610_circ_g.14 AT3G55620_circ_g.1 AT3G55620_circ_g.2 AT3G55620_circ_g.3 AT3G55630_circ_g.1 AT3G55630_circ_g.2 AT3G55630_circ_g.3 AT3G55630_circ_g.4 AT3G55630_circ_g.5 AT3G55630_circ_g.6 AT3G55630_circ_g.7 AT3G55630_circ_g.8 AT3G55630_circ_g.9 AT3G55630_circ_g.10 AT3G55630_circ_g.11 AT3G55630_circ_g.12 AT3G55630_circ_g.13 AT3G55630_circ_g.14 AT3G55640_circ_g.1 AT3G55640_circ_g.2 AT3G55660_circ_g.1 AT3G55660_circ_g.2 AT3G55660_circ_g.3 						
					
						Support reads
						4/1/3
					
						Tissues
						leaf/whole_plant/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  
						
							GT-AG							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
						AT3G55440.1:4

General Information
CircRNA Name	AT3G55440_circ_g.3
ID in PlantcircBase	ath_circ_027642
Alias	At_ciR4182
Organism	Arabidpsis thaliana
Position	chr3: 20554160-20555305 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full
Parent gene	AT3G55440
Parent gene annotation	Triosephosphate isomerase, cytosolic
Parent gene strand	+
Alternative splicing	AT3G55440_circ_g.2 AT3G55440_circ_g.4 AT3G55440_circ_g.5 AT3G55440_circ_g.6 AT3G55440_circ_g.7 AT3G55440_circ_g.8 AT3G55440_circ_g.9 AT3G55440_circ_g.10 AT3G55440_circ_g.11 AT3G55440_circ_g.12 AT3G55440_circ_g.13 AT3G55440_circ_g.14 AT3G55440_circ_g.15 3_circ_ag.16 AT3G55440_circ_g.17 AT3G55440_circ_g.18 AT3G55440_circ_g.19 AT3G55450_circ_g.1 AT3G55450_circ_g.2 AT3G55450_circ_g.3 AT3G55460_circ_g.1 AT3G55460_circ_g.2 AT3G55460_circ_g.3 AT3G55460_circ_g.4 AT3G55460_circ_g.5 AT3G55460_circ_g.6 AT3G55460_circ_g.7 AT3G55470_circ_g.1 AT3G55470_circ_g.2 AT3G55480_circ_g.1 AT3G55480_circ_g.2 AT3G55480_circ_g.3 AT3G55480_circ_g.4 ENSRNA049493723_circ_g.1 AT3G55490_circ_g.1 AT3G55510_circ_g.1 AT3G55510_circ_g.2 AT3G55530_circ_g.1 AT3G55530_circ_g.2 AT3G55530_circ_g.3 AT3G55580_circ_g.1 AT3G55580_circ_g.2 AT3G55600_circ_g.1 AT3G55610_circ_g.1 AT3G55610_circ_g.2 AT3G55610_circ_g.3 AT3G55610_circ_g.4 AT3G55610_circ_g.5 AT3G55610_circ_g.6 AT3G55610_circ_g.7 AT3G55610_circ_g.8 AT3G55610_circ_g.9 AT3G55610_circ_g.10 AT3G55610_circ_g.11 AT3G55610_circ_g.12 AT3G55610_circ_g.13 AT3G55610_circ_g.14 AT3G55620_circ_g.1 AT3G55620_circ_g.2 AT3G55620_circ_g.3 AT3G55630_circ_g.1 AT3G55630_circ_g.2 AT3G55630_circ_g.3 AT3G55630_circ_g.4 AT3G55630_circ_g.5 AT3G55630_circ_g.6 AT3G55630_circ_g.7 AT3G55630_circ_g.8 AT3G55630_circ_g.9 AT3G55630_circ_g.10 AT3G55630_circ_g.11 AT3G55630_circ_g.12 AT3G55630_circ_g.13 AT3G55630_circ_g.14 AT3G55640_circ_g.1 AT3G55640_circ_g.2 AT3G55660_circ_g.1 AT3G55660_circ_g.2 AT3G55660_circ_g.3
Support reads	4/1/3
Tissues	leaf/whole_plant/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	GT-AG 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	AT3G55440.1:4

			
						 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  
						
							CAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCA
TGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGaacggaactgctgaggaggtgaagaaga
ttgtgaacactcttaatgaagctcaggttccttcacaggatgttgtaggtatgtgtagcatctc
aattgctt

									
								

					

						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: 418
Transcript exons: 20554160-20555305
AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC
AGGATGTTGTAGAGGTTGTGGTTAGCCCTCCATATGTTTTTCTTCCCCTGGTTAAGAGCACATT
GAGGTCTGACTTTTTTGTTGCGGCACAAAACTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGT
GAAGTGAGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAA
GGAGGGCAATCCTTAATGAATCAAGCGAGTTCGTCGGAGACAAGGTTGCCTATGCACTTGCTCA
AGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCATG
GATGTTGTGGCTGCCCAGACCAAGGCTATTGCCG
						
					

