Plant Circular RNA Database

Detail information of AT4G00240_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G00240_circ_g.3
					
						ID in PlantcircBase
						ath_circ_029053
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 108794-109175  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT4G00240						
					
						Parent gene annotation
						
							Phospholipase D beta 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G00240_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						root, 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
						AT4G00240.3:2
AT4G00240.2:2
AT4G00240.1:2

General Information
CircRNA Name	AT4G00240_circ_g.3
ID in PlantcircBase	ath_circ_029053
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 108794-109175 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder
Parent gene	AT4G00240
Parent gene annotation	Phospholipase D beta 2
Parent gene strand	-
Alternative splicing	AT4G00240_circ_g.2
Support reads	2
Tissues	root, 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	AT4G00240.3:2 AT4G00240.2:2 AT4G00240.1:2

			
						 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  
						
							TATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACTTGCACTGAGGAGTCCTTGAAAAAACG
GCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATCcgtgaaagtggggttgtgatagtcacca
ttatgatctgtttgcagtgtcctaaacaacggatgttgaggagtatcatatcggccatcacata
gatcaagc

						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: 312
Transcript exons: 108794-108988,109059-109175
CGTGAAAGTGGGGTTGTGATAGTCACCATTATGATCTGTTTGCAGTGTCCTAAACAACGGATGT
TGAGGAGTATCATATCGGCCATCACATAGATCAAGCCCGCCCACAAAAGCTACGATTTTCCTTC
TGTTACCCCCAGCATCGGCATCTACTATTAAGTTTTTTTGGTGGTGTGTATAGATGGTTCCAAC
TTCCCTCTGTTTGACCCAACTATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACTTGCACT
GAGGAGTCCTTGAAAAAACGGCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATC
						
						Genomic sequence
						
							CGTGAAAGTGGGGTTGTGATAGTCACCATTATGATCTGTTTGCAGTGTCCTAAACAACGGATGT
TGAGGAGTATCATATCGGCCATCACATAGATCAAGCCCGCCCACAAAAGCTACGATTTTCCTTC
TGTTACCCCCAGCATCGGCATCTACTATTAAGTTTTTTTGGTGGTGTGTATAGATGGTTCCAAC
TTCCTGATGGACTAAAATATAAATAGAAGCCGGATACCACAACCAAAAAAAAGACCAAAAATTC
ATGTTCTACCCTCTGTTTGACCCAACTATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACT
TGCACTGAGGAGTCCTTGAAAAAACGGCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATC

Sequences
Splice junction sequence	TATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACTTGCACTGAGGAGTCCTTGAAAAAACG GCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATCcgtgaaagtggggttgtgatagtcacca ttatgatctgtttgcagtgtcctaaacaacggatgttgaggagtatcatatcggccatcacata gatcaagc
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: 312 Transcript exons: 108794-108988,109059-109175 CGTGAAAGTGGGGTTGTGATAGTCACCATTATGATCTGTTTGCAGTGTCCTAAACAACGGATGT TGAGGAGTATCATATCGGCCATCACATAGATCAAGCCCGCCCACAAAAGCTACGATTTTCCTTC TGTTACCCCCAGCATCGGCATCTACTATTAAGTTTTTTTGGTGGTGTGTATAGATGGTTCCAAC TTCCCTCTGTTTGACCCAACTATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACTTGCACT GAGGAGTCCTTGAAAAAACGGCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATC
Genomic sequence	CGTGAAAGTGGGGTTGTGATAGTCACCATTATGATCTGTTTGCAGTGTCCTAAACAACGGATGT TGAGGAGTATCATATCGGCCATCACATAGATCAAGCCCGCCCACAAAAGCTACGATTTTCCTTC TGTTACCCCCAGCATCGGCATCTACTATTAAGTTTTTTTGGTGGTGTGTATAGATGGTTCCAAC TTCCTGATGGACTAAAATATAAATAGAAGCCGGATACCACAACCAAAAAAAAGACCAAAAATTC ATGTTCTACCCTCTGTTTGACCCAACTATGTCGCTTTCCAGCATTTCGAGGGCATAGCAAGACT TGCACTGAGGAGTCCTTGAAAAAACGGCGTGTCTCCTCGTCATGGGTTCCCATAACCCCATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.302933376

Conservation Information
Conserved circRNAs	NA
PMCS	0.302933376

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							109167-108796(-)
						
						Potential amino acid sequence
						
							MGTHDEETRRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVA
FVGGLDLCDGRYDTPQHPLFRTLQTDHNGDYHNPTFTDGVMGTHDEETRRFFKDSSVQVLLCPR
NAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVAFVGGLDLCDGRYDTPQHPLFRTLQ
TDHNGDYHNPTFTDGVMGTHDEETRRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKN
LIVDADAGGNRRKIVAFVGGLDLCDGRYDTPQHPLFRTLQTDHNGDYHNPTFTDGVMGTHDEET
RRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVAFVGGLDLC
DGRYDTPQHPLFRTLQTDHNGDYHNPTFT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	109167-108796(-)
Potential amino acid sequence	MGTHDEETRRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVA FVGGLDLCDGRYDTPQHPLFRTLQTDHNGDYHNPTFTDGVMGTHDEETRRFFKDSSVQVLLCPR NAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVAFVGGLDLCDGRYDTPQHPLFRTLQ TDHNGDYHNPTFTDGVMGTHDEETRRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKN LIVDADAGGNRRKIVAFVGGLDLCDGRYDTPQHPLFRTLQTDHNGDYHNPTFTDGVMGTHDEET RRFFKDSSVQVLLCPRNAGKRHSWVKQREVGTIYTHHQKNLIVDADAGGNRRKIVAFVGGLDLC DGRYDTPQHPLFRTLQTDHNGDYHNPTFT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G00240_circ_g.3

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