Plant Circular RNA Database

Detail information of AT3G16320_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G16320_circ_g.2
					
						ID in PlantcircBase
						ath_circ_022140
					
						Alias
						3:5531440-5532795
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5531440-5532795  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G16320						
					
						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1/1
					
						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
						AT3G16320.1:5
AT3G16320.2:5
AT3G16320.3:5
AT3G16320.4:5

General Information
CircRNA Name	AT3G16320_circ_g.2
ID in PlantcircBase	ath_circ_022140
Alias	3:5531440-5532795
Organism	Arabidpsis thaliana
Position	chr3: 5531440-5532795 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G16320
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	+
Alternative splicing	NA
Support reads	1/1
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	AT3G16320.1:5 AT3G16320.2:5 AT3G16320.3:5 AT3G16320.4:5

			
						 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  
						
							GCTACAAGACTACTTCAACGCTGACTCTTCCTTTACTCTTGCTCATCAAAAGTATCCTTATGCT
TTGGAAGGAATGGATACATACTCCACTGTTCTTTATgtaatggatgctctaccgcctctgcttc
ttaagaatatgcgtcgtccagcagtggaaggatctttgatgtctgtacatggagtgcgtgtgcg
tcgaagaa

									
								

					

						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: 705
Transcript exons: 5531440-5531568,5531794-5531971,5532147-5532358,5532475-
5532540,5532676-5532795
GTAATGGATGCTCTACCGCCTCTGCTTCTTAAGAATATGCGTCGTCCAGCAGTGGAAGGATCTT
TGATGTCTGTACATGGAGTGCGTGTGCGTCGAAGAAACTTTTTTAGTGAAGAATTGTCAGCAGA
GGCTCAAGAAGAATCTGGGCGCCGCCGTAGTGCTAGAATAGCAGCAAGGAAAAAGAATCCTATG
TCGCAGTCATTTGGAAAAGATTCCCATTGGTTACATCTTTCACCTTCCGAGTCAAACTATGCAC
CTTCTCTTTCCTCGATGATTGGAAAATGCAGAATCCAAAGCAGCAAAGAAGTGATTCCTGATAC
CGTTACTCTAAATGATCCAGCAACGACGTCAGGCCAGTCTGTAAGTGACATTGGAAGCTCTGTT
GATGATGAGGAAAAGTCAAATCCTAGTGAATCTTCCCCGGATCGTTTCAGCCTTATTTCTGGAA
TTTCAGAAGTGCTAAGCCTTCTGAAAATTCTTGGAGATGGCCACAGGCATTTACATATGTACAA
GTGTCAGGAAGCTTTGTTGGCATATCAAAAGCTATCTCAGAAACAATACAATACACACTGGGTT
CTCATGCAGGTTGGAAAAGCATATTTTGAGCTACAAGACTACTTCAACGCTGACTCTTCCTTTA
CTCTTGCTCATCAAAAGTATCCTTATGCTTTGGAAGGAATGGATACATACTCCACTGTTCTTTA
T
						
					

						Genomic sequence
						
							GTAATGGATGCTCTACCGCCTCTGCTTCTTAAGAATATGCGTCGTCCAGCAGTGGAAGGATCTT
TGATGTCTGTACATGGAGTGCGTGTGCGTCGAAGAAACTTTTTTAGTGAAGAATTGTCAGCAGA
GGTTATATATCTACAATGGGCTTTGAGTGATTTCTTCCTTGTTTTCTTTGCATAAGAGTTTTCT
TATTAATGCATAGGCGAAGAATGATCATCTATCTAGCACTGCAGATATTTTAAGTTTTTAACAT
AGAGCTTCCCCCACCTTGTTTCTATCTTCTAGCTCTATGGCTGGACCATCTAAAGCTACTTGAT
TTATTGGTCTTCTTTTACTTTCCTTATCTTGAAGGCTCAAGAAGAATCTGGGCGCCGCCGTAGT
GCTAGAATAGCAGCAAGGAAAAAGAATCCTATGTCGCAGTCATTTGGAAAAGATTCCCATTGGT
TACATCTTTCACCTTCCGAGTCAAACTATGCACCTTCTCTTTCCTCGATGATTGGAAAATGCAG
AATCCAAAGCAGCAAAGAAGGTGATGTTTTACTATCATATTTTTCTTTTCTGTCTCCCAAACCG
GACTATAGAGCCTCAATTGGTTGTAATTTTTGAAATGGAAAAAGTTAGATCTCTAGTTAAAATT
CATGATGTAATAATATAGGTGGCTTAAGTAATTTACATGACAATAAGACTTGAACATATATGTG
CAGTGATTCCTGATACCGTTACTCTAAATGATCCAGCAACGACGTCAGGCCAGTCTGTAAGTGA
CATTGGAAGCTCTGTTGATGATGAGGAAAAGTCAAATCCTAGTGAATCTTCCCCGGATCGTTTC
AGCCTTATTTCTGGAATTTCAGAAGTGCTAAGCCTTCTGAAAATTCTTGGAGATGGCCACAGGC
ATTTACATATGTACAAGTGTCAGGTACTTTACTAAGACAATGTGTGTATTGGGTTCATATTCTT
CAACTTGAATTCTCTGCTTAAAAGTTAAAGTATCGATGTCGAAGCCTAAAATGACAAAAATGGA
TACTACTGCAGGAAGCTTTGTTGGCATATCAAAAGCTATCTCAGAAACAATACAATACACACTG
GGTTCTCATGCAGGTGATAATATGAATGGCTTTTTCTTTGCTCCTTTTTCATTGGAATGATCTT
ATTTGGTCATTGACGTCATTTTCTAATTCCATTTTGTTGGTTTTTGACACTGAAACTAAAAACC
ATGGATACATTTTGAAATAGGTTGGAAAAGCATATTTTGAGCTACAAGACTACTTCAACGCTGA
CTCTTCCTTTACTCTTGCTCATCAAAAGTATCCTTATGCTTTGGAAGGAATGGATACATACTCC
ACTGTTCTTTAT
						
