Plant Circular RNA Database

Detail information of AT1G47490_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G47490_circ_g.2
					
						ID in PlantcircBase
						ath_circ_006143
					
						Alias
						Ath_circ_FC0675, Ath_circ_FC0676
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 17425407-17426517  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G47490						
					
						Parent gene annotation
						
							Polyadenylate-binding protein RBP47C
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G47490_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G47500_circ_g.1 AT1G47500_circ_g.2 AT1G47500_circ_g.3 AT1G47500_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						root
					
						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  
						
							GT-AG							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
						AT1G47490.1:4
AT1G47490.2:3

General Information
CircRNA Name	AT1G47490_circ_g.2
ID in PlantcircBase	ath_circ_006143
Alias	Ath_circ_FC0675, Ath_circ_FC0676
Organism	Arabidpsis thaliana
Position	chr1: 17425407-17426517 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G47490
Parent gene annotation	Polyadenylate-binding protein RBP47C
Parent gene strand	+
Alternative splicing	AT1G47490_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G47500_circ_g.1 AT1G47500_circ_g.2 AT1G47500_circ_g.3 AT1G47500_circ_g.4
Support reads	1
Tissues	root
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	GT-AG 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	AT1G47490.1:4 AT1G47490.2:3

			
						 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  
						
							CAGACCAAATGCAGAGGAGGCTTTGGAGAAACTAAATGGGACTGTAATTGGAAAACAAACAGTT
CGGCTTTCTTGGGGACGTAATCCCGCCAATAAGCAGagagagattgtttcggtgaaggtgattc
gtaataagaacaatggtttatcagaaggatatggatttgtggagtttgagtcccatgatgtagc
tgataagg

									
								

					

						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: 765
Transcript exons: 17425407-17425884,17426038-17426096,17426210-17426340,17
426421-17426517
AGAGAGATTGTTTCGGTGAAGGTGATTCGTAATAAGAACAATGGTTTATCAGAAGGATATGGAT
TTGTGGAGTTTGAGTCCCATGATGTAGCTGATAAGGTTTTGCGGGAGTTTAACGGGACGACTAT
GCCAAATACTGACCAACCTTTTCGTTTGAACTGGGCTAGTTTTAGCACCGGTGAGAAGCGGTTA
GAGAACAATGGACCTGATCTCTCTATTTTCGTGGGGGATTTGTCACCAGATGTTTCGGATAATT
TGTTGCACGAGACCTTCTCTGAGAAGTATCCGTCGGTTAAAGCTGCGAAAGTTGTCCTTGATGC
TAATACTGGTAGGTCAAAGGGGTATGGGTTTGTGAGGTTTGGTGATGAGAATGAAAGGACCAAA
GCAATGACTGAGATGAATGGTGTTAAATGTTCTAGTAGAGCTATGCGCATCGGTCCTGCTACCC
CGAGGAAGACTAATGGTTATCAACAACAAGGTGGATACATGCCGAATGGTACCTTGACGCGTCC
TGAAGGGGACATAATGAACACAACAATATTTGTTGGAGGGCTTGACTCTAGTGTCACTGATGAA
GACTTAAAGCAACCTTTCAATGAATTCGGGGAAATAGTCTCTGTCAAGATTCCTGTTGGTAAAG
GATGCGGATTTGTTCAGTTTGTTAACAGACCAAATGCAGAGGAGGCTTTGGAGAAACTAAATGG
GACTGTAATTGGAAAACAAACAGTTCGGCTTTCTTGGGGACGTAATCCCGCCAATAAGCAG
						
					

