Plant Circular RNA Database

Detail information of AT2G42500_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G42500_circ_g.4
					
						ID in PlantcircBase
						ath_circ_017951
					
						Alias
						Ath_circ_FC1640
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17698643-17700174  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT2G42500						
					
						Parent gene annotation
						
							Serine/threonine-protein phosphatase PP2A-3 catalytic subunit
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G42500_circ_g.1 AT2G42500_circ_g.2 AT2G42500_circ_g.3 AT2G42500_circ_g.5 AT2G42500_circ_g.6 AT2G42500_circ_g.7 AT2G42500_circ_g.8 AT2G42500_circ_g.9 AT2G42500_circ_g.10 						
					
						Support reads
						4
					
						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  
						
							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
						AT2G42500.5:6
AT2G42500.4:5
AT2G42500.1:5
AT2G42500.2:5
AT2G42500.3:5

General Information
CircRNA Name	AT2G42500_circ_g.4
ID in PlantcircBase	ath_circ_017951
Alias	Ath_circ_FC1640
Organism	Arabidpsis thaliana
Position	chr2: 17698643-17700174 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder
Parent gene	AT2G42500
Parent gene annotation	Serine/threonine-protein phosphatase PP2A-3 catalytic subunit
Parent gene strand	-
Alternative splicing	AT2G42500_circ_g.1 AT2G42500_circ_g.2 AT2G42500_circ_g.3 AT2G42500_circ_g.5 AT2G42500_circ_g.6 AT2G42500_circ_g.7 AT2G42500_circ_g.8 AT2G42500_circ_g.9 AT2G42500_circ_g.10
Support reads	4
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	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	AT2G42500.5:6 AT2G42500.4:5 AT2G42500.1:5 AT2G42500.2:5 AT2G42500.3:5

			
						 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  
						
							AGGAAGTCTAAATATTTCATCTTCGTACCGTAACAGTTTCAACAGAATAATAACCACGGTCCAC
ATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCActgaccaaatgtatatccggcaccccga
ggagagatgccccaaccacatcggtcatcggggtcagaccataataagtcacacatcggccctt
catggggc

									
								

					

						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: 444
Transcript exons: 17698643-17698834,17699176-17699242,17699554-17699594,17
699835-17699906,17700103-17700174
CTGACCAAATGTATATCCGGCACCCCGAGGAGAGATGCCCCAACCACATCGGTCATCGGGGTCA
GACCATAATAAGTCACACATCGGCCCTTCATGGGGCACTTCTTGAACTCGATCAAAATTCCTTA
TGTTGTCAAGGGTCTCGATAGATGGAGATAATCCACCATGAAGGCAAAATATTTCTGACTCAAC
CAAGGCTGTCAGAGGAAAATAGTCGAAGAGGTCTGTAAAGATTTTCCAAACATTTGCGTTGCCG
TACTTTCGTAGACATTCATCATAAAATCCATAAACCTGAGTAATCTGACGACTTTCATGGTTTC
CTCTAAGAATAGTGATTCGCTGAGGATATCGCATCTTTAAGGCGACTAACAGCGTAACAGTTTC
AACAGAATAATAACCACGGTCCACATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCA
						
					

