Plant Circular RNA Database

Detail information of AT3G51840_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G51840_circ_g.2
					
						ID in PlantcircBase
						ath_circ_027033
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 19226435-19228591  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G51840						
					
						Parent gene annotation
						
							Acyl-coenzyme A oxidase 4, peroxisomal
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G51840_circ_g.1 AT3G51840_circ_g.3 AT3G51840_circ_g.4 AT3G51840_circ_g.5 AT3G51840_circ_g.6 AT3G51840_circ_g.7 						
					
						Support reads
						1
					
						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
						AT3G51840.1:10

General Information
CircRNA Name	AT3G51840_circ_g.2
ID in PlantcircBase	ath_circ_027033
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 19226435-19228591 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT3G51840
Parent gene annotation	Acyl-coenzyme A oxidase 4, peroxisomal
Parent gene strand	-
Alternative splicing	AT3G51840_circ_g.1 AT3G51840_circ_g.3 AT3G51840_circ_g.4 AT3G51840_circ_g.5 AT3G51840_circ_g.6 AT3G51840_circ_g.7
Support reads	1
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	AT3G51840.1:10

			
						 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  
						
							GGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAGGTGGCAAAT
CAAAGTATGAACTCTTCACCTTCTTCTCATTACTAGctttcctaaactggcttgacctggagtc
atctgacccgtctcatacagcttgcagagacgccaacccattagaaacatcgcttgaacgttac
ccagcatc

									
								

					

						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: 1067
Transcript exons: 19226435-19226606,19226698-19226774,19226896-19227055,19
227349-19227458,19227562-19227621,19227731-19227804,1922
7914-19228037,19228123-19228200,19228297-19228403,192284
87-19228591
CTTTCCTAAACTGGCTTGACCTGGAGTCATCTGACCCGTCTCATACAGCTTGCAGAGACGCCAA
CCCATTAGAAACATCGCTTGAACGTTACCCAGCATCTGCACAAGCTTCTGTTGGTTTAACTGGA
AAGCAGCCAACGGTGCTCCAAACTGTTTCCTCTCCTTCAGATACCTGTGGCACATATCGTAGAT
TCCCATTGATATGCCGATTGGTTGCCAGGCCACCATTACACGTGAGACAGCCAGAACCTTGCTG
GTGTCCTGAAAAGAATTTACCCCAGGTAACCGATCCTCATCTGGAACAAAGACATTCTGTAGTA
GAATATCTCCATTTTGAACCATACGTAAACCTATTTTATTTGGGATCTTAGTAGCCTTTAGGCC
AGGCGCATCTTTCTTGACTATGAATCCGTTGATTTGGTTAGTTGTTGTATTCCTCGCAAAGATG
ATCAACAGATCTGCAAAGGTGCTGTTTCCAATCCAACGCTTTTGTCCATTAATTTTCCAACCTC
CTTCAACCTTTGTTGCAGTCGTTCCTAGACCACTTGCATCGCTTCCATTGTCGGGCTCTGTCAA
AGCCCAACAAGCCACAGTATTCAATTGAGCCAAAGAAGGCAAATACTTCTCCTTCTGTGCTTCT
GATCCACAGAGTGCAATAGTGAGCATGCCCAAAGAAGAATGCACCAAAATGAAAGTCGAACAAC
TTGCATCAACTCTAGCTATTTCTGCTGTGGCAATTGCATTGGCGGTGATGGAGAGACCAGGACA
TCCATAACCCTTGATCGAGCCACCAGCAACACCCATAGCCCCAAGCTTTGGAGTGATATGGAAT
GGAAATTCTGCTTTCTCCCAGTACTCTGTCATTATTGGAGCAACTTCTTTCTCCATGCATTCCC
TCACTTTCTTCCGGATAGCTTGTTCTTCCGGAGTCAGTAGATCATTGAAATGATAATAGTCTGA
AGTACAAGGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAGGT
GGCAAATCAAAGTATGAACTCTTCACCTTCTTCTCATTACTAG
						
					