						Genomic sequence
						
							AGAGAGATTGTTTCGGTGAAGGTGATTCGTAATAAGAACAATGGTTTATCAGAAGGATATGGAT
TTGTGGAGTTTGAGTCCCATGATGTAGCTGATAAGGTTTTGCGGGAGTTTAACGGGACGACTAT
GCCAAATACTGACCAACCTTTTCGTTTGAACTGGGCTAGTTTTAGCACCGGTGAGAAGCGGTTA
GAGAACAATGGACCTGATCTCTCTATTTTCGTGGGGGATTTGTCACCAGATGTTTCGGATAATT
TGTTGCACGAGACCTTCTCTGAGAAGTATCCGTCGGTTAAAGCTGCGAAAGTTGTCCTTGATGC
TAATACTGGTAGGTCAAAGGGGTATGGGTTTGTGAGGTTTGGTGATGAGAATGAAAGGACCAAA
GCAATGACTGAGATGAATGGTGTTAAATGTTCTAGTAGAGCTATGCGCATCGGTCCTGCTACCC
CGAGGAAGACTAATGGTTATCAACAACAAGGTAAGTTCTTTCCAATGCCACTATCTTTGTTTTA
TAATCTACTTGGATAGTTCTATGAAGTTTCATTAGAAATCTGCTCATTGTTAGGTTCTTGGTAT
TGCAACAATATGTTTTACTCTCTTGTGTACTTTAACTATTTGATGGATTTGGCAGGTGGATACA
TGCCGAATGGTACCTTGACGCGTCCTGAAGGGGACATAATGAACACAACAGTAATTGTTTTTCC
GTAGTATCTTCTTGTTTTCAACCTTTCATGTGAATGTGACAAGAGAAGGTTAATCTTCTTTTGT
TTTTGTTTTCCCCTTTAATCTGTTTTATAACATAGATATTTGTTGGAGGGCTTGACTCTAGTGT
CACTGATGAAGACTTAAAGCAACCTTTCAATGAATTCGGGGAAATAGTCTCTGTCAAGATTCCT
GTTGGTAAAGGATGCGGATTTGTTCAGTTTGTTAACAGGTAAGTATCTTATTTAACTATGAATT
AAGTATTTTCTTATCGTACTATAATCGATTTGATGCTTACACATTTGCTTGCAGACCAAATGCA
GAGGAGGCTTTGGAGAAACTAAATGGGACTGTAATTGGAAAACAAACAGTTCGGCTTTCTTGGG
GACGTAATCCCGCCAATAAGCAG
						
					

			
		