					

			
		

Sequences
Splice junction sequence	GCTACAAGACTACTTCAACGCTGACTCTTCCTTTACTCTTGCTCATCAAAAGTATCCTTATGCT TTGGAAGGAATGGATACATACTCCACTGTTCTTTATgtaatggatgctctaccgcctctgcttc ttaagaatatgcgtcgtccagcagtggaaggatctttgatgtctgtacatggagtgcgtgtgcg tcgaagaa
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: 705 Transcript exons: 5531440-5531568,5531794-5531971,5532147-5532358,5532475- 5532540,5532676-5532795 GTAATGGATGCTCTACCGCCTCTGCTTCTTAAGAATATGCGTCGTCCAGCAGTGGAAGGATCTT TGATGTCTGTACATGGAGTGCGTGTGCGTCGAAGAAACTTTTTTAGTGAAGAATTGTCAGCAGA GGCTCAAGAAGAATCTGGGCGCCGCCGTAGTGCTAGAATAGCAGCAAGGAAAAAGAATCCTATG TCGCAGTCATTTGGAAAAGATTCCCATTGGTTACATCTTTCACCTTCCGAGTCAAACTATGCAC CTTCTCTTTCCTCGATGATTGGAAAATGCAGAATCCAAAGCAGCAAAGAAGTGATTCCTGATAC CGTTACTCTAAATGATCCAGCAACGACGTCAGGCCAGTCTGTAAGTGACATTGGAAGCTCTGTT GATGATGAGGAAAAGTCAAATCCTAGTGAATCTTCCCCGGATCGTTTCAGCCTTATTTCTGGAA TTTCAGAAGTGCTAAGCCTTCTGAAAATTCTTGGAGATGGCCACAGGCATTTACATATGTACAA GTGTCAGGAAGCTTTGTTGGCATATCAAAAGCTATCTCAGAAACAATACAATACACACTGGGTT CTCATGCAGGTTGGAAAAGCATATTTTGAGCTACAAGACTACTTCAACGCTGACTCTTCCTTTA CTCTTGCTCATCAAAAGTATCCTTATGCTTTGGAAGGAATGGATACATACTCCACTGTTCTTTA T
Genomic sequence	GTAATGGATGCTCTACCGCCTCTGCTTCTTAAGAATATGCGTCGTCCAGCAGTGGAAGGATCTT TGATGTCTGTACATGGAGTGCGTGTGCGTCGAAGAAACTTTTTTAGTGAAGAATTGTCAGCAGA GGTTATATATCTACAATGGGCTTTGAGTGATTTCTTCCTTGTTTTCTTTGCATAAGAGTTTTCT TATTAATGCATAGGCGAAGAATGATCATCTATCTAGCACTGCAGATATTTTAAGTTTTTAACAT AGAGCTTCCCCCACCTTGTTTCTATCTTCTAGCTCTATGGCTGGACCATCTAAAGCTACTTGAT TTATTGGTCTTCTTTTACTTTCCTTATCTTGAAGGCTCAAGAAGAATCTGGGCGCCGCCGTAGT GCTAGAATAGCAGCAAGGAAAAAGAATCCTATGTCGCAGTCATTTGGAAAAGATTCCCATTGGT TACATCTTTCACCTTCCGAGTCAAACTATGCACCTTCTCTTTCCTCGATGATTGGAAAATGCAG AATCCAAAGCAGCAAAGAAGGTGATGTTTTACTATCATATTTTTCTTTTCTGTCTCCCAAACCG GACTATAGAGCCTCAATTGGTTGTAATTTTTGAAATGGAAAAAGTTAGATCTCTAGTTAAAATT CATGATGTAATAATATAGGTGGCTTAAGTAATTTACATGACAATAAGACTTGAACATATATGTG CAGTGATTCCTGATACCGTTACTCTAAATGATCCAGCAACGACGTCAGGCCAGTCTGTAAGTGA CATTGGAAGCTCTGTTGATGATGAGGAAAAGTCAAATCCTAGTGAATCTTCCCCGGATCGTTTC AGCCTTATTTCTGGAATTTCAGAAGTGCTAAGCCTTCTGAAAATTCTTGGAGATGGCCACAGGC ATTTACATATGTACAAGTGTCAGGTACTTTACTAAGACAATGTGTGTATTGGGTTCATATTCTT CAACTTGAATTCTCTGCTTAAAAGTTAAAGTATCGATGTCGAAGCCTAAAATGACAAAAATGGA TACTACTGCAGGAAGCTTTGTTGGCATATCAAAAGCTATCTCAGAAACAATACAATACACACTG GGTTCTCATGCAGGTGATAATATGAATGGCTTTTTCTTTGCTCCTTTTTCATTGGAATGATCTT ATTTGGTCATTGACGTCATTTTCTAATTCCATTTTGTTGGTTTTTGACACTGAAACTAAAAACC ATGGATACATTTTGAAATAGGTTGGAAAAGCATATTTTGAGCTACAAGACTACTTCAACGCTGA CTCTTCCTTTACTCTTGCTCATCAAAAGTATCCTTATGCTTTGGAAGGAATGGATACATACTCC ACTGTTCTTTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.206726587

Conservation Information
Conserved circRNAs	NA
PMCS	0.206726587

			
						 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 AT3G16320_circ_g.2

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