Plant Circular RNA Database

Detail information of AT4G11820_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G11820_circ_g.2
					
						ID in PlantcircBase
						ath_circ_030422
					
						Alias
						Ath_circ_FC2602
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7109656-7110409  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT4G11820						
					
						Parent gene annotation
						
							Hydroxymethylglutaryl-CoA synthase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G11820_circ_g.1 AT4G11820_circ_g.3 AT4G11820_circ_g.4 AT4G11820_circ_g.5 AT4G11820_circ_g.6 AT4G11820_circ_g.7 						
					
						Support reads
						9
					
						Tissues
						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
						AT4G11820.2:5
AT4G11820.1:5
AT4G11820.3:5

General Information
CircRNA Name	AT4G11820_circ_g.2
ID in PlantcircBase	ath_circ_030422
Alias	Ath_circ_FC2602
Organism	Arabidpsis thaliana
Position	chr4: 7109656-7110409 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT4G11820
Parent gene annotation	Hydroxymethylglutaryl-CoA synthase
Parent gene strand	-
Alternative splicing	AT4G11820_circ_g.1 AT4G11820_circ_g.3 AT4G11820_circ_g.4 AT4G11820_circ_g.5 AT4G11820_circ_g.6 AT4G11820_circ_g.7
Support reads	9
Tissues	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	AT4G11820.2:5 AT4G11820.1:5 AT4G11820.3:5

			
						 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  
						
							TTGTAACTGTGAAAAGAAACACTTACTTGTTGCATAAATGTTTATAGCAGGAGTCAAGAGCCAT
GAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAACcaaatcattgtgtttcttgtggatgagg
gaagcaaatgcagcgtagagagaagcagtgtacatgttaccgacttcctttggtattaaagtcg
ttggttgc

						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: 435
Transcript exons: 7109656-7109796,7109878-7109965,7110049-7110104,7110184-
7110259,7110336-7110409
CAAATCATTGTGTTTCTTGTGGATGAGGGAAGCAAATGCAGCGTAGAGAGAAGCAGTGTACATG
TTACCGACTTCCTTTGGTATTAAAGTCGTTGGTTGCACTTTAGCATCATAAAACGGTTTCGCAA
TTTGTTGTGACACCTTTTCAAGATCACGGCTTTGGTAACTCTCGTCAAGGGTCAAAGATGAATA
AGGGGTGAACTTTTCTTTGGCAGCCTCGTCAATGGAGCTTGCGTTTCTCAAGAAGTCGTTGTAC
AAGAGACGAGCAAAGCTTTTCTGTACAAGTTTATTGTATGGAGAATGGAAAACAATGTAATCAG
CATCATTTATGGAGAACTCTTTGCCCTCGATCTTCTCGAACTTGTTGCATAAATGTTTATAGCA
GGAGTCAAGAGCCATGAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAAC
						
						Genomic sequence
						
							CAAATCATTGTGTTTCTTGTGGATGAGGGAAGCAAATGCAGCGTAGAGAGAAGCAGTGTACATG
TTACCGACTTCCTTTGGTATTAAAGTCGTTGGTTGCACTTTAGCATCATAAAACGGTTTCGCAA
TTTGTTGTGACACCTGCAAAAGAGACAACAGATTGAGCTATAAATCGGTTTTCTCTCAGTATCA
AAAGCAAAAGAAAAGAGAAATGATGAGAACCTTTTCAAGATCACGGCTTTGGTAACTCTCGTCA
AGGGTCAAAGATGAATAAGGGGTGAACTTTTCTTTGGCAGCCTCGTCAATGGAGCTGCAATAGA
GGAAAGAAAATGTTCACTCACATTTAACAAGTAAAGAACTTTCAATCTGAAAACGTAGTTAATA
AGCAAGAACCTTGCGTTTCTCAAGAAGTCGTTGTACAAGAGACGAGCAAAGCTTTTCTGTACAA
GCTGCAATATCATAGAGGAGAAGACTGGTAAGAGACAATTCAACTAGAACAAAACTATTGTTGG
AGGATTAAGAAATTACTTTATTGTATGGAGAATGGAAAACAATGTAATCAGCATCATTTATGGA
GAACTCTTTGCCCTCGATCTTCTCGAACCTAATAAAAACCAAAGAGTCACACAACAACAGAAGA
AAGAAACTGAGTTTTTGTAACTGTGAAAAGAAACACTTACTTGTTGCATAAATGTTTATAGCAG
GAGTCAAGAGCCATGAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAAC

