Plant Circular RNA Database

Detail information of AT3G19840_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT3G19840_circ_g.7
					
						ID in PlantcircBase
						ath_circ_022805
					
						Alias
						Ath_circ_FC2083
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 6894173-6895988  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G19840						
					
						Parent gene annotation
						
							Pre-mRNA-processing protein 40C
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G19840_circ_g.1 AT3G19840_circ_g.2 AT3G19840_circ_g.3 AT3G19840_circ_g.4 AT3G19840_circ_g.5 AT3G19840_circ_g.6 AT3G19840_circ_g.8 AT3G19840_circ_g.9 AT3G19840_circ_g.10 AT3G19840_circ_g.11 AT3G19840_circ_g.12 						
					
						Support reads
						3
					
						Tissues
						inflorescences
					
						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
						AT3G19840.1:5

General Information
CircRNA Name	AT3G19840_circ_g.7
ID in PlantcircBase	ath_circ_022805
Alias	Ath_circ_FC2083
Organism	Arabidpsis thaliana
Position	chr3: 6894173-6895988 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT3G19840
Parent gene annotation	Pre-mRNA-processing protein 40C
Parent gene strand	+
Alternative splicing	AT3G19840_circ_g.1 AT3G19840_circ_g.2 AT3G19840_circ_g.3 AT3G19840_circ_g.4 AT3G19840_circ_g.5 AT3G19840_circ_g.6 AT3G19840_circ_g.8 AT3G19840_circ_g.9 AT3G19840_circ_g.10 AT3G19840_circ_g.11 AT3G19840_circ_g.12
Support reads	3
Tissues	inflorescences
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	AT3G19840.1:5

			
						 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  
						
							TGCGCACGAGGATAGGGAGGTTTTTTATTATGAGTACATTGCGGAACTAAAAGCTGCACAAAGG
GGAGATGATCATGAGATGAAAGCCAGAGACGAAGAGgaaatgctgaaagagagaggaatagcac
cgttttctaaatgggagaaggaattgccaaaaattatctttgaccctcgctttaaggtctgtca
agcctaaa

