Plant Circular RNA Database

Detail information of AT3G55620_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G55620_circ_g.3
					
						ID in PlantcircBase
						ath_circ_027701
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20634557-20635604  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G55620						
					
						Parent gene annotation
						
							Eukaryotic translation initiation factor 6-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G55440_circ_g.2 AT3G55440_circ_g.3 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 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
						2
					
						Tissues
						whole_plant
					
						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
						AT3G55620.1:5

General Information
CircRNA Name	AT3G55620_circ_g.3
ID in PlantcircBase	ath_circ_027701
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 20634557-20635604 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G55620
Parent gene annotation	Eukaryotic translation initiation factor 6-2
Parent gene strand	+
Alternative splicing	AT3G55440_circ_g.2 AT3G55440_circ_g.3 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 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	2
Tissues	whole_plant
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	AT3G55620.1:5

			
						 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  
						
							TCAAGTTGTGGTCCAGCGAATTGATGAACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAAT
GACTATGTAGCTCTTGCCCACACCGATCTTGATAAGgtgtacgttagcctcctccctctaatgg
cgactcgtaagttttctgcagagcttacttatgatattgttgtgtttactcttctgtgtatttg
accttaat

									
								

					

						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: 393
Transcript exons: 20634557-20634590,20634679-20634775,20634870-20634955,20
635057-20635101,20635474-20635604
GTGTACGTTAGCCTCCTCCCTCTAATGGCGACTCGTCTTCAGTTTGAGAACAACTGCGAAGTTG
GTGTCTTTTCCAAACTCACTAATGCCTATTGCTTAGTCGCTATAGGAGGCTCTGAGAACTTTTA
CAGTGCTTTTGAGTCGGAGTTAGCAGATGTTATCCCTATTGTTAAGACCTCTATTGGAGGAACA
CGAATTATTGGGCGTCTTTGTGCTGGAAACAAGAATGGGCTTCTTGTACCTCATACAACAACTG
ACCAAGAGCTTCAACACTTAAGGAACAGTCTACCTGATCAAGTTGTGGTCCAGCGAATTGATGA
ACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAATGACTATGTAGCTCTTGCCCACACCGAT
CTTGATAAG
						
					

						Genomic sequence
						
							GTGTACGTTAGCCTCCTCCCTCTAATGGCGACTCGTAAGTTTTCTGCAGAGCTTACTTATGATA
TTGTTGTGTTTACTCTTCTGTGTATTTGACCTTAATGGGATTTGTGGGTAATACGCAGGTCTTC
AGTTTGAGAACAACTGCGAAGTTGGTGTCTTTTCCAAACTCACTAATGCCTATTGCTTAGTCGC
TATAGGAGGCTCTGAGAACTTTTACAGGTACCTTTTTTTTTTTTCTCTGTAAAGTTTTCAGTAT
TGTTTTTGCTTCTTCTATTTCACTTTTTTGATGTTTTTGGTTTGATGATTTGTGTAGTGCTTTT
GAGTCGGAGTTAGCAGATGTTATCCCTATTGTTAAGACCTCTATTGGAGGAACACGAATTATTG
GGCGTCTTTGTGCTGGTTAGCTTTCTCAACTAGCTGTTATATTTTCTTGCTTCAAATCATCGTG
ATTATTTCATTACTTTAGCGTAGTGAATGTGGTTTTGTGTTTCTTCGTATAGGAAACAAGAATG
GGCTTCTTGTACCTCATACAACAACTGACCAAGGTAATTTTATACTTCTTTCCTCAGATCGTTT
CTCATAACAATTAAGAATTGATTGTTTAATACCAGCATGATCCAGTTGTCTGAGATAGAGATTG
TAGAGTTTTTGGTGAATATCTTTTATGTAACTTGCCTGAAGCATCTACTCTGCGCCTCTGCCCA
TACCTGTTTCATTTCAGTTTATGAGTGGACTTTTTATAACTGAATAAGCTTTTGGTGAAGATGA
TTTTCCTCCTTAACTTGTTGATGATTTTGTAATGTTGCAATATTTATTGAGTCTCTTGTTCTTT
TATATTAGAAATCTATATAGGTTTTAGGTCTGTAATTGGTTGCATCTCCTGAGTCCTGCTTATT
TTTTTATGTTTACTCGTCCAGAGCTTCAACACTTAAGGAACAGTCTACCTGATCAAGTTGTGGT
CCAGCGAATTGATGAACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAATGACTATGTAGCT
CTTGCCCACACCGATCTTGATAAG
						
