Plant Circular RNA Database

Detail information of AT5G20840_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT5G20840_circ_g.5
					
						ID in PlantcircBase
						ath_circ_039559
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7065723-7067620  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT5G20840						
					
						Parent gene annotation
						
							Phosphoinositide phosphatase SAC4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G20840_circ_g.6 AT5G20840_circ_g.7 AT5G20840_circ_g.8 AT5G20840_circ_g.9 AT5G20840_circ_g.10 AT5G20840_circ_g.11 AT5G20840_circ_g.12 AT5G20840_circ_g.13 						
					
						Support reads
						19
					
						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
						AT5G20840.1:6

General Information
CircRNA Name	AT5G20840_circ_g.5
ID in PlantcircBase	ath_circ_039559
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 7065723-7067620 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT5G20840
Parent gene annotation	Phosphoinositide phosphatase SAC4
Parent gene strand	-
Alternative splicing	AT5G20840_circ_g.6 AT5G20840_circ_g.7 AT5G20840_circ_g.8 AT5G20840_circ_g.9 AT5G20840_circ_g.10 AT5G20840_circ_g.11 AT5G20840_circ_g.12 AT5G20840_circ_g.13
Support reads	19
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	AT5G20840.1:6

			
						 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  
						
							ATGGTCGCATATATTCTTCTGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAGAAGTCT
TTCGTAAGGTCCACCATACACAGGAGTCTCTTGTACtcagacgaagacaagctcatataaccct
caagcttcattgctggtgtaagttgataataaaagaaacctgttagcatcaaagcacaggcagc
tacttttc

									
								

					

						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: 849
Transcript exons: 7065723-7065851,7065953-7066086,7066306-7066403,7066503-
7066690,7066938-7067014,7067398-7067620
TCAGACGAAGACAAGCTCATATAACCCTCAAGCTTCATTGCTGGTGTAAGTTGATAATAAAAGA
AACCTGTTAGCATCAAAGCACAGGCAGCTACTTTTCCAAGAAGTGCCAATACATTTTCTGTTTT
GCTGTGAAAATGTTTGTGCAAGTCCCAGTGGAGGAATCTAAGCCGATTTTCTTCCGGCAGATCT
TTGTTTATAAAGTCAATTGCATTAGCAAACTCTGCCCGGAGAATCGACTCCCTGGGTTTCCTCT
CGTTGGTCTTGATCAAGTTCAGAATAATGATGGGGACTCCATAACGCTCCACAAGATTTTCAAA
GTGAACTCTAGTTGCCTCATAGTTCAGGTCCCTTTTTGACAATACTATATCAGGCTTAACTTTC
ATCCGTGAGGTCTCCTGTGACCAGAATAGAGGGATTGAGCCACGATTCTGCACAACAGAACTTA
TTTGCATGGGACGGTCTACTGGAACATCCTCAGACACTATCTGTTCTGTTTCCACATCATTAGC
AACATTGCCACTTTCGTTTATTCCTCGTTTCAAGTACCTGGTTCCAGCATTATGGCGGGAACGC
CTAGCAATAAGAGTGAGTTTGAAATTCCGTCCAGCTTCGGAAAGTATTGTCTGCTTAAAAAACC
CATACACCAATGCTACAGTCCACAGGGTATTCCGAAGGTGATGTCGAGTTCCCCGAGTCAAGAA
TTCGTTCCACACAAACATTTTCTTATAGAGAGTACCTCCACTCTCATGGTCGCATATATTCTTC
TGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAGAAGTCTTTCGTAAGGTCCACCATAC
ACAGGAGTCTCTTGTAC
						
					