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GAAATGCTGAAAGAGAGAGGAATAGCACCGTTTTCTAAATGGGAGAAGGAATTGCCAAAAATTA
TCTTTGACCCTCGCTTTAAGGTCTGTCAAGCCTAAAGATCGTGACAATATTTTGATATCTTATT
CTATTTTGAAATTCCACGTCCATTGTTTCTTTCCTTGCATGCGTTTGCAACTTGCACATTTCCA
GTTAATGTTATTTGCGTCTATGTCAGCATTGTAACATCCATTCGTTTTGGGTGCTCAAATAGAG
CACAAATTAAAGTTTCCTATAGATTTCCTAGCTCGGTGTAGAAAGAAGTTTACATCTATATTAC
ATTTGGAAACAAGTCTTTCACTTTACTTATATTAGAGTCCATAACTAGTATCCTCACTGATTAA
TTGTTCTGATGCCTTGTATGCTAGCTAAATGATTTTCTGTAGAGAAAGAGTATGCCTTTGGTTC
CTTCCAATGTTAGCTAAGTAAAGTTTTGAGGATGTTAGAGCCATTATGTGATATAGTTTATTCA
CTCCACCCATAATATGTTGTGTCGCCAGAAACTTCATTCTTATTTGCTAATTAGAATGTTAGAG
GAACTATTACTGTGTTAATTTTCCAGCATTCCTGTTACAGTGCCACAGCTTGATCTTTGGACTT
TTTCGATTATGTATTTTTATCCGGAGAGTTCATTTTTCTTGCAGGCAATACCAAGTCATTCTGT
TAGAAGATCATTATTTGAGCAGTACGTAAAGACACGAGCTGAGGAAGAACGTAGGGAAAAGCGT
GCTGCTCATAAGGCAGCTATTGAAGGTTTCAGGCAGTTGCTGGATGATGCGTCTACGGTAAATC
TTTTTAAGGAACTGAATGTATTTTTACTTTGAGCTACCTGACGTCTTTAAACATTTTTATTATT
TGGTTTGGGATGTTCTCAACTTCTATATCTCTTGTGGGAATGTATCCTCATTTTTCCAGGACAT
TGATCAACACACTGACTATCGTGCTTTTAAAAAGAAATGGGGGAATGATCTCCGGTTCGAAGCA
ATTGAGCGTAAGGAGCGGGAGGGTTTACTGAATGAAAGGTACCAATATAGATCTTGAGATCATA
TTCTATGTATGTTGGAAAGTTTGCTTATAGCCTTCAAGTTTACACTGGATGTGTCTTTCCCTGT
TGCTTTGTGATGTTTTGGTTGTAACTGCAGCGGATCCTTTTGGGGAAGTTTTTCCTTGTACAAG
AATGATATGCCCTTTATGATTTTATTTGTCTTCATGTGAGTTTTTGAGTGTTTGATAGTTTATA
CACTGTCTTGGCTCTTATATTTTCCCTGGTTCTGTTGCAGAGTCCTTTCTTTGAAACGAAGTGC
TGAACAAAAGGCACAAGAAATTCGCGCTGCTGCTGCCTCTGATTTCAAGACAATGCTACGGGAA
AGAGAAATATCAATAAATTCACATTGGTCCAAGGTATGTAGCATATTTGTTTCTATCCTTTGCG
ACCAAGAGAGATAGAGTATGGAAAATTTCTAAAGTTTTCAGGAACTTATGGTGTTTGAGGAAAT
TGTAATATTTACTTATTGAAGTTACAAGTATTAATTTTATGTATCTTATCTCTTATCAAATACA
TCATTTGATTGGCACCATTTATAACTGGTTAGCATATTCATACCACCTATATGATATATTTCCA
TATTTTATCAGGTGAAGGATAGTCTGAGAAATGAACCAAGATATAGATCCGTTGCGCACGAGGA
TAGGGAGGTTTTTTATTATGAGTACATTGCGGAACTAAAAGCTGCACAAAGGGGAGATGATCAT
GAGATGAAAGCCAGAGACGAAGAG
						
					

			
		

