Plant Circular RNA Database

Detail information of AT3G59920_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G59920_circ_g.6
					
						ID in PlantcircBase
						ath_circ_028373
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22136267-22137359  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						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.3 AT3G59920_circ_g.4 AT3G59920_circ_g.5 AT3G59920_circ_g.7 AT3G59920_circ_g.8 AT3G59920_circ_g.9 						
					
						Support reads
						3
					
						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
						AT3G59920.1:5

General Information
CircRNA Name	AT3G59920_circ_g.6
ID in PlantcircBase	ath_circ_028373
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 22136267-22137359 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
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.3 AT3G59920_circ_g.4 AT3G59920_circ_g.5 AT3G59920_circ_g.7 AT3G59920_circ_g.8 AT3G59920_circ_g.9
Support reads	3
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	AT3G59920.1:5

			
						 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  
						
							GGGCCATCGCCATTATGAGCCACCCGATTCCGAACACCAATGATTCTCACTCAGTGCAGGTCAT
CATACCCCAGAAACAGTTGGCCCGCAAATCGGATATgaaatatggtcttgatggcaacactatt
gactttattggtcacgcagtggcacttcacacgaatgaccaacatctcgaccaacccgcctttg
atactgta

									
								

					

						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: 483
Transcript exons: 22136267-22136378,22136475-22136555,22136662-22136724,22
136858-22136959,22137235-22137359
GAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAAT
GACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGCTCTATGCGGAATCTC
TTGCACGTTTCCAAGGAACATCTCCATATATTTATCCTCTCTATGGGTTGGGAGAACTACCCCA
GGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAACCTGAGTGCAAG
GTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCA
AAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGGTTAGGAAGATTGGCAGGGTTGCTCG
GGCCATCGCCATTATGAGCCACCCGATTCCGAACACCAATGATTCTCACTCAGTGCAGGTCATC
ATACCCCAGAAACAGTTGGCCCGCAAATCGGATAT
						
					

						Genomic sequence
						
							GAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAAT
GACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGGTGAAATTTTGTCAGA
CTTATCTTTCTTGTTATAACAGTTGTACATTTAGTTCTGAAGCAGCTAAGTTGATATTCTTGCT
TTAAATGGCTGGCTAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACATCTCCATATATT
TATCCTCTCTATGGGTTGGGAGAACTACCCCAGGTTTTTCTGTCATTCTGACCTTTGCCTTCTG
TATGACTTTTCAAGTTTTATATGATTACATTTTTGATTCTTCTGTGACTTCTCTCTCTCTCTTC
TCCTTGTTCAGGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAACC
TGAGTGCAAGGTATTTTCTCTTTGTCTTCATGACAACTCTTTGTTTTCTTTCTTGTTGTGCAAG
TCTGCAAGAGGGGAATGCACCGTAAGATTGTATTGGAGGAACGCTGTACTCATATATAGCAATG
TTAATCTTATGCCAGGTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAG
AGACTGCTAAATGCAAAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGGTAATATTGCA
GTTCTTAGCATGTTTAAATTTTCAATTACTGTGTCCATACTTATCCACGTCAGGAGGATCGTTA
TAAAGTTGCTGTTCATGAAACTTGTGACTTTTGCCGTTGGCCTGTTCATTATGTTGGTTGATTG
CCATAGTTTTTATATTCATTCACACACTTAGTTCTTCTCTTCTTGTAATGACTAGACTGTGGTC
TTGTTCAGGATTTTTGGAAAAATCTATTCCTTTTTGTTGTTTTTTATATGATGATTAATCACAT
TCAAACAGGTTAGGAAGATTGGCAGGGTTGCTCGGGCCATCGCCATTATGAGCCACCCGATTCC
GAACACCAATGATTCTCACTCAGTGCAGGTCATCATACCCCAGAAACAGTTGGCCCGCAAATCG
GATAT
						
					

			
		