						Genomic sequence
						
							TCAGACGAAGACAAGCTCATATAACCCTCAAGCTTCATTGCTGGTGTAAGTTGATAATAAAAGA
AACCTGTTAGCATCAAAGCACAGGCAGCTACTTTTCCAAGAAGTGCCAATACATTTTCTGTTTT
GCTGAAATAAAGACAAAGAAGAGAGAAAACTGGTTATTATCTAAAAATGTATTGATAGATATTC
ATTATTTGAAGCAGCTGGAACGCAAATTAAAAGGATACCTGTGAAAATGTTTGTGCAAGTCCCA
GTGGAGGAATCTAAGCCGATTTTCTTCCGGCAGATCTTTGTTTATAAAGTCAATTGCATTAGCA
AACTCTGCCCGGAGAATCGACTCCCTGGGTTTCCTCTCGTTGGTCTATTGATTGTCAAAAGTAA
CAAGAAATATCAGTGAAAGCGTCGAGGTGTGAGAGCATCAAAAATATAGTACACACTCGTTTCA
TTGATAGTTTAACTAGAATAAGGTATTAAGGTGTAAGAAGATGCGTCACTTGCCAATACACAAG
GTACCCAGGGAAGTGAGGACTAGGCGTGAAAGATGATAAGAACGTGAAACAAGCTAGATTAGGC
AACTCACCTTGATCAAGTTCAGAATAATGATGGGGACTCCATAACGCTCCACAAGATTTTCAAA
GTGAACTCTAGTTGCCTCATAGTTCAGGTCCCTTTTTGACACTGGGATTGAGATTGAGGTGTTT
AAACACAAAGAAAAGAGAGAGAGAGGGAGGAAGAAAGATGACCAGGCAGTATTTTATTTAGTAT
AATAACACTTACATACTATATCAGGCTTAACTTTCATCCGTGAGGTCTCCTGTGACCAGAATAG
AGGGATTGAGCCACGATTCTGCACAACAGAACTTATTTGCATGGGACGGTCTACTGGAACATCC
TCAGACACTATCTGTTCTGTTTCCACATCATTAGCAACATTGCCACTTTCGTTTATTCCTCGTT
TCAAGTACCTAAAATCATAAGGAGTTTAAGAGAAAATAAGCATAATAACTACCCTTATGCCTCA
AGTGAAGATATATAATTTAAATCTCATAATGTTAAAAAGACCCTCGAGATGGAAAAACTTCTTA
TTTGATTAACAGTGTGGACTTTATTTGCAATGATTTCATGCTACTGCTAAAAAGTAGAATACAG
AGCGACTTATAATAGTCACGTTTACCACAGAAATGGAAACTAGGGAGTGATGAAATCTGATACC
TGGTTCCAGCATTATGGCGGGAACGCCTAGCAATAAGAGTGAGTTTGAAATTCCGTCCAGCTTC
GGAAAGTATTGTCTACATGCACAGCAAAACAAGGTTCAGCATCCATGAATCTAAACAGTACTGT
GCGATTATGAAGGTATATGAAAATAAAGATGCCAGAGTATTATAGCTGTATCTGAAGTAGCACG
ACCAAGTATATCAAAATTGATAGTCAACTATTAAAAATTTGCATATGAGACAAAAAGCTTCTTT
CCAGACCTTTTAGGCAAGACAGGACTGATGAAAAAAAAAAAAAAAAAAAAGGCAAGACAGGACT
TGATTTAGGGAAGCAAAATAGTGATCCTAAAGAAAATGGTACACAAATAAAAAGACTACAAAAG
AAAAACAATTGAAGTCGGGCAAACTTTCTTTCCTCTGGGTAGTAAGTGAGGTGCAGAAAAACAT
ACAATTCTCACCTGCTTAAAAAACCCATACACCAATGCTACAGTCCACAGGGTATTCCGAAGGT
GATGTCGAGTTCCCCGAGTCAAGAATTCGTTCCACACAAACATTTTCTTATAGAGAGTACCTCC
ACTCTCATGGTCGCATATATTCTTCTGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAG
AAGTCTTTCGTAAGGTCCACCATACACAGGAGTCTCTTGTAC
						
					

			
		