						Genomic sequence
						
							AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC
AGGATGTTGTAGGTATGTGTAGCATCTCAATTGCTTTGACGACATTATGGCTTTTTTTTTAATT
TCCATGTCTATGAAATCTTAAGTAGTGACAAATATTTTGGGCATACAATTACAAACCTGTTTCA
ATGTACATCGATGTTCTATAGTGTTTATGCTTCTTAGGAACCATGGATAGATCTAGTGTTTGTT
GTTAGTTAAAATGTTCTTTATCATATACTTGTTATGGTTCTATCTTTGTTGATAGTTATAAGTA
TGTTTGTTCTTGTATTAATAATTTGATGAAATTTTACTAAATGCAGAGGTTGTGGTTAGCCCTC
CATATGTTTTTCTTCCCCTGGTTAAGAGCACATTGAGGTCTGACTTTTTTGTTGCGGCACAAAA
CTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGTGAAGTGAGGTGAGATTCTAACCATTGGTGT
ATACTTTAAGCTGTTTTACCATTATTGCTTCATGCAGTAAATATTTATGGTTTTGAAAATGAAT
ATGATTGTGTTTATAAACGAATCGATTTTTCCATCTGTTCTTCTTCTTTATCTTCTTTCCTATA
AGAATTGTGTAACCTAAGTGATTAAGAAAACAACTAGTAGTTGGTAGTAAGACCATGATTGGAT
TCGTGCCTGGTTAGACAAGTAGGTGTAATATGATTTACCTGTCTATGGAATGCTTTCATAGGAA
GAAAAGATATATTCTGTGGTGCCTGTATTTCCTGCTCTTATGCATTGTGTAATTTGTGTGTTTT
AGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAAGGAGGG
CAATCCTTAATGAATCAAGCGAGGTTGGTGACTTTACATGATAAAATAATTTTCTGGAGACTCA
AATAGCTTTTAAATTCATGATTTTGGTTTTTGACCTCTATCCTACATTTGTAGTTCGTCGGAGA
CAAGGTTGCCTATGCACTTGCTCAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAG
GAGCGGGAAGCTGGATCGACCATGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCG
						
					

			
		

Sequences
Splice junction sequence	CAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCA TGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGaacggaactgctgaggaggtgaagaaga ttgtgaacactcttaatgaagctcaggttccttcacaggatgttgtaggtatgtgtagcatctc aattgctt
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: 418 Transcript exons: 20554160-20555305 AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC AGGATGTTGTAGAGGTTGTGGTTAGCCCTCCATATGTTTTTCTTCCCCTGGTTAAGAGCACATT GAGGTCTGACTTTTTTGTTGCGGCACAAAACTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGT GAAGTGAGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAA GGAGGGCAATCCTTAATGAATCAAGCGAGTTCGTCGGAGACAAGGTTGCCTATGCACTTGCTCA AGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCATG GATGTTGTGGCTGCCCAGACCAAGGCTATTGCCG
Genomic sequence	AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC AGGATGTTGTAGGTATGTGTAGCATCTCAATTGCTTTGACGACATTATGGCTTTTTTTTTAATT TCCATGTCTATGAAATCTTAAGTAGTGACAAATATTTTGGGCATACAATTACAAACCTGTTTCA ATGTACATCGATGTTCTATAGTGTTTATGCTTCTTAGGAACCATGGATAGATCTAGTGTTTGTT GTTAGTTAAAATGTTCTTTATCATATACTTGTTATGGTTCTATCTTTGTTGATAGTTATAAGTA TGTTTGTTCTTGTATTAATAATTTGATGAAATTTTACTAAATGCAGAGGTTGTGGTTAGCCCTC CATATGTTTTTCTTCCCCTGGTTAAGAGCACATTGAGGTCTGACTTTTTTGTTGCGGCACAAAA CTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGTGAAGTGAGGTGAGATTCTAACCATTGGTGT ATACTTTAAGCTGTTTTACCATTATTGCTTCATGCAGTAAATATTTATGGTTTTGAAAATGAAT ATGATTGTGTTTATAAACGAATCGATTTTTCCATCTGTTCTTCTTCTTTATCTTCTTTCCTATA AGAATTGTGTAACCTAAGTGATTAAGAAAACAACTAGTAGTTGGTAGTAAGACCATGATTGGAT TCGTGCCTGGTTAGACAAGTAGGTGTAATATGATTTACCTGTCTATGGAATGCTTTCATAGGAA GAAAAGATATATTCTGTGGTGCCTGTATTTCCTGCTCTTATGCATTGTGTAATTTGTGTGTTTT AGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAAGGAGGG CAATCCTTAATGAATCAAGCGAGGTTGGTGACTTTACATGATAAAATAATTTTCTGGAGACTCA AATAGCTTTTAAATTCATGATTTTGGTTTTTGACCTCTATCCTACATTTGTAGTTCGTCGGAGA CAAGGTTGCCTATGCACTTGCTCAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAG GAGCGGGAAGCTGGATCGACCATGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211400671

Conservation Information
Conserved circRNAs	NA
PMCS	0.211400671

			
						 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;Chu et al., 2017;Pan et al., 2017

circRNA

Detail information of AT3G55440_circ_g.3

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