Plant Circular RNA Database

Detail information of AT4G24520_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G24520_circ_g.3
					
						ID in PlantcircBase
						ath_circ_032570
					
						Alias
						Ath_circ_FC2790
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12663232-12664287  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT4G24520						
					
						Parent gene annotation
						
							NADPH--cytochrome P450 reductase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G24520_circ_g.1 AT4G24520_circ_g.2 AT4G24520_circ_g.4 AT4G24520_circ_g.5 AT4G24520_circ_g.6 AT4G24520_circ_g.7 AT4G24520_circ_g.8 						
					
						Support reads
						9
					
						Tissues
						whole_plant
					
						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
						AT4G24520.1:5
AT4G24520.2:5

General Information
CircRNA Name	AT4G24520_circ_g.3
ID in PlantcircBase	ath_circ_032570
Alias	Ath_circ_FC2790
Organism	Arabidpsis thaliana
Position	chr4: 12663232-12664287 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT4G24520
Parent gene annotation	NADPH--cytochrome P450 reductase
Parent gene strand	-
Alternative splicing	AT4G24520_circ_g.1 AT4G24520_circ_g.2 AT4G24520_circ_g.4 AT4G24520_circ_g.5 AT4G24520_circ_g.6 AT4G24520_circ_g.7 AT4G24520_circ_g.8
Support reads	9
Tissues	whole_plant
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	AT4G24520.1:5 AT4G24520.2:5

			
						 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  
						
							CAGCAAAAAATACACCTAGTGGGGGTTTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACT
TCTCTGACTTGCAACAATCCATTGTGAGTACTCATCctgctcctgaacaatggtgtgtagagtt
cggtggacgtccctcgccatgcccttagcatcaccgcatacatagagatatccttcttccttta
ttagatcc

									
								

					

						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: 714
Transcript exons: 12663232-12663345,12663429-12663551,12663642-12663869,12
663940-12664036,12664136-12664287
CTGCTCCTGAACAATGGTGTGTAGAGTTCGGTGGACGTCCCTCGCCATGCCCTTAGCATCACCG
CATACATAGAGATATCCTTCTTCCTTTATTAGATCCCAAACTTGTGCTGCCTTCTCCATCATCT
TATGTTGAACATACTCCTTCTGAGCTCCTTCACGGGAGAATGCCATGATGAGCTCAGATATTAC
GCCTTGATCAACAAAATTATTGAGCTCATCCTCGTATATAAAGTCCATCTGTCGATTTCTACAC
CCAAAGAAGAGCAAAGATGAACCTAGTTCTTCTCCATCTTCTTTTAGTGCCATCCTTTCCTGCA
GAAAACCTCTAAAAGGTGCCAGCCCAGTCCCAGGTCCCACCATAACGATTGGAGTTGAAGGGTT
GGATGGTAACTTGAAATTAGATGCTCGAATAAAGATTGGGGCTCCACTACATTCATGACTTTTC
TCCGCAGGAACTGCATTCTTCATCCACGTAGAACACACACCCTTGTGGATTCTACCAGTAGGAG
TTGGACCATATACTAGTGCGGATGTAACATGAACTCTACTTGGCGCCAATCTTGGCGAGGATGA
GATGGAGTAGTAACGAGGTTGTAGACGAGGAGCTATTGCAGCAAAAAATACACCTAGTGGGGGT
TTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACTTCTCTGACTTGCAACAATCCATTGTG
AGTACTCATC
						
					

