Plant Circular RNA Database

Detail information of AT5G01670_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G01670_circ_g.3
					
						ID in PlantcircBase
						ath_circ_035915
					
						Alias
						5:252298-253428
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 252298-253428  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G01670						
					
						Parent gene annotation
						
							NAD(P)-linked oxidoreductase superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G01670_circ_g.1 AT5G01670_circ_g.2 AT5G01670_circ_g.4 AT5G01670_circ_g.5 AT5G01670_circ_g.6 AT5G01670_circ_g.7 AT5G01670_circ_g.8 AT5G01670_circ_g.9 AT5G01670_circ_g.10 AT5G01670_circ_g.11 						
					
						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
						AT5G01670.2:5
AT5G01670.1:6

General Information
CircRNA Name	AT5G01670_circ_g.3
ID in PlantcircBase	ath_circ_035915
Alias	5:252298-253428
Organism	Arabidpsis thaliana
Position	chr5: 252298-253428 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G01670
Parent gene annotation	NAD(P)-linked oxidoreductase superfamily protein
Parent gene strand	+
Alternative splicing	AT5G01670_circ_g.1 AT5G01670_circ_g.2 AT5G01670_circ_g.4 AT5G01670_circ_g.5 AT5G01670_circ_g.6 AT5G01670_circ_g.7 AT5G01670_circ_g.8 AT5G01670_circ_g.9 AT5G01670_circ_g.10 AT5G01670_circ_g.11
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	AT5G01670.2:5 AT5G01670.1:6

			
						 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  
						
							TAAGTCATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGATCCCTGAA
CAAGACTTCCAAGCTCTCAACAGCATCACTGACCAGggtggctataggcacatagatacagctt
gggagtatggtgatcagagagaggtttctttctctatctctctttgttacttactactactact
acttgttt

									
								

					

						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: 735
Transcript exons: 252298-252348,252448-252521,252603-252690,252762-252968,
253043-253114,253186-253428
GGTGGCTATAGGCACATAGATACAGCTTGGGAGTATGGTGATCAGAGAGAGGTCGGTCAAGGAA
TAAAGAGGGCGATGCACGCTGGCCTTGAAAGGAGGGACCTCTTTGTGACCTCGAAGCTTTGGTG
CACTGAGTTATCTCCTGAGAGAGTGCGTCCTGCTCTGCAAAACACCCTTAAAGAGCTTCAATTA
GAGTACCTTGATCTCTACTTGATTCACTGGCCTATCCGGCTAAGAGAAGGAGCCAGTAAGCCAC
CAAAGGCAGGGGACGTTCTTGACTTTGACATGGAAGGAGTTTGGAGAGAAATGGAGAATCTTTC
CAAGGACAGTCTCGTCAGGAATATCGGTGTCTGTAACTTTACAGTCACTAAGCTCAATAAGCTG
CTAGGATTTGCTGAACTGATCCCTGCCGTTTGCCAGATGGAAATGCATCCTGGTTGGAGAAACG
ATAGGATACTCGAATTCTGCAAGAAGAATGAGATCCATGTTACTGCCTATTCTCCATTGGGATC
TCAAGAAGGCGGGAGAGATCTGATACACGATCAGACGGTGGATAGGATAGCGAAGAAGCTGAAT
AAGACACCGGGACAGATTCTAGTGAAATGGGGTTTGCAGAGAGGAACAAGTGTCATCCCTAAGT
CATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGATCCCTGAACAAGA
CTTCCAAGCTCTCAACAGCATCACTGACCAG
						
					

						Genomic sequence
						
							GGTGGCTATAGGCACATAGATACAGCTTGGGAGTATGGTGATCAGAGAGAGGTTTCTTTCTCTA
TCTCTCTTTGTTACTTACTACTACTACTACTTGTTTTGTCTGAAAGTTTTGAGTTTAGAGGTAA
ACAAGTCTTACTCTTTTTTAAGGTCGGTCAAGGAATAAAGAGGGCGATGCACGCTGGCCTTGAA
AGGAGGGACCTCTTTGTGACCTCGAAGCTTTGGTACACATTAATTTTAAGAAAAATGATTAATT
TATCATCGCCACTGATGAATGTTTTGGTTGGTACATGTTTAAACAAAAGGTGCACTGAGTTATC
TCCTGAGAGAGTGCGTCCTGCTCTGCAAAACACCCTTAAAGAGCTTCAATTAGAGTACCTTGAT
CTCTACTTGGTAAGTTGTGAATCAAGTTTTAGTCTTTCTTGTTACTCTTCTTCCTCTCTTTACA
ATTCAATTTTCTGCAGATTCACTGGCCTATCCGGCTAAGAGAAGGAGCCAGTAAGCCACCAAAG
GCAGGGGACGTTCTTGACTTTGACATGGAAGGAGTTTGGAGAGAAATGGAGAATCTTTCCAAGG
ACAGTCTCGTCAGGAATATCGGTGTCTGTAACTTTACAGTCACTAAGCTCAATAAGCTGCTAGG
ATTTGCTGAACTGATCCCTGCCGTTTGCCAGGTATAGGTTCTTCATTTCACATGTGAAAGTTCA
TTGAAAAACTTTTGTAGTGAGTTTGTTAGCTTGGCCCTCAGATGGAAATGCATCCTGGTTGGAG
AAACGATAGGATACTCGAATTCTGCAAGAAGAATGAGATCCATGTTACTGTGAGTACTAATATG
ATTCTTGATCCATTGTATCTGGAAAAATATTCACTGTTTCAATTGGAACTTTGAAGGCCTATTC
TCCATTGGGATCTCAAGAAGGCGGGAGAGATCTGATACACGATCAGACGGTGGATAGGATAGCG
AAGAAGCTGAATAAGACACCGGGACAGATTCTAGTGAAATGGGGTTTGCAGAGAGGAACAAGTG
TCATCCCTAAGTCATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGAT
CCCTGAACAAGACTTCCAAGCTCTCAACAGCATCACTGACCAG
						
