Plant Circular RNA Database

Detail information of AT3G59920_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G59920_circ_g.3
					
						ID in PlantcircBase
						ath_circ_028370
					
						Alias
						At_ciR5027
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22135561-22136959  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT3G59920						
					
						Parent gene annotation
						
							Guanosine nucleotide diphosphate dissociation inhibitor
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G59920_circ_g.1 AT3G59920_circ_g.2 AT3G59920_circ_g.4 AT3G59920_circ_g.5 AT3G59920_circ_g.6 AT3G59920_circ_g.7 AT3G59920_circ_g.8 AT3G59920_circ_g.9 						
					
						Support reads
						2
					
						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  
						
							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
						AT3G59920.1:7

General Information
CircRNA Name	AT3G59920_circ_g.3
ID in PlantcircBase	ath_circ_028370
Alias	At_ciR5027
Organism	Arabidpsis thaliana
Position	chr3: 22135561-22136959 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT3G59920
Parent gene annotation	Guanosine nucleotide diphosphate dissociation inhibitor
Parent gene strand	+
Alternative splicing	AT3G59920_circ_g.1 AT3G59920_circ_g.2 AT3G59920_circ_g.4 AT3G59920_circ_g.5 AT3G59920_circ_g.6 AT3G59920_circ_g.7 AT3G59920_circ_g.8 AT3G59920_circ_g.9
Support reads	2
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	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	AT3G59920.1:7

			
						 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  
						
							AGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCAAA
AAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGgtgcttcacatggacaggaatgactact
atggtggagaatcaacttcccttaatctcaatcagctttggaagaagttcaggggagaagagaa
ggctcctg

									
								

					

						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: 786
Transcript exons: 22135561-22135707,22135797-22135904,22135998-22136170,22
136267-22136378,22136475-22136555,22136662-22136724,2213
6858-22136959
GTGCTTCACATGGACAGGAATGACTACTATGGTGGAGAATCAACTTCCCTTAATCTCAATCAGC
TTTGGAAGAAGTTCAGGGGAGAAGAGAAGGCTCCTGAGCATTTAGGCGCTAGCCGGGATTACAA
TGTTGACATGATGCCTAAGTTTATGATGGGAAATGGCAAGCTTGTTCGTACCCTTATTCATACA
GATGTTACAAAGTATTTGTCCTTCAAAGCTGTTGATGGAAGCTATGTTTTCGTCAAAGGAAAGG
TTCAAAAGGTGCCAGCTACTCCTATGGAGGCCCTGAAATCTTCTCTCATGGGCATATTTGAGAA
ACGTCGAGCCGGCAAGTTTTTCAGTTTTGTTCAAGAATACGATGAGAAGGACCCAAAAACACAC
GATGGAATGGATTTGACCAGAGTTACAACAAAGGAACTGATTGCGAAATATGGTCTTGATGGCA
ACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAATGACCAACATCTCGACCAACC
CGCCTTTGATACTGTAATGAGAATGAAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACA
TCTCCATATATTTATCCTCTCTATGGGTTGGGAGAACTACCCCAGGCATTTGCACGACTTAGTG
CTGTCTATGGTGGCACATATATGTTGAACAAACCTGAGTGCAAGGTAGAGTTTGACGAGGGAGG
TAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCAAAAAGATTGTGTGTGACCCT
TCATACCTGCCGAACAAG
						
					

