Plant Circular RNA Database

Detail information of AT1G68890_circ_g.8

			
						 General Information
					
						CircRNA Name
						AT1G68890_circ_g.8
					
						ID in PlantcircBase
						ath_circ_009257
					
						Alias
						At_ciR5484
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 25903443-25905719  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT1G68890						
					
						Parent gene annotation
						
							Protein PHYLLO, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G68890_circ_g.6 AT1G68890_circ_g.7 AT1G68890_circ_g.9 AT1G68890_circ_g.10 AT1G68890_circ_g.11 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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
						AT1G68890.1:6
AT1G68890.2:6

General Information
CircRNA Name	AT1G68890_circ_g.8
ID in PlantcircBase	ath_circ_009257
Alias	At_ciR5484
Organism	Arabidpsis thaliana
Position	chr1: 25903443-25905719 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT1G68890
Parent gene annotation	Protein PHYLLO, chloroplastic
Parent gene strand	+
Alternative splicing	AT1G68890_circ_g.6 AT1G68890_circ_g.7 AT1G68890_circ_g.9 AT1G68890_circ_g.10 AT1G68890_circ_g.11
Support reads	2
Tissues	leaf
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	AT1G68890.1:6 AT1G68890.2:6

			
						 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  
						
							TAAGTTGATTGAGCAAATTACTCCTGGGAAAGTAACCATAGTTGGATATTCCATGGGAGCAAGG
ATAGCACTGTACATGGCTTTGAGGTTTAGCAACAAGgttgcacctctgaacagtaatgtagaga
acttaatggatgttgaggggcagcttcagttagttcttcacctcatgaatgaagctaaatttag
ttacatgc