Sequences
Splice junction sequence	CAGACCAAATGCAGAGGAGGCTTTGGAGAAACTAAATGGGACTGTAATTGGAAAACAAACAGTT CGGCTTTCTTGGGGACGTAATCCCGCCAATAAGCAGagagagattgtttcggtgaaggtgattc gtaataagaacaatggtttatcagaaggatatggatttgtggagtttgagtcccatgatgtagc tgataagg
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: 765 Transcript exons: 17425407-17425884,17426038-17426096,17426210-17426340,17 426421-17426517 AGAGAGATTGTTTCGGTGAAGGTGATTCGTAATAAGAACAATGGTTTATCAGAAGGATATGGAT TTGTGGAGTTTGAGTCCCATGATGTAGCTGATAAGGTTTTGCGGGAGTTTAACGGGACGACTAT GCCAAATACTGACCAACCTTTTCGTTTGAACTGGGCTAGTTTTAGCACCGGTGAGAAGCGGTTA GAGAACAATGGACCTGATCTCTCTATTTTCGTGGGGGATTTGTCACCAGATGTTTCGGATAATT TGTTGCACGAGACCTTCTCTGAGAAGTATCCGTCGGTTAAAGCTGCGAAAGTTGTCCTTGATGC TAATACTGGTAGGTCAAAGGGGTATGGGTTTGTGAGGTTTGGTGATGAGAATGAAAGGACCAAA GCAATGACTGAGATGAATGGTGTTAAATGTTCTAGTAGAGCTATGCGCATCGGTCCTGCTACCC CGAGGAAGACTAATGGTTATCAACAACAAGGTGGATACATGCCGAATGGTACCTTGACGCGTCC TGAAGGGGACATAATGAACACAACAATATTTGTTGGAGGGCTTGACTCTAGTGTCACTGATGAA GACTTAAAGCAACCTTTCAATGAATTCGGGGAAATAGTCTCTGTCAAGATTCCTGTTGGTAAAG GATGCGGATTTGTTCAGTTTGTTAACAGACCAAATGCAGAGGAGGCTTTGGAGAAACTAAATGG GACTGTAATTGGAAAACAAACAGTTCGGCTTTCTTGGGGACGTAATCCCGCCAATAAGCAG
Genomic sequence	AGAGAGATTGTTTCGGTGAAGGTGATTCGTAATAAGAACAATGGTTTATCAGAAGGATATGGAT TTGTGGAGTTTGAGTCCCATGATGTAGCTGATAAGGTTTTGCGGGAGTTTAACGGGACGACTAT GCCAAATACTGACCAACCTTTTCGTTTGAACTGGGCTAGTTTTAGCACCGGTGAGAAGCGGTTA GAGAACAATGGACCTGATCTCTCTATTTTCGTGGGGGATTTGTCACCAGATGTTTCGGATAATT TGTTGCACGAGACCTTCTCTGAGAAGTATCCGTCGGTTAAAGCTGCGAAAGTTGTCCTTGATGC TAATACTGGTAGGTCAAAGGGGTATGGGTTTGTGAGGTTTGGTGATGAGAATGAAAGGACCAAA GCAATGACTGAGATGAATGGTGTTAAATGTTCTAGTAGAGCTATGCGCATCGGTCCTGCTACCC CGAGGAAGACTAATGGTTATCAACAACAAGGTAAGTTCTTTCCAATGCCACTATCTTTGTTTTA TAATCTACTTGGATAGTTCTATGAAGTTTCATTAGAAATCTGCTCATTGTTAGGTTCTTGGTAT TGCAACAATATGTTTTACTCTCTTGTGTACTTTAACTATTTGATGGATTTGGCAGGTGGATACA TGCCGAATGGTACCTTGACGCGTCCTGAAGGGGACATAATGAACACAACAGTAATTGTTTTTCC GTAGTATCTTCTTGTTTTCAACCTTTCATGTGAATGTGACAAGAGAAGGTTAATCTTCTTTTGT TTTTGTTTTCCCCTTTAATCTGTTTTATAACATAGATATTTGTTGGAGGGCTTGACTCTAGTGT CACTGATGAAGACTTAAAGCAACCTTTCAATGAATTCGGGGAAATAGTCTCTGTCAAGATTCCT GTTGGTAAAGGATGCGGATTTGTTCAGTTTGTTAACAGGTAAGTATCTTATTTAACTATGAATT AAGTATTTTCTTATCGTACTATAATCGATTTGATGCTTACACATTTGCTTGCAGACCAAATGCA GAGGAGGCTTTGGAGAAACTAAATGGGACTGTAATTGGAAAACAAACAGTTCGGCTTTCTTGGG GACGTAATCCCGCCAATAAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.339013143

Conservation Information
Conserved circRNAs	NA
PMCS	0.339013143

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17425533-17426514(+)
						
						Potential amino acid sequence
						
							MPNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLD
ANTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTR
PEGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLN
GTVIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTM
PNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDA
NTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRP
EGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNG
TVIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTMP
NTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDAN
TGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRPE
GDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGT
VIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTMPN
TDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDANT
GRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRPEG
DIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGTV
IGKQTVRLSWGRNPANKQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17425533-17426514(+)
Potential amino acid sequence	MPNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLD ANTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTR PEGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLN GTVIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTM PNTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDA NTGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRP EGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNG TVIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTMP NTDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDAN TGRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRPE GDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGT VIGKQTVRLSWGRNPANKQREIVSVKVIRNKNNGLSEGYGFVEFESHDVADKVLREFNGTTMPN TDQPFRLNWASFSTGEKRLENNGPDLSIFVGDLSPDVSDNLLHETFSEKYPSVKAAKVVLDANT GRSKGYGFVRFGDENERTKAMTEMNGVKCSSRAMRIGPATPRKTNGYQQQGGYMPNGTLTRPEG DIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGTV IGKQTVRLSWGRNPANKQ(+)
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 AT1G47490_circ_g.2

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