						Genomic sequence
						
							GTGCTTCACATGGACAGGAATGACTACTATGGTGGAGAATCAACTTCCCTTAATCTCAATCAGC
TTTGGAAGAAGTTCAGGGGAGAAGAGAAGGCTCCTGAGCATTTAGGCGCTAGCCGGGATTACAA
TGTTGACATGATGCCTAAGGTATTATAGCTAGCTGCCATTTGTTTTGTTTTTATGCTAATCTTA
TCAATGTCACTTACTAACTCTTGTCTCTCAATGCCATTGACCAGTTTATGATGGGAAATGGCAA
GCTTGTTCGTACCCTTATTCATACAGATGTTACAAAGTATTTGTCCTTCAAAGCTGTTGATGGA
AGCTATGTTTTCGTCAAAGGAAAGGTACAAACTTCTCATTTGATGTATTTGTTGCTGACATTTT
AAAATATCATTTTGCTGATAACTCTTAAATTGTTGATGAAAATTTTCCTGCAGGTTCAAAAGGT
GCCAGCTACTCCTATGGAGGCCCTGAAATCTTCTCTCATGGGCATATTTGAGAAACGTCGAGCC
GGCAAGTTTTTCAGTTTTGTTCAAGAATACGATGAGAAGGACCCAAAAACACACGATGGAATGG
ATTTGACCAGAGTTACAACAAAGGAACTGATTGCGTAAGCTTGATGTTCTAATGCCTTCTAGAG
TTTATGGTGTTACTGACTTTCAAGTGAGGATATACGTGGCTAACCATTTATGTGACACTTTTGC
AGGAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGA
ATGACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGGTGAAATTTTGTCA
GACTTATCTTTCTTGTTATAACAGTTGTACATTTAGTTCTGAAGCAGCTAAGTTGATATTCTTG
CTTTAAATGGCTGGCTAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACATCTCCATATA
TTTATCCTCTCTATGGGTTGGGAGAACTACCCCAGGTTTTTCTGTCATTCTGACCTTTGCCTTC
TGTATGACTTTTCAAGTTTTATATGATTACATTTTTGATTCTTCTGTGACTTCTCTCTCTCTCT
TCTCCTTGTTCAGGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAA
CCTGAGTGCAAGGTATTTTCTCTTTGTCTTCATGACAACTCTTTGTTTTCTTTCTTGTTGTGCA
AGTCTGCAAGAGGGGAATGCACCGTAAGATTGTATTGGAGGAACGCTGTACTCATATATAGCAA
TGTTAATCTTATGCCAGGTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGG
AGAGACTGCTAAATGCAAAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAG
						
					

			
		