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GTTGCACCTCTGAACAGTAATGTAGAGAACTTAATGGATGTTGAGGGGCAGCTTCAGTTAGTTC
TTCACCTCATGAATGAAGCTAAATTTAGTTACATGCTTCCTTTGTTAAATGGCTCGATTTCTTC
CTGGATTTGGAGTGAACTTGGAATTACTGTAAGCTTACCTAGCCTTAGTTCTGTCTGAAGAAAA
TTAGTTTATCCACACAGCTGATGTCAGATGTAAGCTTACCTAGGCTTATCAATTTCCTTCTTTT
GTCTCAGGCATCATCGATTTTCCCTAGTGTCAGATGTGGTCTGGAAATGGCTCTTCTAAACGCA
ATGGCAGTAAGACATGATTCTAGTTTGTTGGGGATACTTCATTATCAGAAAGAAGAAAATGGTT
CTGCTCAGCCACACTCTGTTCAAATATGTGCCCTTCTTGATTCTGAAGGTACTCCACTGGAGGT
CGCATACGTTGCTAGAAAACTTGTTCAAGAAGGGTTCAGTGCTATTAAACTTAAAGTAAGCCAA
CGTTCCTTAATCATACAAACAAGATGCTCGATCATCAAGTAAGATAGGCGGATAATTATTTTAT
TTTATGATTGAATGGTGGCTTTCTCAACGTTCAGTGCTATTAAACTTATGGTTGAGTTTTAGCA
TTTCATGCATAAATTGAAGTGGTTGGCTTTCTCACTTTGCGAATTTCAAGCTATTGATTGCTGA
CTGGTGGATAAACCTGCCTAAAATGACAGGTTGGTCGTCGAGTGAGCTCTGTTCAAGATGCTTT
AGTTATGCAAGAAGTAAGGAGAGCCGTTGGCGTTCAAATTGAACTCCGTGCAGATGCAAATTGT
CGTTGGACTTTTGAAGAGGCTAGAGAGTTTGGTTTATTGGTGAACAGCTGTAATTTAAAATATA
TTGAGGTCTGCTTCTGTATGAATTATTGCTATCTGATTGTGTTATGAAGTATTACTCCAAAATA
ACTGATTTCTCTTGCCTATATAACTTCAGTGACAAACGTTTTGTATATCTCAGGAACCTGTCCA
GAATAAAGATGACCTTATAAGGTTTCATGAAGAAACTGGATTACCAGTGGCACTTGATGAGACT
CTTGATGATTTTGAGGAATGTCCTCTGCGTATGCTTACCAAATATACGCACCCTGGAATAGTTG
CTGTTGTAAGCCCCTGGTCATTTTTTACAACATGTACATGAGCCTGACACTGTCAAAAGATATT
TTCTTTCTTGTGTGCTTATTTCTTCGTTGATCATTTCGTCTTGCTCCCTTTTTTAATTGATTTG
GAGATGGTTTATTAGTTTTTATTGTTACGATCAATCATATATCATTTTAAATATCGGCTCTATC
TTATGTCATTTTTGCTTTCAAACTAAATAGTCTTGACTTTGTTTTATCATACTTGGAGTTGTAG
GTTATTAAACCAAGTGTTGTGGGAGGGTTTGAGAATGCAGCACTGATTGCTCGGTGGGCACAGC
AGCATGGAAAGATGGCTGTTATAAGTGCTGCATATGAAAGTGGCCTAGGTTTATCAGCATATAT
TTTATTTGCATCATATTTGGAGATGGAGAACGTGAAAGCATCCACAGAGCAGAAGCAAGGAACG
CCCCCTTCTGTAGCCCATGGTCTTGGAACTTACCGGTGGCTTAGTGAAGACGTAATGATGAATA
CATTAGGGATATTTCGTAGCCCTTACAGTGGATTTGTTGAAGGATTTATTGCTGATGCTAGTAG
AAATCTAAAGGATGTTAAGATAAACAACGATGTTATTGTTAGAACCAGTAAAGGAATTCCTGTT
CGGAGGTATGAACTGAGGGTGGATGTAGATGGTTTCTCTCATTTCATAAGAGTCCATGACGTTG
GGGAGAATGCAGAAGTAAGCTTGTCCTTGTTTGTAATTTTGTATCTCCGAAGCTAAAAAGACAT
AAAAGCTGTTCTTGGTCAATTACTCTCTTGTTTTTCACTCTGCTGTAATGTATTTTTCAGGGAA
GTGTAGCTTTGTTTCTTCATGGATTTCTTGGAACTGGTGAAGAATGGATCCCCATCATGACGGG
TATCTCAGGATCTGCGAGATGCATTTCAGTCGATATTCCTGGTCACGGAAGGTCAAGGGTACAA
AGTCATGCTAGTGAGACCCAGACGTCCCCAACTTTCTCAATGGAGATGATAGCGGAGGCATTGT
ATAAGTTGATTGAGCAAATTACTCCTGGGAAAGTAACCATAGTTGGATATTCCATGGGAGCAAG
GATAGCACTGTACATGGCTTTGAGGTTTAGCAACAAG
						
					

			
		

