Plant Circular RNA Database

Detail information of AT4G20430_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G20430_circ_g.3
					
						ID in PlantcircBase
						ath_circ_031883
					
						Alias
						Ath_circ_FC2730
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 11018520-11019211  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT4G20430						
					
						Parent gene annotation
						
							Subtilisin-like protease SBT2.2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G20430_circ_g.1 AT4G20430_circ_g.2 						
					
						Support reads
						8
					
						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
						AT4G20430.1:2
AT4G20430.3:2
AT4G20430.2:3

General Information
CircRNA Name	AT4G20430_circ_g.3
ID in PlantcircBase	ath_circ_031883
Alias	Ath_circ_FC2730
Organism	Arabidpsis thaliana
Position	chr4: 11018520-11019211 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circRNA_finder
Parent gene	AT4G20430
Parent gene annotation	Subtilisin-like protease SBT2.2
Parent gene strand	-
Alternative splicing	AT4G20430_circ_g.1 AT4G20430_circ_g.2
Support reads	8
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	AT4G20430.1:2 AT4G20430.3:2 AT4G20430.2:3

			
						 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  
						
							CATTCACCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAG
AGATCATTGTGTACTTCTTGCCTTCATCTGTACGAActtcaaactcagtggattcagtggcagc
ggaactccaagcgccccaaatggaatttccaggagctacaagatttggtttcaaaatgtcggcg
tcgttaaa

									
								

					

						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: 534
Transcript exons: 11018520-11018790,11018877-11019054,11019127-11019211
CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC
TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT
GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG
CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA
GTACTTGAGTAAAACCTTGGAATCTTCTGCGGATGGAATTATGATCCCGGGCATGTCCATCGGT
GTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAGAACACAACACCCTTTGCAGATA
GATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCCCGAGGACGAAACGGATAGAGTA
GATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAGAGATCATTGTGTAC
TTCTTGCCTTCATCTGTACGAA
Transcript length: 606
Transcript exons: 11018520-11018790,11018877-11019211
CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC
TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT
GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG
CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA
GTACTTGAGTAAAACCTTGGAATCTTCTGCGGATGGAATTATGATCCCGGGCATGTCCATCGGT
GTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAGAACACAACACCCTTTGCAGATA
GATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCCCGAGGACGAAACGGATAGAGTA
GCTACATATCAGTAGATTCCCACGGATAACATCTTTATCGAAGCTGCCATAGTCTTGGCATTCA
CCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAGAGATCA
TTGTGTACTTCTTGCCTTCATCTGTACGAA
						
					

						Genomic sequence
						
							CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC
TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT
GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG
CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA
GTACTTGAGTAAAACCTATATATGAATTAACATGTCGTTATTAGATTGCTCTTCAAGAAGAATC
AAGAAAAGAAGTGATATGTTTCTAGTTATATTCTCACCTTGGAATCTTCTGCGGATGGAATTAT
GATCCCGGGCATGTCCATCGGTGTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAG
AACACAACACCCTTTGCAGATAGATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCC
CGAGGACGAAACGGATAGAGTAGCTACATATCAGTAGATTCCCACGGATAACATCTTTATCGAA
GCTGCCATAGTCTTGGCATTCACCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTC
AACGCATCAAGAGCAGAGATCATTGTGTACTTCTTGCCTTCATCTGTACGAA
						
					

			
		