Sequences
Splice junction sequence	ATGGTCGCATATATTCTTCTGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAGAAGTCT TTCGTAAGGTCCACCATACACAGGAGTCTCTTGTACtcagacgaagacaagctcatataaccct caagcttcattgctggtgtaagttgataataaaagaaacctgttagcatcaaagcacaggcagc tacttttc
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: 849 Transcript exons: 7065723-7065851,7065953-7066086,7066306-7066403,7066503- 7066690,7066938-7067014,7067398-7067620 TCAGACGAAGACAAGCTCATATAACCCTCAAGCTTCATTGCTGGTGTAAGTTGATAATAAAAGA AACCTGTTAGCATCAAAGCACAGGCAGCTACTTTTCCAAGAAGTGCCAATACATTTTCTGTTTT GCTGTGAAAATGTTTGTGCAAGTCCCAGTGGAGGAATCTAAGCCGATTTTCTTCCGGCAGATCT TTGTTTATAAAGTCAATTGCATTAGCAAACTCTGCCCGGAGAATCGACTCCCTGGGTTTCCTCT CGTTGGTCTTGATCAAGTTCAGAATAATGATGGGGACTCCATAACGCTCCACAAGATTTTCAAA GTGAACTCTAGTTGCCTCATAGTTCAGGTCCCTTTTTGACAATACTATATCAGGCTTAACTTTC ATCCGTGAGGTCTCCTGTGACCAGAATAGAGGGATTGAGCCACGATTCTGCACAACAGAACTTA TTTGCATGGGACGGTCTACTGGAACATCCTCAGACACTATCTGTTCTGTTTCCACATCATTAGC AACATTGCCACTTTCGTTTATTCCTCGTTTCAAGTACCTGGTTCCAGCATTATGGCGGGAACGC CTAGCAATAAGAGTGAGTTTGAAATTCCGTCCAGCTTCGGAAAGTATTGTCTGCTTAAAAAACC CATACACCAATGCTACAGTCCACAGGGTATTCCGAAGGTGATGTCGAGTTCCCCGAGTCAAGAA TTCGTTCCACACAAACATTTTCTTATAGAGAGTACCTCCACTCTCATGGTCGCATATATTCTTC TGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAGAAGTCTTTCGTAAGGTCCACCATAC ACAGGAGTCTCTTGTAC
Genomic sequence	TCAGACGAAGACAAGCTCATATAACCCTCAAGCTTCATTGCTGGTGTAAGTTGATAATAAAAGA AACCTGTTAGCATCAAAGCACAGGCAGCTACTTTTCCAAGAAGTGCCAATACATTTTCTGTTTT GCTGAAATAAAGACAAAGAAGAGAGAAAACTGGTTATTATCTAAAAATGTATTGATAGATATTC ATTATTTGAAGCAGCTGGAACGCAAATTAAAAGGATACCTGTGAAAATGTTTGTGCAAGTCCCA GTGGAGGAATCTAAGCCGATTTTCTTCCGGCAGATCTTTGTTTATAAAGTCAATTGCATTAGCA AACTCTGCCCGGAGAATCGACTCCCTGGGTTTCCTCTCGTTGGTCTATTGATTGTCAAAAGTAA CAAGAAATATCAGTGAAAGCGTCGAGGTGTGAGAGCATCAAAAATATAGTACACACTCGTTTCA TTGATAGTTTAACTAGAATAAGGTATTAAGGTGTAAGAAGATGCGTCACTTGCCAATACACAAG GTACCCAGGGAAGTGAGGACTAGGCGTGAAAGATGATAAGAACGTGAAACAAGCTAGATTAGGC AACTCACCTTGATCAAGTTCAGAATAATGATGGGGACTCCATAACGCTCCACAAGATTTTCAAA GTGAACTCTAGTTGCCTCATAGTTCAGGTCCCTTTTTGACACTGGGATTGAGATTGAGGTGTTT AAACACAAAGAAAAGAGAGAGAGAGGGAGGAAGAAAGATGACCAGGCAGTATTTTATTTAGTAT AATAACACTTACATACTATATCAGGCTTAACTTTCATCCGTGAGGTCTCCTGTGACCAGAATAG AGGGATTGAGCCACGATTCTGCACAACAGAACTTATTTGCATGGGACGGTCTACTGGAACATCC TCAGACACTATCTGTTCTGTTTCCACATCATTAGCAACATTGCCACTTTCGTTTATTCCTCGTT TCAAGTACCTAAAATCATAAGGAGTTTAAGAGAAAATAAGCATAATAACTACCCTTATGCCTCA AGTGAAGATATATAATTTAAATCTCATAATGTTAAAAAGACCCTCGAGATGGAAAAACTTCTTA TTTGATTAACAGTGTGGACTTTATTTGCAATGATTTCATGCTACTGCTAAAAAGTAGAATACAG AGCGACTTATAATAGTCACGTTTACCACAGAAATGGAAACTAGGGAGTGATGAAATCTGATACC TGGTTCCAGCATTATGGCGGGAACGCCTAGCAATAAGAGTGAGTTTGAAATTCCGTCCAGCTTC GGAAAGTATTGTCTACATGCACAGCAAAACAAGGTTCAGCATCCATGAATCTAAACAGTACTGT GCGATTATGAAGGTATATGAAAATAAAGATGCCAGAGTATTATAGCTGTATCTGAAGTAGCACG ACCAAGTATATCAAAATTGATAGTCAACTATTAAAAATTTGCATATGAGACAAAAAGCTTCTTT CCAGACCTTTTAGGCAAGACAGGACTGATGAAAAAAAAAAAAAAAAAAAAGGCAAGACAGGACT TGATTTAGGGAAGCAAAATAGTGATCCTAAAGAAAATGGTACACAAATAAAAAGACTACAAAAG AAAAACAATTGAAGTCGGGCAAACTTTCTTTCCTCTGGGTAGTAAGTGAGGTGCAGAAAAACAT ACAATTCTCACCTGCTTAAAAAACCCATACACCAATGCTACAGTCCACAGGGTATTCCGAAGGT GATGTCGAGTTCCCCGAGTCAAGAATTCGTTCCACACAAACATTTTCTTATAGAGAGTACCTCC ACTCTCATGGTCGCATATATTCTTCTGGAAACTTCGCATTATATTGTAAGAATAGCTGAAAAAG AAGTCTTTCGTAAGGTCCACCATACACAGGAGTCTCTTGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.275508557