Sequences
Splice junction sequence	TAAGTTGATTGAGCAAATTACTCCTGGGAAAGTAACCATAGTTGGATATTCCATGGGAGCAAGG ATAGCACTGTACATGGCTTTGAGGTTTAGCAACAAGgttgcacctctgaacagtaatgtagaga acttaatggatgttgaggggcagcttcagttagttcttcacctcatgaatgaagctaaatttag ttacatgc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GTTGCACCTCTGAACAGTAATGTAGAGAACTTAATGGATGTTGAGGGGCAGCTTCAGTTAGTTC TTCACCTCATGAATGAAGCTAAATTTAGTTACATGCTTCCTTTGTTAAATGGCTCGATTTCTTC CTGGATTTGGAGTGAACTTGGAATTACTGTAAGCTTACCTAGCCTTAGTTCTGTCTGAAGAAAA TTAGTTTATCCACACAGCTGATGTCAGATGTAAGCTTACCTAGGCTTATCAATTTCCTTCTTTT GTCTCAGGCATCATCGATTTTCCCTAGTGTCAGATGTGGTCTGGAAATGGCTCTTCTAAACGCA ATGGCAGTAAGACATGATTCTAGTTTGTTGGGGATACTTCATTATCAGAAAGAAGAAAATGGTT CTGCTCAGCCACACTCTGTTCAAATATGTGCCCTTCTTGATTCTGAAGGTACTCCACTGGAGGT CGCATACGTTGCTAGAAAACTTGTTCAAGAAGGGTTCAGTGCTATTAAACTTAAAGTAAGCCAA CGTTCCTTAATCATACAAACAAGATGCTCGATCATCAAGTAAGATAGGCGGATAATTATTTTAT TTTATGATTGAATGGTGGCTTTCTCAACGTTCAGTGCTATTAAACTTATGGTTGAGTTTTAGCA TTTCATGCATAAATTGAAGTGGTTGGCTTTCTCACTTTGCGAATTTCAAGCTATTGATTGCTGA CTGGTGGATAAACCTGCCTAAAATGACAGGTTGGTCGTCGAGTGAGCTCTGTTCAAGATGCTTT AGTTATGCAAGAAGTAAGGAGAGCCGTTGGCGTTCAAATTGAACTCCGTGCAGATGCAAATTGT CGTTGGACTTTTGAAGAGGCTAGAGAGTTTGGTTTATTGGTGAACAGCTGTAATTTAAAATATA TTGAGGTCTGCTTCTGTATGAATTATTGCTATCTGATTGTGTTATGAAGTATTACTCCAAAATA ACTGATTTCTCTTGCCTATATAACTTCAGTGACAAACGTTTTGTATATCTCAGGAACCTGTCCA GAATAAAGATGACCTTATAAGGTTTCATGAAGAAACTGGATTACCAGTGGCACTTGATGAGACT CTTGATGATTTTGAGGAATGTCCTCTGCGTATGCTTACCAAATATACGCACCCTGGAATAGTTG CTGTTGTAAGCCCCTGGTCATTTTTTACAACATGTACATGAGCCTGACACTGTCAAAAGATATT TTCTTTCTTGTGTGCTTATTTCTTCGTTGATCATTTCGTCTTGCTCCCTTTTTTAATTGATTTG GAGATGGTTTATTAGTTTTTATTGTTACGATCAATCATATATCATTTTAAATATCGGCTCTATC TTATGTCATTTTTGCTTTCAAACTAAATAGTCTTGACTTTGTTTTATCATACTTGGAGTTGTAG GTTATTAAACCAAGTGTTGTGGGAGGGTTTGAGAATGCAGCACTGATTGCTCGGTGGGCACAGC AGCATGGAAAGATGGCTGTTATAAGTGCTGCATATGAAAGTGGCCTAGGTTTATCAGCATATAT TTTATTTGCATCATATTTGGAGATGGAGAACGTGAAAGCATCCACAGAGCAGAAGCAAGGAACG CCCCCTTCTGTAGCCCATGGTCTTGGAACTTACCGGTGGCTTAGTGAAGACGTAATGATGAATA CATTAGGGATATTTCGTAGCCCTTACAGTGGATTTGTTGAAGGATTTATTGCTGATGCTAGTAG AAATCTAAAGGATGTTAAGATAAACAACGATGTTATTGTTAGAACCAGTAAAGGAATTCCTGTT CGGAGGTATGAACTGAGGGTGGATGTAGATGGTTTCTCTCATTTCATAAGAGTCCATGACGTTG GGGAGAATGCAGAAGTAAGCTTGTCCTTGTTTGTAATTTTGTATCTCCGAAGCTAAAAAGACAT AAAAGCTGTTCTTGGTCAATTACTCTCTTGTTTTTCACTCTGCTGTAATGTATTTTTCAGGGAA GTGTAGCTTTGTTTCTTCATGGATTTCTTGGAACTGGTGAAGAATGGATCCCCATCATGACGGG TATCTCAGGATCTGCGAGATGCATTTCAGTCGATATTCCTGGTCACGGAAGGTCAAGGGTACAA AGTCATGCTAGTGAGACCCAGACGTCCCCAACTTTCTCAATGGAGATGATAGCGGAGGCATTGT ATAAGTTGATTGAGCAAATTACTCCTGGGAAAGTAACCATAGTTGGATATTCCATGGGAGCAAG GATAGCACTGTACATGGCTTTGAGGTTTAGCAACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.162516608

Conservation Information
Conserved circRNAs	NA
PMCS	0.162516608

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							25903476-25905716(+)
						
					