					

			
		

Sequences
Splice junction sequence	TCAAGTTGTGGTCCAGCGAATTGATGAACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAAT GACTATGTAGCTCTTGCCCACACCGATCTTGATAAGgtgtacgttagcctcctccctctaatgg cgactcgtaagttttctgcagagcttacttatgatattgttgtgtttactcttctgtgtatttg accttaat
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: 393 Transcript exons: 20634557-20634590,20634679-20634775,20634870-20634955,20 635057-20635101,20635474-20635604 GTGTACGTTAGCCTCCTCCCTCTAATGGCGACTCGTCTTCAGTTTGAGAACAACTGCGAAGTTG GTGTCTTTTCCAAACTCACTAATGCCTATTGCTTAGTCGCTATAGGAGGCTCTGAGAACTTTTA CAGTGCTTTTGAGTCGGAGTTAGCAGATGTTATCCCTATTGTTAAGACCTCTATTGGAGGAACA CGAATTATTGGGCGTCTTTGTGCTGGAAACAAGAATGGGCTTCTTGTACCTCATACAACAACTG ACCAAGAGCTTCAACACTTAAGGAACAGTCTACCTGATCAAGTTGTGGTCCAGCGAATTGATGA ACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAATGACTATGTAGCTCTTGCCCACACCGAT CTTGATAAG
Genomic sequence	GTGTACGTTAGCCTCCTCCCTCTAATGGCGACTCGTAAGTTTTCTGCAGAGCTTACTTATGATA TTGTTGTGTTTACTCTTCTGTGTATTTGACCTTAATGGGATTTGTGGGTAATACGCAGGTCTTC AGTTTGAGAACAACTGCGAAGTTGGTGTCTTTTCCAAACTCACTAATGCCTATTGCTTAGTCGC TATAGGAGGCTCTGAGAACTTTTACAGGTACCTTTTTTTTTTTTCTCTGTAAAGTTTTCAGTAT TGTTTTTGCTTCTTCTATTTCACTTTTTTGATGTTTTTGGTTTGATGATTTGTGTAGTGCTTTT GAGTCGGAGTTAGCAGATGTTATCCCTATTGTTAAGACCTCTATTGGAGGAACACGAATTATTG GGCGTCTTTGTGCTGGTTAGCTTTCTCAACTAGCTGTTATATTTTCTTGCTTCAAATCATCGTG ATTATTTCATTACTTTAGCGTAGTGAATGTGGTTTTGTGTTTCTTCGTATAGGAAACAAGAATG GGCTTCTTGTACCTCATACAACAACTGACCAAGGTAATTTTATACTTCTTTCCTCAGATCGTTT CTCATAACAATTAAGAATTGATTGTTTAATACCAGCATGATCCAGTTGTCTGAGATAGAGATTG TAGAGTTTTTGGTGAATATCTTTTATGTAACTTGCCTGAAGCATCTACTCTGCGCCTCTGCCCA TACCTGTTTCATTTCAGTTTATGAGTGGACTTTTTATAACTGAATAAGCTTTTGGTGAAGATGA TTTTCCTCCTTAACTTGTTGATGATTTTGTAATGTTGCAATATTTATTGAGTCTCTTGTTCTTT TATATTAGAAATCTATATAGGTTTTAGGTCTGTAATTGGTTGCATCTCCTGAGTCCTGCTTATT TTTTTATGTTTACTCGTCCAGAGCTTCAACACTTAAGGAACAGTCTACCTGATCAAGTTGTGGT CCAGCGAATTGATGAACGTCTGTCTGCTCTTGGAAATTGCATTGCCTGCAATGACTATGTAGCT CTTGCCCACACCGATCTTGATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.200879256

Conservation Information
Conserved circRNAs	NA
PMCS	0.200879256

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20634581-20635601(+)
						
						Potential amino acid sequence
						
							MATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRIIGRLCA
GNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLDKVYVSL
LPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRIIGR
LCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLDKVY
VSLLPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRI
IGRLCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLD
KVYVSLLPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGG
TRIIGRLCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHT
DLDK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20634581-20635601(+)
Potential amino acid sequence	MATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRIIGRLCA GNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLDKVYVSL LPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRIIGR LCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLDKVY VSLLPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGGTRI IGRLCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHTDLD KVYVSLLPLMATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSIGG TRIIGRLCAGNKNGLLVPHTTTDQELQHLRNSLPDQVVVQRIDERLSALGNCIACNDYVALAHT DLDK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G55620_circ_g.3

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