Sequences
Splice junction sequence	GGGCCATCGCCATTATGAGCCACCCGATTCCGAACACCAATGATTCTCACTCAGTGCAGGTCAT CATACCCCAGAAACAGTTGGCCCGCAAATCGGATATgaaatatggtcttgatggcaacactatt gactttattggtcacgcagtggcacttcacacgaatgaccaacatctcgaccaacccgcctttg atactgta
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: 483 Transcript exons: 22136267-22136378,22136475-22136555,22136662-22136724,22 136858-22136959,22137235-22137359 GAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAAT GACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGCTCTATGCGGAATCTC TTGCACGTTTCCAAGGAACATCTCCATATATTTATCCTCTCTATGGGTTGGGAGAACTACCCCA GGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAACCTGAGTGCAAG GTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAGAGACTGCTAAATGCA AAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGGTTAGGAAGATTGGCAGGGTTGCTCG GGCCATCGCCATTATGAGCCACCCGATTCCGAACACCAATGATTCTCACTCAGTGCAGGTCATC ATACCCCAGAAACAGTTGGCCCGCAAATCGGATAT
Genomic sequence	GAAATATGGTCTTGATGGCAACACTATTGACTTTATTGGTCACGCAGTGGCACTTCACACGAAT GACCAACATCTCGACCAACCCGCCTTTGATACTGTAATGAGAATGAAGGTGAAATTTTGTCAGA CTTATCTTTCTTGTTATAACAGTTGTACATTTAGTTCTGAAGCAGCTAAGTTGATATTCTTGCT TTAAATGGCTGGCTAGCTCTATGCGGAATCTCTTGCACGTTTCCAAGGAACATCTCCATATATT TATCCTCTCTATGGGTTGGGAGAACTACCCCAGGTTTTTCTGTCATTCTGACCTTTGCCTTCTG TATGACTTTTCAAGTTTTATATGATTACATTTTTGATTCTTCTGTGACTTCTCTCTCTCTCTTC TCCTTGTTCAGGCATTTGCACGACTTAGTGCTGTCTATGGTGGCACATATATGTTGAACAAACC TGAGTGCAAGGTATTTTCTCTTTGTCTTCATGACAACTCTTTGTTTTCTTTCTTGTTGTGCAAG TCTGCAAGAGGGGAATGCACCGTAAGATTGTATTGGAGGAACGCTGTACTCATATATAGCAATG TTAATCTTATGCCAGGTAGAGTTTGACGAGGGAGGTAAGGTTATTGGTGTAACATCTGAGGGAG AGACTGCTAAATGCAAAAAGATTGTGTGTGACCCTTCATACCTGCCGAACAAGGTAATATTGCA GTTCTTAGCATGTTTAAATTTTCAATTACTGTGTCCATACTTATCCACGTCAGGAGGATCGTTA TAAAGTTGCTGTTCATGAAACTTGTGACTTTTGCCGTTGGCCTGTTCATTATGTTGGTTGATTG CCATAGTTTTTATATTCATTCACACACTTAGTTCTTCTCTTCTTGTAATGACTAGACTGTGGTC TTGTTCAGGATTTTTGGAAAAATCTATTCCTTTTTGTTGTTTTTTATATGATGATTAATCACAT TCAAACAGGTTAGGAAGATTGGCAGGGTTGCTCGGGCCATCGCCATTATGAGCCACCCGATTCC GAACACCAATGATTCTCACTCAGTGCAGGTCATCATACCCCAGAAACAGTTGGCCCGCAAATCG GATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.221653987

Conservation Information
Conserved circRNAs	NA
PMCS	0.221653987

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22136367-22137356(+)
						
						Potential amino acid sequence
						
							MRMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGV
TSEGETAKCKKIVCDPSYLPNKVRKIGRVARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKSDM
KYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPYIYPLYGLGELPQ
AFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYLPNKVRKIGRVAR
AIAIMSHPIPNTNDSHSVQVIIPQKQLARKSDMKYGLDGNTIDFIGHAVALHTNDQHLDQPAFD
TVMRMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVI
GVTSEGETAKCKKIVCDPSYLPNKVRKIGRVARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKS
DMKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPYIYPLYGLGEL
PQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYLPNKVRKIGRV
ARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKSD(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22136367-22137356(+)
Potential amino acid sequence	MRMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGV TSEGETAKCKKIVCDPSYLPNKVRKIGRVARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKSDM KYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPYIYPLYGLGELPQ AFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYLPNKVRKIGRVAR AIAIMSHPIPNTNDSHSVQVIIPQKQLARKSDMKYGLDGNTIDFIGHAVALHTNDQHLDQPAFD TVMRMKLYAESLARFQGTSPYIYPLYGLGELPQAFARLSAVYGGTYMLNKPECKVEFDEGGKVI GVTSEGETAKCKKIVCDPSYLPNKVRKIGRVARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKS DMKYGLDGNTIDFIGHAVALHTNDQHLDQPAFDTVMRMKLYAESLARFQGTSPYIYPLYGLGEL PQAFARLSAVYGGTYMLNKPECKVEFDEGGKVIGVTSEGETAKCKKIVCDPSYLPNKVRKIGRV ARAIAIMSHPIPNTNDSHSVQVIIPQKQLARKSD(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G59920_circ_g.6

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