Plant Circular RNA Database

Detail information of AT3G17880_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G17880_circ_g.1
					
						ID in PlantcircBase
						ath_circ_022458
					
						Alias
						3:6123961-6125089
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 6123961-6125089  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G17880						
					
						Parent gene annotation
						
							TPR repeat-containing thioredoxin TDX
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_igg.3 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4 AT3G17880_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT3G17880.2:6
AT3G17880.1:6

General Information
CircRNA Name	AT3G17880_circ_g.1
ID in PlantcircBase	ath_circ_022458
Alias	3:6123961-6125089
Organism	Arabidpsis thaliana
Position	chr3: 6123961-6125089 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G17880
Parent gene annotation	TPR repeat-containing thioredoxin TDX
Parent gene strand	+
Alternative splicing	3_circ_igg.3 AT3G17880_circ_g.2 AT3G17880_circ_g.3 AT3G17880_circ_g.4 AT3G17880_circ_g.5
Support reads	2
Tissues	root
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	AT3G17880.2:6 AT3G17880.1:6

			
						 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  
						
							AAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGG
GCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAGgaaagagattatgaagataaggctgaga
caaaacccagtttctctcctaaacatgatgatgatgatgatgatattatggagtctgatgttga
actcgaca

									
								

					

						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: 630
Transcript exons: 6123961-6124101,6124197-6124284,6124361-6124441,6124525-
6124589,6124749-6124889,6124976-6125089
GAAAGAGATTATGAAGATAAGGCTGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATG
ATGATGATATTATGGAGTCTGATGTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGA
GCCTCCTCAGCCGATGGGAGACCCTACTGCTGAAGTGACCGATGAAAATAGGGATGATGCTCAG
TCAGAGAAGAGCAAAGCTATGGAGGCAATCTCTGATGGGAGGTTTGACGAAGCTATAGAGCATC
TAACAAAAGCTGTCATGCTAAATCCTACTTCAGCGATTCTCTACGCCACTAGAGCTAGTGTGTT
TTTAAAAGTTAAGAAGCCAAATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGTTCAACTCT
GATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAATGGGAAGAGG
CTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGACAATGCTTAA
GAAGGTTGAACCCAATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAA
GAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG
						
					

						Genomic sequence
						
							GAAAGAGATTATGAAGATAAGGCTGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATG
ATGATGATATTATGGAGTCTGATGTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGA
GCCTCCTCAGCCGGTAGGTGTTGAAGTTATCATCTTTGGATATTATGTGGTGCTTGTGTCTCTA
TGCATTTTTTTACCTGATTGGATGATTTTACTTTCTTGTCTTAGATGGGAGACCCTACTGCTGA
AGTGACCGATGAAAATAGGGATGATGCTCAGTCAGAGAAGAGCAAAGCTATGGAGGCAATCTCT
GATGGTACATAACTACCGTTGAAATTGGTTTTGATTATCTACTTCATAAGATTTCTCCTTAATG
CTTGATTGGTATACAGGGAGGTTTGACGAAGCTATAGAGCATCTAACAAAAGCTGTCATGCTAA
ATCCTACTTCAGCGATTCTCTACGCCACTAGAGGTAACTTTCTTTTACTAGTTCACTCTCCCTT
TTCGGCTGAATGTGGGTGATAATACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTT
TAAAAGTTAAGAAGCCAAATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGGTGATCATTTC
TCTTGACATAAACTTGTTTTGTTTGTGCTGAAAATGGATTTGGTAAAACAAGTTTATGTCTCAA
TAGTTTTATGGCTTGGGAGAGTGATTTTATATCTCAATGGTTTTCTTCCATAAACAAGCTAAAC
TAGTTTATTTTGGGGTTTAGTTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGC
TAAGGCCATGTTAGGCCAATGGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGAT
TACGATGAGGAGATAGGGACAATGCTTAAGAAGGTAATTGCGGAAACCTCTTGATATCACTGTA
TGGTCCTTGAGTTTTACAGTACCAAATATATATGCTGAAAATGTGTACTTCCCAGGTTGAACCC
AATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCC
AAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG
						