Sequences
Splice junction sequence	AGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCAAA AAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGgtgcttcacatggacaggaatgactact atggtggagaatcaacttcccttaatctcaatcagctttggaagaagttcaggggagaagagaa ggctcctg
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: 786 Transcript exons: 22135561-22135707,22135797-22135904,22135998-22136170,22 136267-22136378,22136475-22136555,22136662-22136724,2213 6858-22136959 GTGCTTCACATGGACAGGAATGACTACTATGGTGGAGAATCAACTTCCCTTAATCTCAATCAGC TTTGGAAGAAGTTCAGGGGAGAAGAGAAGGCTCCTGAGCATTTAGGCGCTAGCCGGGATTACAA TGTTGACATGATGCCTAAGTTTATGATGGGAAATGGCAAGCTTGTTCGTACCCTTATTCATACA GATGTTACAAAGTATTTGTCCTTCAAAGCTGTTGATGGAAGCTATGTTTTCGTCAAAGGAAAGG TTCAAAAGGTGCCAGCTACTCCTATGGAGGCCCTGAAATCTTCTCTCATGGGCATATTTGAGAA ACGTCGAGCCGGCAAGTTTTTCAGTTTTGTTCAAGAATACGATGAGAAGGACCCAAAAACACAC GATGGAATGGATTTGACCAGAGTTACAACAAAGGAACTGATTGCGAAATATGGTCTTGATGGCA ACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAATGACCAACATCTCGACCAACC CGCCTTTGATACTGTAATGAGAATGAAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACA TCTCCATATATTTATCCTCTCTATGGGTTGGGAGAACTACCCCAGGCATTTGCACGACTTAGTG CTGTCTATGGTGGCACATATATGTTGAACAAACCTGAGTGCAAGGTAGAGTTTGACGAGGGAGG TAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCAAAAAGATTGTGTGTGACCCT TCATACCTGCCGAACAAG
Genomic sequence	GTGCTTCACATGGACAGGAATGACTACTATGGTGGAGAATCAACTTCCCTTAATCTCAATCAGC TTTGGAAGAAGTTCAGGGGAGAAGAGAAGGCTCCTGAGCATTTAGGCGCTAGCCGGGATTACAA TGTTGACATGATGCCTAAGGTATTATAGCTAGCTGCCATTTGTTTTGTTTTTATGCTAATCTTA TCAATGTCACTTACTAACTCTTGTCTCTCAATGCCATTGACCAGTTTATGATGGGAAATGGCAA GCTTGTTCGTACCCTTATTCATACAGATGTTACAAAGTATTTGTCCTTCAAAGCTGTTGATGGA AGCTATGTTTTCGTCAAAGGAAAGGTACAAACTTCTCATTTGATGTATTTGTTGCTGACATTTT AAAATATCATTTTGCTGATAACTCTTAAATTGTTGATGAAAATTTTCCTGCAGGTTCAAAAGGT GCCAGCTACTCCTATGGAGGCCCTGAAATCTTCTCTCATGGGCATATTTGAGAAACGTCGAGCC GGCAAGTTTTTCAGTTTTGTTCAAGAATACGATGAGAAGGACCCAAAAACACACGATGGAATGG ATTTGACCAGAGTTACAACAAAGGAACTGATTGCGTAAGCTTGATGTTCTAATGCCTTCTAGAG TTTATGGTGTTACTGACTTTCAAGTGAGGATATACGTGGCTAACCATTTATGTGACACTTTTGC AGGAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGA ATGACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGGTGAAATTTTGTCA GACTTATCTTTCTTGTTATAACAGTTGTACATTTAGTTCTGAAGCAGCTAAGTTGATATTCTTG CTTTAAATGGCTGGCTAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACATCTCCATATA TTTATCCTCTCTATGGGTTGGGAGAACTACCCCAGGTTTTTCTGTCATTCTGACCTTTGCCTTC TGTATGACTTTTCAAGTTTTATATGATTACATTTTTGATTCTTCTGTGACTTCTCTCTCTCTCT TCTCCTTGTTCAGGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAA CCTGAGTGCAAGGTATTTTCTCTTTGTCTTCATGACAACTCTTTGTTTTCTTTCTTGTTGTGCA AGTCTGCAAGAGGGGAATGCACCGTAAGATTGTATTGGAGGAACGCTGTACTCATATATAGCAA TGTTAATCTTATGCCAGGTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGG AGAGACTGCTAAATGCAAAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24921115

Conservation Information
Conserved circRNAs	NA
PMCS	0.24921115

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22135570-22136956(+)
						
						Potential amino acid sequence
						
							MDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNGKLVRTLIHTDVT
KYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQEYDEKDPKTHDGM
DLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPY
IYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYL
PNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNGKLVRTL
IHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQEYDEKDP
KTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARF
QGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIV
CDPSYLPNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNG
KLVRTLIHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQE
YDEKDPKTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYA
ESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETA
KCKKIVCDPSYLPNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPK
FMMGNGKLVRTLIHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKF
FSFVQEYDEKDPKTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVM
RMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVT
SEGETAKCKKIVCDPSYLPNK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22135570-22136956(+)
Potential amino acid sequence	MDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNGKLVRTLIHTDVT KYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQEYDEKDPKTHDGM DLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPY IYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYL PNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNGKLVRTL IHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQEYDEKDP KTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARF QGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIV CDPSYLPNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPKFMMGNG KLVRTLIHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKFFSFVQE YDEKDPKTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYA ESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETA KCKKIVCDPSYLPNKVLHMDRNDYYGGESTSLNLNQLWKKFRGEEKAPEHLGASRDYNVDMMPK FMMGNGKLVRTLIHTDVTKYLSFKAVDGSYVFVKGKVQKVPATPMEALKSSLMGIFEKRRAGKF FSFVQEYDEKDPKTHDGMDLTRVTTKELIAKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVM RMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVT SEGETAKCKKIVCDPSYLPNK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT3G59920_circ_g.3

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