						Genomic sequence
						
							CTGCTCCTGAACAATGGTGTGTAGAGTTCGGTGGACGTCCCTCGCCATGCCCTTAGCATCACCG
CATACATAGAGATATCCTTCTTCCTTTATTAGATCCCAAACTTGTGCTGCCTGAACAAATAGAA
AATGCAAAATTAAAGAGATTATGTGACATTCCTTTTCCCAAAGTATGATGCATCACTTGATATA
TTTACCTTCTCCATCATCTTATGTTGAACATACTCCTTCTGAGCTCCTTCACGGGAGAATGCCA
TGATGAGCTCAGATATTACGCCTTGATCAACAAAATTATTGAGCTCATCCTCGTATATAAAGTC
CTGCAACATACATATAAGCACTCAGCAGAAGCTCAACATGCATGATGACACAGCAAATGAAGAA
GGTGTTTTTGGTTGTGAAAGTCTCACCATCTGTCGATTTCTACACCCAAAGAAGAGCAAAGATG
AACCTAGTTCTTCTCCATCTTCTTTTAGTGCCATCCTTTCCTGCAGAAAACCTCTAAAAGGTGC
CAGCCCAGTCCCAGGTCCCACCATAACGATTGGAGTTGAAGGGTTGGATGGTAACTTGAAATTA
GATGCTCGAATAAAGATTGGGGCTCCACTACATTCATGACTTTTCTCCGCAGGAACTGCATTCT
GAATTTTTCAAACTGTTAAGAAAAAAAACAGTGAACTGGCAGATAGTCAAAAAGAAGGTAAGAA
GTACCTTCATCCACGTAGAACACACACCCTTGTGGATTCTACCAGTAGGAGTTGGACCATATAC
TAGTGCGGATGTAACATGAACTCTACTTGGCGCCAATCTGTATTGTAAAAAACGGTAAAGAGTG
ATTTGAATGCCAGAGACGATCAAGAATAGTTTTCCTTCTGCCACAAAATATATTTCAAAAATAA
ATAATCACCTTGGCGAGGATGAGATGGAGTAGTAACGAGGTTGTAGACGAGGAGCTATTGCAGC
AAAAAATACACCTAGTGGGGGTTTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACTTCTC
TGACTTGCAACAATCCATTGTGAGTACTCATC
						
					

			
		

Sequences
Splice junction sequence	CAGCAAAAAATACACCTAGTGGGGGTTTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACT TCTCTGACTTGCAACAATCCATTGTGAGTACTCATCctgctcctgaacaatggtgtgtagagtt cggtggacgtccctcgccatgcccttagcatcaccgcatacatagagatatccttcttccttta ttagatcc
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: 714 Transcript exons: 12663232-12663345,12663429-12663551,12663642-12663869,12 663940-12664036,12664136-12664287 CTGCTCCTGAACAATGGTGTGTAGAGTTCGGTGGACGTCCCTCGCCATGCCCTTAGCATCACCG CATACATAGAGATATCCTTCTTCCTTTATTAGATCCCAAACTTGTGCTGCCTTCTCCATCATCT TATGTTGAACATACTCCTTCTGAGCTCCTTCACGGGAGAATGCCATGATGAGCTCAGATATTAC GCCTTGATCAACAAAATTATTGAGCTCATCCTCGTATATAAAGTCCATCTGTCGATTTCTACAC CCAAAGAAGAGCAAAGATGAACCTAGTTCTTCTCCATCTTCTTTTAGTGCCATCCTTTCCTGCA GAAAACCTCTAAAAGGTGCCAGCCCAGTCCCAGGTCCCACCATAACGATTGGAGTTGAAGGGTT GGATGGTAACTTGAAATTAGATGCTCGAATAAAGATTGGGGCTCCACTACATTCATGACTTTTC TCCGCAGGAACTGCATTCTTCATCCACGTAGAACACACACCCTTGTGGATTCTACCAGTAGGAG TTGGACCATATACTAGTGCGGATGTAACATGAACTCTACTTGGCGCCAATCTTGGCGAGGATGA GATGGAGTAGTAACGAGGTTGTAGACGAGGAGCTATTGCAGCAAAAAATACACCTAGTGGGGGT TTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACTTCTCTGACTTGCAACAATCCATTGTG AGTACTCATC
Genomic sequence	CTGCTCCTGAACAATGGTGTGTAGAGTTCGGTGGACGTCCCTCGCCATGCCCTTAGCATCACCG CATACATAGAGATATCCTTCTTCCTTTATTAGATCCCAAACTTGTGCTGCCTGAACAAATAGAA AATGCAAAATTAAAGAGATTATGTGACATTCCTTTTCCCAAAGTATGATGCATCACTTGATATA TTTACCTTCTCCATCATCTTATGTTGAACATACTCCTTCTGAGCTCCTTCACGGGAGAATGCCA TGATGAGCTCAGATATTACGCCTTGATCAACAAAATTATTGAGCTCATCCTCGTATATAAAGTC CTGCAACATACATATAAGCACTCAGCAGAAGCTCAACATGCATGATGACACAGCAAATGAAGAA GGTGTTTTTGGTTGTGAAAGTCTCACCATCTGTCGATTTCTACACCCAAAGAAGAGCAAAGATG AACCTAGTTCTTCTCCATCTTCTTTTAGTGCCATCCTTTCCTGCAGAAAACCTCTAAAAGGTGC CAGCCCAGTCCCAGGTCCCACCATAACGATTGGAGTTGAAGGGTTGGATGGTAACTTGAAATTA GATGCTCGAATAAAGATTGGGGCTCCACTACATTCATGACTTTTCTCCGCAGGAACTGCATTCT GAATTTTTCAAACTGTTAAGAAAAAAAACAGTGAACTGGCAGATAGTCAAAAAGAAGGTAAGAA GTACCTTCATCCACGTAGAACACACACCCTTGTGGATTCTACCAGTAGGAGTTGGACCATATAC TAGTGCGGATGTAACATGAACTCTACTTGGCGCCAATCTGTATTGTAAAAAACGGTAAAGAGTG ATTTGAATGCCAGAGACGATCAAGAATAGTTTTCCTTCTGCCACAAAATATATTTCAAAAATAA ATAATCACCTTGGCGAGGATGAGATGGAGTAGTAACGAGGTTGTAGACGAGGAGCTATTGCAGC AAAAAATACACCTAGTGGGGGTTTTGCAGATGGAAAAGCAGCCATCACCTCTAAAAGACTTCTC TGACTTGCAACAATCCATTGTGAGTACTCATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.342295283