					

			
		

Sequences
Splice junction sequence	AAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCCAAAGG GCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAGgaaagagattatgaagataaggctgaga caaaacccagtttctctcctaaacatgatgatgatgatgatgatattatggagtctgatgttga actcgaca
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: 630 Transcript exons: 6123961-6124101,6124197-6124284,6124361-6124441,6124525- 6124589,6124749-6124889,6124976-6125089 GAAAGAGATTATGAAGATAAGGCTGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATG ATGATGATATTATGGAGTCTGATGTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGA GCCTCCTCAGCCGATGGGAGACCCTACTGCTGAAGTGACCGATGAAAATAGGGATGATGCTCAG TCAGAGAAGAGCAAAGCTATGGAGGCAATCTCTGATGGGAGGTTTGACGAAGCTATAGAGCATC TAACAAAAGCTGTCATGCTAAATCCTACTTCAGCGATTCTCTACGCCACTAGAGCTAGTGTGTT TTTAAAAGTTAAGAAGCCAAATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGTTCAACTCT GATTCAGCTAAGGGGTACAAATCACGAGGTATGGCTAAGGCCATGTTAGGCCAATGGGAAGAGG CTGCAGCTGATCTACATGTCGCATCAAAATTAGATTACGATGAGGAGATAGGGACAATGCTTAA GAAGGTTGAACCCAATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAA GAAAAGGAGCTCCAAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG
Genomic sequence	GAAAGAGATTATGAAGATAAGGCTGAGACAAAACCCAGTTTCTCTCCTAAACATGATGATGATG ATGATGATATTATGGAGTCTGATGTTGAACTCGACAACTCTGATGTAGTTGAACCAGACAATGA GCCTCCTCAGCCGGTAGGTGTTGAAGTTATCATCTTTGGATATTATGTGGTGCTTGTGTCTCTA TGCATTTTTTTACCTGATTGGATGATTTTACTTTCTTGTCTTAGATGGGAGACCCTACTGCTGA AGTGACCGATGAAAATAGGGATGATGCTCAGTCAGAGAAGAGCAAAGCTATGGAGGCAATCTCT GATGGTACATAACTACCGTTGAAATTGGTTTTGATTATCTACTTCATAAGATTTCTCCTTAATG CTTGATTGGTATACAGGGAGGTTTGACGAAGCTATAGAGCATCTAACAAAAGCTGTCATGCTAA ATCCTACTTCAGCGATTCTCTACGCCACTAGAGGTAACTTTCTTTTACTAGTTCACTCTCCCTT TTCGGCTGAATGTGGGTGATAATACTCAATATTTGTGATTGTTGTCCTGCAGCTAGTGTGTTTT TAAAAGTTAAGAAGCCAAATGCTGCAATTCGTGATGCCAACGTAGCGTTACAGGTGATCATTTC TCTTGACATAAACTTGTTTTGTTTGTGCTGAAAATGGATTTGGTAAAACAAGTTTATGTCTCAA TAGTTTTATGGCTTGGGAGAGTGATTTTATATCTCAATGGTTTTCTTCCATAAACAAGCTAAAC TAGTTTATTTTGGGGTTTAGTTCAACTCTGATTCAGCTAAGGGGTACAAATCACGAGGTATGGC TAAGGCCATGTTAGGCCAATGGGAAGAGGCTGCAGCTGATCTACATGTCGCATCAAAATTAGAT TACGATGAGGAGATAGGGACAATGCTTAAGAAGGTAATTGCGGAAACCTCTTGATATCACTGTA TGGTCCTTGAGTTTTACAGTACCAAATATATATGCTGAAAATGTGTACTTCCCAGGTTGAACCC AATGCAAAGAGAATCGAAGAACACCGCAGGAAATACCAACGCCTGAGGAAAGAAAAGGAGCTCC AAAGGGCTGAACGCGAGAGACGGAAACAGCAAGAAGCCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.199396622

Conservation Information
Conserved circRNAs	NA
PMCS	0.199396622

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5658 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	ath-miR5658
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G17880_circ_g.1

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