						Genomic sequence
						
							CTGACCAAATGTATATCCGGCACCCCGAGGAGAGATGCCCCAACCACATCGGTCATCGGGGTCA
GACCATAATAAGTCACACATCGGCCCTTCATGGGGCACTTCTTGAACTCGATCAAAATTCCTTA
TGTTGTCAAGGGTCTCGATAGATGGAGATAATCCACCATGAAGGCAAAATATTTCTGACTCAAC
CTGCAGGGAAAAAACATAATGATTTGATGATTCCCAAAAATTTGTGTAGAAAATACCAACGATT
TAGTCAGATAAGGCATACATGAAATCTTCCATATATAACAGATCTCCATTCTTTGCATTTTTCA
GAATACTAACGTCTTGCAATTGATGTGACACTAGCAAAAGAAATACGACAGCACAGTACAAAAG
TACTACTTTGGTTCCAAATAATACTGCCAGCACAAGACAAAGAACTGATCATCTATATTAATTG
ACTACCGGACGAGGATAGACTTATATGTGAACCCCCACTAACAAAAAAGGAAGAAAAATGTGAG
ACATGTATGATAGGTACTAACCAAGGCTGTCAGAGGAAAATAGTCGAAGAGGTCTGTAAAGATT
TTCCAAACATTTGCGTTGCCGTACCTAAAAAGGAAAACATGGTTTGTTAAATTTATTGCAAAAT
CTATATCCCAAATAAGCTGCAAACTAGGATGTGTAAGATTATACAACATAGAACAATACTATAA
GCAAGTAATCATAAGCCCAAAGGATTAACAGAAACAGGAAGTAAAGAAAGAAAAGACAATTTTG
GACAGGCTACCATACACACATACAATGCAACAGCAAAAATATAAGGACAATAGTAATGCTAATA
ATAATTAAAAAAATTGTTTAAATGCATTAGAAAATAAGGATTTTTTTTCCAGTATAAGGATTTT
TTCCAGGAGACTCACTTTCGTAGACATTCATCATAAAATCCATAAACCTGAGTAATCTGCGAGA
TGGAAGAAAAAGAAGAAAAGCCTGTGTCAGATTAAAATAGTAATATGATAAAAAAAATGTGCAC
AAAACGAATTTTGTAGACAAAACAGAGACTTATAAAAAAGGAAATTGTGTGTCAACCAAGATCT
CAACGATGGAAAAGACTGGATACACAATGAAGTACTGTATTTAACATCAGAAGGTGAATTTACA
AGTGGAACCAGAGTAATAAAATCATAAAGCATTAGTCTACCTGACGACTTTCATGGTTTCCTCT
AAGAATAGTGATTCGCTGAGGATATCGCATCTTTAAGGCGACTAACAGCTGGAAAGAGAATAAG
AAAGAGAAACAGTATCAGCATACTTCATAGTCACACCCAAAATATATACATTGTAAAGAAAAAA
ATATCCGTCAAGTTAATGGTATCTTGTTACCAATATAAAAAGACAATGACTGGCTTGCCAATCA
GCCTACTCTTAAATGAATAAAAAAAGGAAGTCTAAATATTTCATCTTCGTACCGTAACAGTTTC
AACAGAATAATAACCACGGTCCACATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCA
						
					

			
		