Conservation Information
Conserved circRNAs	NA
PMCS	0.342295283

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12664237-12663234(-)
						
						Potential amino acid sequence
						
							MAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTGRIHKGVCSTW
MKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQERMALKEDGEEL
GSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIMAFSREGAQKEYVQHKMMEKAAQVWDLIK
EEGYLYVCGDAKGMARDVHRTLHTIVQEQDEYSQWIVASQRSLLEVMAAFPSAKPPLGVFFAAI
APRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTGRIHKGVCSTWMKNAVPAEKSHECSGAPI
FIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQERMALKEDGEELGSSLLFFGCRNRQMDFIY
EDELNNFVDQGVISELIMAFSREGAQKEYVQHKMMEKAAQVWDLIKEEGYLYVCGDAKGMARDV
HRTLHTIVQEQDEYSQWIVASQRSLLEVMAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLA
PSRVHVTSALVYGPTPTGRIHKGVCSTWMKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIV
MVGPGTGLAPFRGFLQERMALKEDGEELGSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIM
AFSREGAQKEYVQHKMMEKAAQVWDLIKEEGYLYVCGDAKGMARDVHRTLHTIVQEQDEYSQWI
VASQRSLLEVMAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTG
RIHKGVCSTWMKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQER
MALKEDGEELGSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIMAFSREGAQKEYVQHKMME
KAAQVWDLIKEEGYLYVCGDAKGMARDVHRTLHTIVQEQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12664237-12663234(-)
Potential amino acid sequence	MAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTGRIHKGVCSTW MKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQERMALKEDGEEL GSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIMAFSREGAQKEYVQHKMMEKAAQVWDLIK EEGYLYVCGDAKGMARDVHRTLHTIVQEQDEYSQWIVASQRSLLEVMAAFPSAKPPLGVFFAAI APRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTGRIHKGVCSTWMKNAVPAEKSHECSGAPI FIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQERMALKEDGEELGSSLLFFGCRNRQMDFIY EDELNNFVDQGVISELIMAFSREGAQKEYVQHKMMEKAAQVWDLIKEEGYLYVCGDAKGMARDV HRTLHTIVQEQDEYSQWIVASQRSLLEVMAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLA PSRVHVTSALVYGPTPTGRIHKGVCSTWMKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIV MVGPGTGLAPFRGFLQERMALKEDGEELGSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIM AFSREGAQKEYVQHKMMEKAAQVWDLIKEEGYLYVCGDAKGMARDVHRTLHTIVQEQDEYSQWI VASQRSLLEVMAAFPSAKPPLGVFFAAIAPRLQPRYYSISSSPRLAPSRVHVTSALVYGPTPTG RIHKGVCSTWMKNAVPAEKSHECSGAPIFIRASNFKLPSNPSTPIVMVGPGTGLAPFRGFLQER MALKEDGEELGSSLLFFGCRNRQMDFIYEDELNNFVDQGVISELIMAFSREGAQKEYVQHKMME KAAQVWDLIKEEGYLYVCGDAKGMARDVHRTLHTIVQEQ(-)
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 AT4G24520_circ_g.3

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