Sequences
Splice junction sequence	CATTCACCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAG AGATCATTGTGTACTTCTTGCCTTCATCTGTACGAActtcaaactcagtggattcagtggcagc ggaactccaagcgccccaaatggaatttccaggagctacaagatttggtttcaaaatgtcggcg tcgttaaa
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: 534 Transcript exons: 11018520-11018790,11018877-11019054,11019127-11019211 CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA GTACTTGAGTAAAACCTTGGAATCTTCTGCGGATGGAATTATGATCCCGGGCATGTCCATCGGT GTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAGAACACAACACCCTTTGCAGATA GATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCCCGAGGACGAAACGGATAGAGTA GATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAGAGATCATTGTGTAC TTCTTGCCTTCATCTGTACGAA Transcript length: 606 Transcript exons: 11018520-11018790,11018877-11019211 CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA GTACTTGAGTAAAACCTTGGAATCTTCTGCGGATGGAATTATGATCCCGGGCATGTCCATCGGT GTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAGAACACAACACCCTTTGCAGATA GATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCCCGAGGACGAAACGGATAGAGTA GCTACATATCAGTAGATTCCCACGGATAACATCTTTATCGAAGCTGCCATAGTCTTGGCATTCA CCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTCAACGCATCAAGAGCAGAGATCA TTGTGTACTTCTTGCCTTCATCTGTACGAA
Genomic sequence	CTTCAAACTCAGTGGATTCAGTGGCAGCGGAACTCCAAGCGCCCCAAATGGAATTTCCAGGAGC TACAAGATTTGGTTTCAAAATGTCGGCGTCGTTAAAAAGGCTGTCTTGTGGATCAGGTCCTCTT GCTGAGTAGTACATAATCTTAGGAGCTCTGTTACTGAAGTTAGCATTTTGTCCACCTGCAATGG CTGCAACTGCTCCAAATCTAACAATCTCCTTGGTTGTTCCATCTCTTACAAGAGAAGAGTTATA GTACTTGAGTAAAACCTATATATGAATTAACATGTCGTTATTAGATTGCTCTTCAAGAAGAATC AAGAAAAGAAGTGATATGTTTCTAGTTATATTCTCACCTTGGAATCTTCTGCGGATGGAATTAT GATCCCGGGCATGTCCATCGGTGTAGGATTAATCTGAAAACCAAGAACATAAGGGTCCATGTAG AACACAACACCCTTTGCAGATAGATTCTTGGCAACAGCTAAAGCTTGTTTAATAGTGGAAAGCC CGAGGACGAAACGGATAGAGTAGCTACATATCAGTAGATTCCCACGGATAACATCTTTATCGAA GCTGCCATAGTCTTGGCATTCACCTACATACATGTCTTTGTCTACTACTGAACTTTTGTTCTTC AACGCATCAAGAGCAGAGATCATTGTGTACTTCTTGCCTTCATCTGTACGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.421153314

Conservation Information
Conserved circRNAs	NA
PMCS	0.421153314

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11019183-11018522(-)
						
						Potential amino acid sequence
						
							MISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSYSIRFVLGLSTIKQALAVAKN
LSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYYNSSLVRDGTTKEIVRFGAVA
AIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVAPGNSIWGAWSSAATESTEFE
VRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSYSIRFVLGLST
IKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYYNSSLVRDGTT
KEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVAPGNSIWGAWS
SAATESTEFEVRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSY
SIRFVLGLSTIKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYY
NSSLVRDGTTKEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVA
PGNSIWGAWSSAATESTEFEVRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDV
IRGNLLICSYSIRFVLGLSTIKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSA
EDSKVLLKYYNSSLVRDGTTKEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFND
ADILKPNLVAPGNSIWGAWSSAATESTEFE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11019183-11018522(-)
Potential amino acid sequence	MISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSYSIRFVLGLSTIKQALAVAKN LSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYYNSSLVRDGTTKEIVRFGAVA AIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVAPGNSIWGAWSSAATESTEFE VRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSYSIRFVLGLST IKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYYNSSLVRDGTT KEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVAPGNSIWGAWS SAATESTEFEVRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDVIRGNLLICSY SIRFVLGLSTIKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSAEDSKVLLKYY NSSLVRDGTTKEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFNDADILKPNLVA PGNSIWGAWSSAATESTEFEVRTDEGKKYTMISALDALKNKSSVVDKDMYVGECQDYGSFDKDV IRGNLLICSYSIRFVLGLSTIKQALAVAKNLSAKGVVFYMDPYVLGFQINPTPMDMPGIIIPSA EDSKVLLKYYNSSLVRDGTTKEIVRFGAVAAIAGGQNANFSNRAPKIMYYSARGPDPQDSLFND ADILKPNLVAPGNSIWGAWSSAATESTEFE(-)
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 AT4G20430_circ_g.3

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