Sequences
Splice junction sequence	TGCGCACGAGGATAGGGAGGTTTTTTATTATGAGTACATTGCGGAACTAAAAGCTGCACAAAGG GGAGATGATCATGAGATGAAAGCCAGAGACGAAGAGgaaatgctgaaagagagaggaatagcac cgttttctaaatgggagaaggaattgccaaaaattatctttgaccctcgctttaaggtctgtca agcctaaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GAAATGCTGAAAGAGAGAGGAATAGCACCGTTTTCTAAATGGGAGAAGGAATTGCCAAAAATTA TCTTTGACCCTCGCTTTAAGGTCTGTCAAGCCTAAAGATCGTGACAATATTTTGATATCTTATT CTATTTTGAAATTCCACGTCCATTGTTTCTTTCCTTGCATGCGTTTGCAACTTGCACATTTCCA GTTAATGTTATTTGCGTCTATGTCAGCATTGTAACATCCATTCGTTTTGGGTGCTCAAATAGAG CACAAATTAAAGTTTCCTATAGATTTCCTAGCTCGGTGTAGAAAGAAGTTTACATCTATATTAC ATTTGGAAACAAGTCTTTCACTTTACTTATATTAGAGTCCATAACTAGTATCCTCACTGATTAA TTGTTCTGATGCCTTGTATGCTAGCTAAATGATTTTCTGTAGAGAAAGAGTATGCCTTTGGTTC CTTCCAATGTTAGCTAAGTAAAGTTTTGAGGATGTTAGAGCCATTATGTGATATAGTTTATTCA CTCCACCCATAATATGTTGTGTCGCCAGAAACTTCATTCTTATTTGCTAATTAGAATGTTAGAG GAACTATTACTGTGTTAATTTTCCAGCATTCCTGTTACAGTGCCACAGCTTGATCTTTGGACTT TTTCGATTATGTATTTTTATCCGGAGAGTTCATTTTTCTTGCAGGCAATACCAAGTCATTCTGT TAGAAGATCATTATTTGAGCAGTACGTAAAGACACGAGCTGAGGAAGAACGTAGGGAAAAGCGT GCTGCTCATAAGGCAGCTATTGAAGGTTTCAGGCAGTTGCTGGATGATGCGTCTACGGTAAATC TTTTTAAGGAACTGAATGTATTTTTACTTTGAGCTACCTGACGTCTTTAAACATTTTTATTATT TGGTTTGGGATGTTCTCAACTTCTATATCTCTTGTGGGAATGTATCCTCATTTTTCCAGGACAT TGATCAACACACTGACTATCGTGCTTTTAAAAAGAAATGGGGGAATGATCTCCGGTTCGAAGCA ATTGAGCGTAAGGAGCGGGAGGGTTTACTGAATGAAAGGTACCAATATAGATCTTGAGATCATA TTCTATGTATGTTGGAAAGTTTGCTTATAGCCTTCAAGTTTACACTGGATGTGTCTTTCCCTGT TGCTTTGTGATGTTTTGGTTGTAACTGCAGCGGATCCTTTTGGGGAAGTTTTTCCTTGTACAAG AATGATATGCCCTTTATGATTTTATTTGTCTTCATGTGAGTTTTTGAGTGTTTGATAGTTTATA CACTGTCTTGGCTCTTATATTTTCCCTGGTTCTGTTGCAGAGTCCTTTCTTTGAAACGAAGTGC TGAACAAAAGGCACAAGAAATTCGCGCTGCTGCTGCCTCTGATTTCAAGACAATGCTACGGGAA AGAGAAATATCAATAAATTCACATTGGTCCAAGGTATGTAGCATATTTGTTTCTATCCTTTGCG ACCAAGAGAGATAGAGTATGGAAAATTTCTAAAGTTTTCAGGAACTTATGGTGTTTGAGGAAAT TGTAATATTTACTTATTGAAGTTACAAGTATTAATTTTATGTATCTTATCTCTTATCAAATACA TCATTTGATTGGCACCATTTATAACTGGTTAGCATATTCATACCACCTATATGATATATTTCCA TATTTTATCAGGTGAAGGATAGTCTGAGAAATGAACCAAGATATAGATCCGTTGCGCACGAGGA TAGGGAGGTTTTTTATTATGAGTACATTGCGGAACTAAAAGCTGCACAAAGGGGAGATGATCAT GAGATGAAAGCCAGAGACGAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.169307746

Conservation Information
Conserved circRNAs	NA
PMCS	0.169307746

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6894176-6895985(+)
						
						Potential amino acid sequence
						
							MLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERREKRAAHKAAIEG
FRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKRSAEQKAQEIRAA
AASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAELKAAQRGDDHEMK
ARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERREKRAAH
KAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKRSAEQKA
QEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAELKAAQRG
DDHEMKARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERR
EKRAAHKAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKR
SAEQKAQEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAEL
KAAQRGDDHEMKARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTR
AEEERREKRAAHKAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNER
VLSLKRSAEQKAQEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYY
EYIAELKAAQRGDDHEMKARDEE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6894176-6895985(+)
Potential amino acid sequence	MLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERREKRAAHKAAIEG FRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKRSAEQKAQEIRAA AASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAELKAAQRGDDHEMK ARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERREKRAAH KAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKRSAEQKA QEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAELKAAQRG DDHEMKARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTRAEEERR EKRAAHKAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNERVLSLKR SAEQKAQEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYYEYIAEL KAAQRGDDHEMKARDEEEMLKERGIAPFSKWEKELPKIIFDPRFKAIPSHSVRRSLFEQYVKTR AEEERREKRAAHKAAIEGFRQLLDDASTDIDQHTDYRAFKKKWGNDLRFEAIERKEREGLLNER VLSLKRSAEQKAQEIRAAAASDFKTMLREREISINSHWSKVKDSLRNEPRYRSVAHEDREVFYY EYIAELKAAQRGDDHEMKARDEE(+)
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 AT3G19840_circ_g.7

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