Sequences
Splice junction sequence	TTGTAACTGTGAAAAGAAACACTTACTTGTTGCATAAATGTTTATAGCAGGAGTCAAGAGCCAT GAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAACcaaatcattgtgtttcttgtggatgagg gaagcaaatgcagcgtagagagaagcagtgtacatgttaccgacttcctttggtattaaagtcg ttggttgc
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: 435 Transcript exons: 7109656-7109796,7109878-7109965,7110049-7110104,7110184- 7110259,7110336-7110409 CAAATCATTGTGTTTCTTGTGGATGAGGGAAGCAAATGCAGCGTAGAGAGAAGCAGTGTACATG TTACCGACTTCCTTTGGTATTAAAGTCGTTGGTTGCACTTTAGCATCATAAAACGGTTTCGCAA TTTGTTGTGACACCTTTTCAAGATCACGGCTTTGGTAACTCTCGTCAAGGGTCAAAGATGAATA AGGGGTGAACTTTTCTTTGGCAGCCTCGTCAATGGAGCTTGCGTTTCTCAAGAAGTCGTTGTAC AAGAGACGAGCAAAGCTTTTCTGTACAAGTTTATTGTATGGAGAATGGAAAACAATGTAATCAG CATCATTTATGGAGAACTCTTTGCCCTCGATCTTCTCGAACTTGTTGCATAAATGTTTATAGCA GGAGTCAAGAGCCATGAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAAC
Genomic sequence	CAAATCATTGTGTTTCTTGTGGATGAGGGAAGCAAATGCAGCGTAGAGAGAAGCAGTGTACATG TTACCGACTTCCTTTGGTATTAAAGTCGTTGGTTGCACTTTAGCATCATAAAACGGTTTCGCAA TTTGTTGTGACACCTGCAAAAGAGACAACAGATTGAGCTATAAATCGGTTTTCTCTCAGTATCA AAAGCAAAAGAAAAGAGAAATGATGAGAACCTTTTCAAGATCACGGCTTTGGTAACTCTCGTCA AGGGTCAAAGATGAATAAGGGGTGAACTTTTCTTTGGCAGCCTCGTCAATGGAGCTGCAATAGA GGAAAGAAAATGTTCACTCACATTTAACAAGTAAAGAACTTTCAATCTGAAAACGTAGTTAATA AGCAAGAACCTTGCGTTTCTCAAGAAGTCGTTGTACAAGAGACGAGCAAAGCTTTTCTGTACAA GCTGCAATATCATAGAGGAGAAGACTGGTAAGAGACAATTCAACTAGAACAAAACTATTGTTGG AGGATTAAGAAATTACTTTATTGTATGGAGAATGGAAAACAATGTAATCAGCATCATTTATGGA GAACTCTTTGCCCTCGATCTTCTCGAACCTAATAAAAACCAAAGAGTCACACAACAACAGAAGA AAGAAACTGAGTTTTTGTAACTGTGAAAAGAAACACTTACTTGTTGCATAAATGTTTATAGCAG GAGTCAAGAGCCATGAGGTAGCAAGTCTGTGAAAGCTTACCATCAACAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.262702834

Conservation Information
Conserved circRNAs	NA
PMCS	0.262702834

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7110374-7109658(-)
						
						Potential amino acid sequence
						
							MALDSCYKHLCNKFEKIEGKEFSINDADYIVFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAK
EKFTPYSSLTLDESYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHK
KHNDLVVDGKLSQTCYLMALDSCYKHLCNKFEKIEGKEFSINDADYIVFHSPYNKLVQKSFARL
LYNDFLRNASSIDEAAKEKFTPYSSLTLDESYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVG
NMYTASLYAAFASLIHKKHNDLVVDGKLSQTCYLMALDSCYKHLCNKFEKIEGKEFSINDADYI
VFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAKEKFTPYSSLTLDESYQSRDLEKVSQQIAKP
FYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHKKHNDLVVDGKLSQTCYLMALDSCYKHLCNK
FEKIEGKEFSINDADYIVFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAKEKFTPYSSLTLDE
SYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHKKHNDL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7110374-7109658(-)
Potential amino acid sequence	MALDSCYKHLCNKFEKIEGKEFSINDADYIVFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAK EKFTPYSSLTLDESYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHK KHNDLVVDGKLSQTCYLMALDSCYKHLCNKFEKIEGKEFSINDADYIVFHSPYNKLVQKSFARL LYNDFLRNASSIDEAAKEKFTPYSSLTLDESYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVG NMYTASLYAAFASLIHKKHNDLVVDGKLSQTCYLMALDSCYKHLCNKFEKIEGKEFSINDADYI VFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAKEKFTPYSSLTLDESYQSRDLEKVSQQIAKP FYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHKKHNDLVVDGKLSQTCYLMALDSCYKHLCNK FEKIEGKEFSINDADYIVFHSPYNKLVQKSFARLLYNDFLRNASSIDEAAKEKFTPYSSLTLDE SYQSRDLEKVSQQIAKPFYDAKVQPTTLIPKEVGNMYTASLYAAFASLIHKKHNDL(-)
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 AT4G11820_circ_g.2

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