						Genomic sequence
						
							CTTTCCTAAACTGGCTTGACCTGGAGTCATCTGACCCGTCTCATACAGCTTGCAGAGACGCCAA
CCCATTAGAAACATCGCTTGAACGTTACCCAGCATCTGCACAAGCTTCTGTTGGTTTAACTGGA
AAGCAGCCAACGGTGCTCCAAACTGTTTCCTCTCCTTCAGATACCTTGAAACAATACATATTAA
TGGAAAACTGTAAGTAACGAAATGAAAGCTCATACTAGGATTACAGAGATCTGGCGGTTTCCCG
GAAATACCTGTGGCACATATCGTAGATTCCCATTGATATGCCGATTGGTTGCCAGGCCACCATT
ACACGTGAGACAGCCAGAACCTATTCAAGTGTAGACAAACATTTAATTATAACAAAGAAAAGAG
GAAGATGTGACGTTTTTCTGGTGATAAAGTATTTTAGAGCATTTTGGGGTTATGTAGTAGAATT
ATCACAACAGTACCTTGCTGGTGTCCTGAAAAGAATTTACCCCAGGTAACCGATCCTCATCTGG
AACAAAGACATTCTGTAGTAGAATATCTCCATTTTGAACCATACGTAAACCTATTTTATTTGGG
ATCTTAGTAGCCTTTAGGCCAGGCGCATCTTTCTTGACTATGAATCTGAAAGAGGGTTGCTGAT
AAGTTTCTAATGCAGGAAATATAGTCTATATAAGATGAATGAGGAGCCAGACATTAGTCCAGTA
TGCACTTGATAACGGTCCTTACCAAATTTATTGTTCAGAACATTCAATTGCGTAGCAACCTATT
TAGCATTCTTTATGAAAATGGATTTTTACAGCACTACCATAAGATGAAATCAAGAGCCACCTCA
TTACCTTCAGTTTTCTGGGAACGACCTCTACACCTAAGATACAAAATCTGAGAGATCTAAGAAA
GCCAATAATCTGACTTACCCGTTGATTTGGTTAGTTGTTGTATTCCTCGCAAAGATGATCAACA
GATCTGCAAAGGTGCTGTTTCCAATCCAACGCTTTTGTCCATTAATTTTCCAACCTCCTTCAAC
CTGATACAGTAAACCAGTCAAAACAATGAAACATTACTGTACTTGCATAAGTATAGAAAGATAG
ATACAAGTAACTGAATACTAGGAGAGAAGGCAGCCCCACCTTTGTTGCAGTCGTTCCTAGACCA
CTTGCATCGCTTCCATTGTCGGGCTCTGTCAAAGCCTTTATAGAAGTCCAATATAGGTAATGGT
ATCAACAGGATGTTTGTATAACACAATAAAACACTATTCAAGGGATGCAAATCATCTAATTCCA
AGATCCACGTACTCACCCAACAAGCCACAGTATTCAATTGAGCCAAAGAAGGCAAATACTTCTC
CTTCTGTGCTTCTGATCCACAGAGTGCTATTCTTGACAAAATCAAAGGAAATAAACTTATGCAA
ATCCTAGAATGATCTTTACTAGGACAACTAAATATTAAACAAGCTTAGAAATAAATATTAGGTG
CTCTTACCAATAGTGAGCATGCCCAAAGAAGAATGCACCAAAATGAAAGTCGAACAACTTGCAT
CAACTCTAGCTATTTCTGCTGTGGCAATTGCATTGGCGGTGATGGAGAGACCAGGACATCCATA
ACCCTAAGAAGTCAAACCAAATCAATACTGAAGCTTCTATCCACATAATCAAACAAACAAAAAC
CCAGAGACAGGCATTGCAAATTACCTTGATCGAGCCACCAGCAACACCCATAGCCCCAAGCTTT
GGAGTGATATGGAATGGAAATTCTGCTTTCTCCCAGTACTGAGTAAAACCCAAAGGAAGAACAA
TGAGATAACGCTAACTATACAATCAAAGCAAACAAAGAAAAAACAAAACACGTCGAACATGAAG
ATCTACCTCTGTCATTATTGGAGCAACTTCTTTCTCCATGCATTCCCTCACTTTCTTCCGGATA
GCTTGTTCTTCCGGAGTCAGTAGATCATTGAAATGATAATAGTCTGAAGCTGTAAACAGTATAT
CCACAAATGAGACAGAGAAACACAATAAATCATCAAAATATAAATCCTCTGGAAGAAGAAATCC
TTACTACAAGGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAG
GTGGCAAATCAAAGTATGAACTCTTCACCTTCTTCTCATTACTAG
						
