Plant Circular RNA Database

Detail information of AT3G13040_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G13040_circ_g.6
					
						ID in PlantcircBase
						ath_circ_021343
					
						Alias
						Ath_circ_FC1948, AT3G13040_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 4173866-4174517  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, CIRI2
					
						Parent gene
						
							AT3G13040						
					
						Parent gene annotation
						
							Myb family transcription factor PHL6
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						73
					
						Tissues
						root, leaf, 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  
						
							CT-AC							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
						AT3G13040.2:1
AT3G13040.3:1
AT3G13040.1:1

General Information
CircRNA Name	AT3G13040_circ_g.6
ID in PlantcircBase	ath_circ_021343
Alias	Ath_circ_FC1948, AT3G13040_C1
Organism	Arabidpsis thaliana
Position	chr3: 4173866-4174517 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, CIRI2
Parent gene	AT3G13040
Parent gene annotation	Myb family transcription factor PHL6
Parent gene strand	-
Alternative splicing	NA
Support reads	73
Tissues	root, leaf, 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	CT-AC 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	AT3G13040.2:1 AT3G13040.3:1 AT3G13040.1:1

			
						 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  
						
							GAGAAGCCTGTGTCTGTTCATGATTGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACA
AGATCCCCCATTAGTTTGCAGTTAGCATCCAAGCCGatcaagcctgggagtttcagcgcggtct
gtgatagccagctcaagttcatcagacaggaactgtaattccatttgatctgataagcaatagc
tgtcattc

									
								

					

						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: 198
Transcript exons: 4173866-4174036,4174491-4174517
ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT
AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT
CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGATTAGTTTGCAGTTAGCATCC
AAGCCG
Transcript length: 268
Transcript exons: 4173866-4173976,4174351-4174451,4174462-4174517
ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT
AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAGGACTGGAGATAAAGAA
GAAGAGCAAGCTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTC
TGTTCATGATTGCTTTGATGATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA
GCATCCAAGCCG
Transcript length: 652
Transcript exons: 4173866-4174517
ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT
AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT
CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGCGACCCGGAGTTGCCTCCATC
ACATTGATTGCCCAAATCCTCAGTGAAAATAGATGGAGATCTTGCAGACTCCACACCAGAAGCT
GAGTGGGTGTAAGAGGAGGGATCAGGGAGGAAAGGAAGACTGTTTCCTAGATGTTTCTGAGTCT
CAGAGGTTGAAGATGATGACAAGTAGAGGTTTGTGCAAAAGGTGGAAGACCGAGAGAAGGTGCT
CTGAGAACTATTCTTTGGCCATAGCTGACCAGGTGAATCTGGAGATTGTGACCTTATGAAAGGA
GTTTTCCGGTGTTCTGGCTGGACATTCAGAAAGTTATGGACTGGAGATAAAGAAGAAGAGCAAG
CTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTCTGTTCATGAT
TGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA
GCATCCAAGCCG
						
					

						Genomic sequence
						
							ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT
AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT
CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGCGACCCGGAGTTGCCTCCATC
ACATTGATTGCCCAAATCCTCAGTGAAAATAGATGGAGATCTTGCAGACTCCACACCAGAAGCT
GAGTGGGTGTAAGAGGAGGGATCAGGGAGGAAAGGAAGACTGTTTCCTAGATGTTTCTGAGTCT
CAGAGGTTGAAGATGATGACAAGTAGAGGTTTGTGCAAAAGGTGGAAGACCGAGAGAAGGTGCT
CTGAGAACTATTCTTTGGCCATAGCTGACCAGGTGAATCTGGAGATTGTGACCTTATGAAAGGA
GTTTTCCGGTGTTCTGGCTGGACATTCAGAAAGTTATGGACTGGAGATAAAGAAGAAGAGCAAG
CTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTCTGTTCATGAT
TGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA
GCATCCAAGCCG
						
					

			
		

Sequences
Splice junction sequence	GAGAAGCCTGTGTCTGTTCATGATTGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACA AGATCCCCCATTAGTTTGCAGTTAGCATCCAAGCCGatcaagcctgggagtttcagcgcggtct gtgatagccagctcaagttcatcagacaggaactgtaattccatttgatctgataagcaatagc tgtcattc
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: 198 Transcript exons: 4173866-4174036,4174491-4174517 ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGATTAGTTTGCAGTTAGCATCC AAGCCG Transcript length: 268 Transcript exons: 4173866-4173976,4174351-4174451,4174462-4174517 ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAGGACTGGAGATAAAGAA GAAGAGCAAGCTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTC TGTTCATGATTGCTTTGATGATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA GCATCCAAGCCG Transcript length: 652 Transcript exons: 4173866-4174517 ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGCGACCCGGAGTTGCCTCCATC ACATTGATTGCCCAAATCCTCAGTGAAAATAGATGGAGATCTTGCAGACTCCACACCAGAAGCT GAGTGGGTGTAAGAGGAGGGATCAGGGAGGAAAGGAAGACTGTTTCCTAGATGTTTCTGAGTCT CAGAGGTTGAAGATGATGACAAGTAGAGGTTTGTGCAAAAGGTGGAAGACCGAGAGAAGGTGCT CTGAGAACTATTCTTTGGCCATAGCTGACCAGGTGAATCTGGAGATTGTGACCTTATGAAAGGA GTTTTCCGGTGTTCTGGCTGGACATTCAGAAAGTTATGGACTGGAGATAAAGAAGAAGAGCAAG CTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTCTGTTCATGAT TGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA GCATCCAAGCCG
Genomic sequence	ATCAAGCCTGGGAGTTTCAGCGCGGTCTGTGATAGCCAGCTCAAGTTCATCAGACAGGAACTGT AATTCCATTTGATCTGATAAGCAATAGCTGTCATTCGAACAGCCAAAATCATGAAAATCGCCAT CGGAACAAGCATCTCCAGAAAGATTAAGGAAGTCTTTGAGAAGCGACCCGGAGTTGCCTCCATC ACATTGATTGCCCAAATCCTCAGTGAAAATAGATGGAGATCTTGCAGACTCCACACCAGAAGCT GAGTGGGTGTAAGAGGAGGGATCAGGGAGGAAAGGAAGACTGTTTCCTAGATGTTTCTGAGTCT CAGAGGTTGAAGATGATGACAAGTAGAGGTTTGTGCAAAAGGTGGAAGACCGAGAGAAGGTGCT CTGAGAACTATTCTTTGGCCATAGCTGACCAGGTGAATCTGGAGATTGTGACCTTATGAAAGGA GTTTTCCGGTGTTCTGGCTGGACATTCAGAAAGTTATGGACTGGAGATAAAGAAGAAGAGCAAG CTTGACCAAGTTTTTTATTGCATTCATCTGTTGCCGCTGAGAGAAGCCTGTGTCTGTTCATGAT TGCTTTGATGTACATCAACAATCAAAACTGTCTCTTGACAAGATCCCCCATTAGTTTGCAGTTA GCATCCAAGCCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.577647989

Conservation Information
Conserved circRNAs	NA
PMCS	0.577647989

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

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

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT3G13040_circ_g.6

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