					

			
		

Sequences
Splice junction sequence	TAAGTCATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGATCCCTGAA CAAGACTTCCAAGCTCTCAACAGCATCACTGACCAGggtggctataggcacatagatacagctt gggagtatggtgatcagagagaggtttctttctctatctctctttgttacttactactactact acttgttt
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: 735 Transcript exons: 252298-252348,252448-252521,252603-252690,252762-252968, 253043-253114,253186-253428 GGTGGCTATAGGCACATAGATACAGCTTGGGAGTATGGTGATCAGAGAGAGGTCGGTCAAGGAA TAAAGAGGGCGATGCACGCTGGCCTTGAAAGGAGGGACCTCTTTGTGACCTCGAAGCTTTGGTG CACTGAGTTATCTCCTGAGAGAGTGCGTCCTGCTCTGCAAAACACCCTTAAAGAGCTTCAATTA GAGTACCTTGATCTCTACTTGATTCACTGGCCTATCCGGCTAAGAGAAGGAGCCAGTAAGCCAC CAAAGGCAGGGGACGTTCTTGACTTTGACATGGAAGGAGTTTGGAGAGAAATGGAGAATCTTTC CAAGGACAGTCTCGTCAGGAATATCGGTGTCTGTAACTTTACAGTCACTAAGCTCAATAAGCTG CTAGGATTTGCTGAACTGATCCCTGCCGTTTGCCAGATGGAAATGCATCCTGGTTGGAGAAACG ATAGGATACTCGAATTCTGCAAGAAGAATGAGATCCATGTTACTGCCTATTCTCCATTGGGATC TCAAGAAGGCGGGAGAGATCTGATACACGATCAGACGGTGGATAGGATAGCGAAGAAGCTGAAT AAGACACCGGGACAGATTCTAGTGAAATGGGGTTTGCAGAGAGGAACAAGTGTCATCCCTAAGT CATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGATCCCTGAACAAGA CTTCCAAGCTCTCAACAGCATCACTGACCAG
Genomic sequence	GGTGGCTATAGGCACATAGATACAGCTTGGGAGTATGGTGATCAGAGAGAGGTTTCTTTCTCTA TCTCTCTTTGTTACTTACTACTACTACTACTTGTTTTGTCTGAAAGTTTTGAGTTTAGAGGTAA ACAAGTCTTACTCTTTTTTAAGGTCGGTCAAGGAATAAAGAGGGCGATGCACGCTGGCCTTGAA AGGAGGGACCTCTTTGTGACCTCGAAGCTTTGGTACACATTAATTTTAAGAAAAATGATTAATT TATCATCGCCACTGATGAATGTTTTGGTTGGTACATGTTTAAACAAAAGGTGCACTGAGTTATC TCCTGAGAGAGTGCGTCCTGCTCTGCAAAACACCCTTAAAGAGCTTCAATTAGAGTACCTTGAT CTCTACTTGGTAAGTTGTGAATCAAGTTTTAGTCTTTCTTGTTACTCTTCTTCCTCTCTTTACA ATTCAATTTTCTGCAGATTCACTGGCCTATCCGGCTAAGAGAAGGAGCCAGTAAGCCACCAAAG GCAGGGGACGTTCTTGACTTTGACATGGAAGGAGTTTGGAGAGAAATGGAGAATCTTTCCAAGG ACAGTCTCGTCAGGAATATCGGTGTCTGTAACTTTACAGTCACTAAGCTCAATAAGCTGCTAGG ATTTGCTGAACTGATCCCTGCCGTTTGCCAGGTATAGGTTCTTCATTTCACATGTGAAAGTTCA TTGAAAAACTTTTGTAGTGAGTTTGTTAGCTTGGCCCTCAGATGGAAATGCATCCTGGTTGGAG AAACGATAGGATACTCGAATTCTGCAAGAAGAATGAGATCCATGTTACTGTGAGTACTAATATG ATTCTTGATCCATTGTATCTGGAAAAATATTCACTGTTTCAATTGGAACTTTGAAGGCCTATTC TCCATTGGGATCTCAAGAAGGCGGGAGAGATCTGATACACGATCAGACGGTGGATAGGATAGCG AAGAAGCTGAATAAGACACCGGGACAGATTCTAGTGAAATGGGGTTTGCAGAGAGGAACAAGTG TCATCCCTAAGTCATTGAATCCAGAGAGGATCAAAGAGAACATCAAAGTGTTTGATTGGGTGAT CCCTGAACAAGACTTCCAAGCTCTCAACAGCATCACTGACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.219971637

Conservation Information
Conserved circRNAs	NA
PMCS	0.219971637

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G01670_circ_g.3

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