					

			
		

Sequences
Splice junction sequence	GGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAGGTGGCAAAT CAAAGTATGAACTCTTCACCTTCTTCTCATTACTAGctttcctaaactggcttgacctggagtc atctgacccgtctcatacagcttgcagagacgccaacccattagaaacatcgcttgaacgttac ccagcatc
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: 1067 Transcript exons: 19226435-19226606,19226698-19226774,19226896-19227055,19 227349-19227458,19227562-19227621,19227731-19227804,1922 7914-19228037,19228123-19228200,19228297-19228403,192284 87-19228591 CTTTCCTAAACTGGCTTGACCTGGAGTCATCTGACCCGTCTCATACAGCTTGCAGAGACGCCAA CCCATTAGAAACATCGCTTGAACGTTACCCAGCATCTGCACAAGCTTCTGTTGGTTTAACTGGA AAGCAGCCAACGGTGCTCCAAACTGTTTCCTCTCCTTCAGATACCTGTGGCACATATCGTAGAT TCCCATTGATATGCCGATTGGTTGCCAGGCCACCATTACACGTGAGACAGCCAGAACCTTGCTG GTGTCCTGAAAAGAATTTACCCCAGGTAACCGATCCTCATCTGGAACAAAGACATTCTGTAGTA GAATATCTCCATTTTGAACCATACGTAAACCTATTTTATTTGGGATCTTAGTAGCCTTTAGGCC AGGCGCATCTTTCTTGACTATGAATCCGTTGATTTGGTTAGTTGTTGTATTCCTCGCAAAGATG ATCAACAGATCTGCAAAGGTGCTGTTTCCAATCCAACGCTTTTGTCCATTAATTTTCCAACCTC CTTCAACCTTTGTTGCAGTCGTTCCTAGACCACTTGCATCGCTTCCATTGTCGGGCTCTGTCAA AGCCCAACAAGCCACAGTATTCAATTGAGCCAAAGAAGGCAAATACTTCTCCTTCTGTGCTTCT GATCCACAGAGTGCAATAGTGAGCATGCCCAAAGAAGAATGCACCAAAATGAAAGTCGAACAAC TTGCATCAACTCTAGCTATTTCTGCTGTGGCAATTGCATTGGCGGTGATGGAGAGACCAGGACA TCCATAACCCTTGATCGAGCCACCAGCAACACCCATAGCCCCAAGCTTTGGAGTGATATGGAAT GGAAATTCTGCTTTCTCCCAGTACTCTGTCATTATTGGAGCAACTTCTTTCTCCATGCATTCCC TCACTTTCTTCCGGATAGCTTGTTCTTCCGGAGTCAGTAGATCATTGAAATGATAATAGTCTGA AGTACAAGGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAGGT GGCAAATCAAAGTATGAACTCTTCACCTTCTTCTCATTACTAG
Genomic sequence	CTTTCCTAAACTGGCTTGACCTGGAGTCATCTGACCCGTCTCATACAGCTTGCAGAGACGCCAA CCCATTAGAAACATCGCTTGAACGTTACCCAGCATCTGCACAAGCTTCTGTTGGTTTAACTGGA AAGCAGCCAACGGTGCTCCAAACTGTTTCCTCTCCTTCAGATACCTTGAAACAATACATATTAA TGGAAAACTGTAAGTAACGAAATGAAAGCTCATACTAGGATTACAGAGATCTGGCGGTTTCCCG GAAATACCTGTGGCACATATCGTAGATTCCCATTGATATGCCGATTGGTTGCCAGGCCACCATT ACACGTGAGACAGCCAGAACCTATTCAAGTGTAGACAAACATTTAATTATAACAAAGAAAAGAG