Sequences
Splice junction sequence	AGGAAGTCTAAATATTTCATCTTCGTACCGTAACAGTTTCAACAGAATAATAACCACGGTCCAC ATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCActgaccaaatgtatatccggcaccccga ggagagatgccccaaccacatcggtcatcggggtcagaccataataagtcacacatcggccctt catggggc
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: 444 Transcript exons: 17698643-17698834,17699176-17699242,17699554-17699594,17 699835-17699906,17700103-17700174 CTGACCAAATGTATATCCGGCACCCCGAGGAGAGATGCCCCAACCACATCGGTCATCGGGGTCA GACCATAATAAGTCACACATCGGCCCTTCATGGGGCACTTCTTGAACTCGATCAAAATTCCTTA TGTTGTCAAGGGTCTCGATAGATGGAGATAATCCACCATGAAGGCAAAATATTTCTGACTCAAC CAAGGCTGTCAGAGGAAAATAGTCGAAGAGGTCTGTAAAGATTTTCCAAACATTTGCGTTGCCG TACTTTCGTAGACATTCATCATAAAATCCATAAACCTGAGTAATCTGACGACTTTCATGGTTTC CTCTAAGAATAGTGATTCGCTGAGGATATCGCATCTTTAAGGCGACTAACAGCGTAACAGTTTC AACAGAATAATAACCACGGTCCACATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCA
Genomic sequence	CTGACCAAATGTATATCCGGCACCCCGAGGAGAGATGCCCCAACCACATCGGTCATCGGGGTCA GACCATAATAAGTCACACATCGGCCCTTCATGGGGCACTTCTTGAACTCGATCAAAATTCCTTA TGTTGTCAAGGGTCTCGATAGATGGAGATAATCCACCATGAAGGCAAAATATTTCTGACTCAAC CTGCAGGGAAAAAACATAATGATTTGATGATTCCCAAAAATTTGTGTAGAAAATACCAACGATT TAGTCAGATAAGGCATACATGAAATCTTCCATATATAACAGATCTCCATTCTTTGCATTTTTCA GAATACTAACGTCTTGCAATTGATGTGACACTAGCAAAAGAAATACGACAGCACAGTACAAAAG TACTACTTTGGTTCCAAATAATACTGCCAGCACAAGACAAAGAACTGATCATCTATATTAATTG ACTACCGGACGAGGATAGACTTATATGTGAACCCCCACTAACAAAAAAGGAAGAAAAATGTGAG ACATGTATGATAGGTACTAACCAAGGCTGTCAGAGGAAAATAGTCGAAGAGGTCTGTAAAGATT TTCCAAACATTTGCGTTGCCGTACCTAAAAAGGAAAACATGGTTTGTTAAATTTATTGCAAAAT CTATATCCCAAATAAGCTGCAAACTAGGATGTGTAAGATTATACAACATAGAACAATACTATAA GCAAGTAATCATAAGCCCAAAGGATTAACAGAAACAGGAAGTAAAGAAAGAAAAGACAATTTTG GACAGGCTACCATACACACATACAATGCAACAGCAAAAATATAAGGACAATAGTAATGCTAATA ATAATTAAAAAAATTGTTTAAATGCATTAGAAAATAAGGATTTTTTTTCCAGTATAAGGATTTT TTCCAGGAGACTCACTTTCGTAGACATTCATCATAAAATCCATAAACCTGAGTAATCTGCGAGA TGGAAGAAAAAGAAGAAAAGCCTGTGTCAGATTAAAATAGTAATATGATAAAAAAAATGTGCAC AAAACGAATTTTGTAGACAAAACAGAGACTTATAAAAAAGGAAATTGTGTGTCAACCAAGATCT CAACGATGGAAAAGACTGGATACACAATGAAGTACTGTATTTAACATCAGAAGGTGAATTTACA AGTGGAACCAGAGTAATAAAATCATAAAGCATTAGTCTACCTGACGACTTTCATGGTTTCCTCT AAGAATAGTGATTCGCTGAGGATATCGCATCTTTAAGGCGACTAACAGCTGGAAAGAGAATAAG AAAGAGAAACAGTATCAGCATACTTCATAGTCACACCCAAAATATATACATTGTAAAGAAAAAA ATATCCGTCAAGTTAATGGTATCTTGTTACCAATATAAAAAGACAATGACTGGCTTGCCAATCA GCCTACTCTTAAATGAATAAAAAAAGGAAGTCTAAATATTTCATCTTCGTACCGTAACAGTTTC AACAGAATAATAACCACGGTCCACATAGTCTCCCATAAACAGGTAATTGGTATCAGGGCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.244572911

Conservation Information
Conserved circRNAs	NA
PMCS	0.244572911

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17700151-17698645(-)
						
						Potential amino acid sequence
						
							MGDYVDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIF
TDLFDYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWG
ISPRGAGYTFGQCPDTNYLFMGDYVDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQV
YGFYDECLRKYGNANVWKIFTDLFDYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVP
HEGPMCDLLWSDPDDRCGWGISPRGAGYTFGQCPDTNYLFMGDYVDRGYYSVETVTLLVALKMR
YPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIFTDLFDYFPLTALVESEIFCLHGGL
SPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWGISPRGAGYTFGQCPDTNYLFMGDY
VDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIFTDLF
DYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWGISPR
GAGYTFGQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17700151-17698645(-)
Potential amino acid sequence	MGDYVDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIF TDLFDYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWG ISPRGAGYTFGQCPDTNYLFMGDYVDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQV YGFYDECLRKYGNANVWKIFTDLFDYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVP HEGPMCDLLWSDPDDRCGWGISPRGAGYTFGQCPDTNYLFMGDYVDRGYYSVETVTLLVALKMR YPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIFTDLFDYFPLTALVESEIFCLHGGL SPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWGISPRGAGYTFGQCPDTNYLFMGDY VDRGYYSVETVTLLVALKMRYPQRITILRGNHESRQITQVYGFYDECLRKYGNANVWKIFTDLF DYFPLTALVESEIFCLHGGLSPSIETLDNIRNFDRVQEVPHEGPMCDLLWSDPDDRCGWGISPR GAGYTFGQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT2G42500_circ_g.4

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