Conservation Information
Conserved circRNAs	NA
PMCS	0.275508557

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7067602-7065725(-)
						
						Potential amino acid sequence
						
							MVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRGTRHHLRNTLWTVALVYG
FFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVETEQIVSEDVPVDRPMQI
SSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLVERYGVPIIILNLIKTNE
RKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENVLALLGKVAACALMLTGF
FYYQLTPAMKLEGYMSLSSSEYKRLLCMVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKM
FVWNEFLTRGTRHHLRNTLWTVALVYGFFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGIN
ESGNVANDVETEQIVSEDVPVDRPMQISSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYE
ATRVHFENLVERYGVPIIILNLIKTNERKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLH
KHFHSKTENVLALLGKVAACALMLTGFFYYQLTPAMKLEGYMSLSSSEYKRLLCMVDLTKDFFF
SYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRGTRHHLRNTLWTVALVYGFFKQTILSEA
GRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVETEQIVSEDVPVDRPMQISSVVQNRGSI
PLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLVERYGVPIIILNLIKTNERKPRESILRA
EFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENVLALLGKVAACALMLTGFFYYQLTPAMK
LEGYMSLSSSEYKRLLCMVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRG
TRHHLRNTLWTVALVYGFFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVE
TEQIVSEDVPVDRPMQISSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLV
ERYGVPIIILNLIKTNERKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENV
LALLGKVAACALMLTGFFYYQLTPAMKLEGYMSLSSS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7067602-7065725(-)
Potential amino acid sequence	MVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRGTRHHLRNTLWTVALVYG FFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVETEQIVSEDVPVDRPMQI SSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLVERYGVPIIILNLIKTNE RKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENVLALLGKVAACALMLTGF FYYQLTPAMKLEGYMSLSSSEYKRLLCMVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKM FVWNEFLTRGTRHHLRNTLWTVALVYGFFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGIN ESGNVANDVETEQIVSEDVPVDRPMQISSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYE ATRVHFENLVERYGVPIIILNLIKTNERKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLH KHFHSKTENVLALLGKVAACALMLTGFFYYQLTPAMKLEGYMSLSSSEYKRLLCMVDLTKDFFF SYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRGTRHHLRNTLWTVALVYGFFKQTILSEA GRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVETEQIVSEDVPVDRPMQISSVVQNRGSI PLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLVERYGVPIIILNLIKTNERKPRESILRA EFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENVLALLGKVAACALMLTGFFYYQLTPAMK LEGYMSLSSSEYKRLLCMVDLTKDFFFSYSYNIMRSFQKNICDHESGGTLYKKMFVWNEFLTRG TRHHLRNTLWTVALVYGFFKQTILSEAGRNFKLTLIARRSRHNAGTRYLKRGINESGNVANDVE TEQIVSEDVPVDRPMQISSVVQNRGSIPLFWSQETSRMKVKPDIVLSKRDLNYEATRVHFENLV ERYGVPIIILNLIKTNERKPRESILRAEFANAIDFINKDLPEENRLRFLHWDLHKHFHSKTENV LALLGKVAACALMLTGFFYYQLTPAMKLEGYMSLSSS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G20840_circ_g.5

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