						Potential amino acid sequence
						
							MDVEGQLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVR
HDSSLLGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSS
VQDALVMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEE
TGLPVALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISA
AYESGLGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYS
GFVEGFIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVAL
FLHGFLGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLI
EQITPGKVTIVGYSMGARIALYMALRFSNKVAPLNSNVENLMDVEGQLQLVLHLMNEAKFSYML
PLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVRHDSSLLGILHYQKEENGSAQPHS
VQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSSVQDALVMQEVRRAVGVQIELRAD
ANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEETGLPVALDETLDDFEECPLRMLT
KYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISAAYESGLGLSAYILFASYLEMENV
KASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYSGFVEGFIADASRNLKDVKINNDV
IVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVALFLHGFLGTGEEWIPIMTGISGSA
RCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLIEQITPGKVTIVGYSMGARIALYM
ALRFSNKVAPLNSNVENLMDVEGQLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIF
PSVRCGLEMALLNAMAVRHDSSLLGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKL
VQEGFSAIKLKVGRRVSSVQDALVMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLK
YIEEPVQNKDDLIRFHEETGLPVALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENA
ALIARWAQQHGKMAVISAAYESGLGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRW
LSEDVMMNTLGIFRSPYSGFVEGFIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFS
HFIRVHDVGENAEGSVALFLHGFLGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQ
TSPTFSMEMIAEALYKLIEQITPGKVTIVGYSMGARIALYMALRFSNKVAPLNSNVENLMDVEG
QLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVRHDSSL
LGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSSVQDAL
VMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEETGLPV
ALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISAAYESG
LGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYSGFVEG
FIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVALFLHGF
LGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLIEQITP
GKVTIVGYSMGARIALYMALRFSNK(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	25903476-25905716(+)
Potential amino acid sequence	MDVEGQLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVR HDSSLLGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSS VQDALVMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEE TGLPVALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISA AYESGLGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYS GFVEGFIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVAL FLHGFLGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLI EQITPGKVTIVGYSMGARIALYMALRFSNKVAPLNSNVENLMDVEGQLQLVLHLMNEAKFSYML PLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVRHDSSLLGILHYQKEENGSAQPHS VQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSSVQDALVMQEVRRAVGVQIELRAD ANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEETGLPVALDETLDDFEECPLRMLT KYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISAAYESGLGLSAYILFASYLEMENV KASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYSGFVEGFIADASRNLKDVKINNDV IVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVALFLHGFLGTGEEWIPIMTGISGSA RCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLIEQITPGKVTIVGYSMGARIALYM ALRFSNKVAPLNSNVENLMDVEGQLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIF PSVRCGLEMALLNAMAVRHDSSLLGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKL VQEGFSAIKLKVGRRVSSVQDALVMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLK YIEEPVQNKDDLIRFHEETGLPVALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENA ALIARWAQQHGKMAVISAAYESGLGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRW LSEDVMMNTLGIFRSPYSGFVEGFIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFS HFIRVHDVGENAEGSVALFLHGFLGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQ TSPTFSMEMIAEALYKLIEQITPGKVTIVGYSMGARIALYMALRFSNKVAPLNSNVENLMDVEG QLQLVLHLMNEAKFSYMLPLLNGSISSWIWSELGITASSIFPSVRCGLEMALLNAMAVRHDSSL LGILHYQKEENGSAQPHSVQICALLDSEGTPLEVAYVARKLVQEGFSAIKLKVGRRVSSVQDAL VMQEVRRAVGVQIELRADANCRWTFEEAREFGLLVNSCNLKYIEEPVQNKDDLIRFHEETGLPV ALDETLDDFEECPLRMLTKYTHPGIVAVVIKPSVVGGFENAALIARWAQQHGKMAVISAAYESG LGLSAYILFASYLEMENVKASTEQKQGTPPSVAHGLGTYRWLSEDVMMNTLGIFRSPYSGFVEG FIADASRNLKDVKINNDVIVRTSKGIPVRRYELRVDVDGFSHFIRVHDVGENAEGSVALFLHGF LGTGEEWIPIMTGISGSARCISVDIPGHGRSRVQSHASETQTSPTFSMEMIAEALYKLIEQITP GKVTIVGYSMGARIALYMALRFSNK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT1G68890_circ_g.8

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