GAAGATGTGACGTTTTTCTGGTGATAAAGTATTTTAGAGCATTTTGGGGTTATGTAGTAGAATT ATCACAACAGTACCTTGCTGGTGTCCTGAAAAGAATTTACCCCAGGTAACCGATCCTCATCTGG AACAAAGACATTCTGTAGTAGAATATCTCCATTTTGAACCATACGTAAACCTATTTTATTTGGG ATCTTAGTAGCCTTTAGGCCAGGCGCATCTTTCTTGACTATGAATCTGAAAGAGGGTTGCTGAT AAGTTTCTAATGCAGGAAATATAGTCTATATAAGATGAATGAGGAGCCAGACATTAGTCCAGTA TGCACTTGATAACGGTCCTTACCAAATTTATTGTTCAGAACATTCAATTGCGTAGCAACCTATT TAGCATTCTTTATGAAAATGGATTTTTACAGCACTACCATAAGATGAAATCAAGAGCCACCTCA TTACCTTCAGTTTTCTGGGAACGACCTCTACACCTAAGATACAAAATCTGAGAGATCTAAGAAA GCCAATAATCTGACTTACCCGTTGATTTGGTTAGTTGTTGTATTCCTCGCAAAGATGATCAACA GATCTGCAAAGGTGCTGTTTCCAATCCAACGCTTTTGTCCATTAATTTTCCAACCTCCTTCAAC CTGATACAGTAAACCAGTCAAAACAATGAAACATTACTGTACTTGCATAAGTATAGAAAGATAG ATACAAGTAACTGAATACTAGGAGAGAAGGCAGCCCCACCTTTGTTGCAGTCGTTCCTAGACCA CTTGCATCGCTTCCATTGTCGGGCTCTGTCAAAGCCTTTATAGAAGTCCAATATAGGTAATGGT ATCAACAGGATGTTTGTATAACACAATAAAACACTATTCAAGGGATGCAAATCATCTAATTCCA AGATCCACGTACTCACCCAACAAGCCACAGTATTCAATTGAGCCAAAGAAGGCAAATACTTCTC CTTCTGTGCTTCTGATCCACAGAGTGCTATTCTTGACAAAATCAAAGGAAATAAACTTATGCAA ATCCTAGAATGATCTTTACTAGGACAACTAAATATTAAACAAGCTTAGAAATAAATATTAGGTG CTCTTACCAATAGTGAGCATGCCCAAAGAAGAATGCACCAAAATGAAAGTCGAACAACTTGCAT CAACTCTAGCTATTTCTGCTGTGGCAATTGCATTGGCGGTGATGGAGAGACCAGGACATCCATA ACCCTAAGAAGTCAAACCAAATCAATACTGAAGCTTCTATCCACATAATCAAACAAACAAAAAC CCAGAGACAGGCATTGCAAATTACCTTGATCGAGCCACCAGCAACACCCATAGCCCCAAGCTTT GGAGTGATATGGAATGGAAATTCTGCTTTCTCCCAGTACTGAGTAAAACCCAAAGGAAGAACAA TGAGATAACGCTAACTATACAATCAAAGCAAACAAAGAAAAAACAAAACACGTCGAACATGAAG ATCTACCTCTGTCATTATTGGAGCAACTTCTTTCTCCATGCATTCCCTCACTTTCTTCCGGATA GCTTGTTCTTCCGGAGTCAGTAGATCATTGAAATGATAATAGTCTGAAGCTGTAAACAGTATAT CCACAAATGAGACAGAGAAACACAATAAATCATCAAAATATAAATCCTCTGGAAGAAGAAATCC TTACTACAAGGTGGAAATGTAGAGGCTGGAGTTGCTTGAGGAAATGCTACAGACATTTCCATAG GTGGCAAATCAAAGTATGAACTCTTCACCTTCTTCTCATTACTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.213582986

Conservation Information
Conserved circRNAs	NA
PMCS	0.213582986

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G51840_circ_g.2

Address

Any questions?

Supported by