Plant Circular RNA Database

Detail information of AT3G57300_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G57300_circ_g.2
					
						ID in PlantcircBase
						ath_circ_027942
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 21199876-21201673  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT3G57300						
					
						Parent gene annotation
						
							DNA helicase INO80-like protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G57300_circ_g.1 AT3G57300_circ_g.3 AT3G57300_circ_g.4 AT3G57300_circ_g.5 AT3G57300_circ_g.6 AT3G57300_circ_g.7 AT3G57300_circ_g.8 						
					
						Support reads
						1
					
						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  
						
							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
						AT3G57300.2:5
AT3G57300.1:5
AT3G57300.3:5
AT3G57300.4:5

General Information
CircRNA Name	AT3G57300_circ_g.2
ID in PlantcircBase	ath_circ_027942
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 21199876-21201673 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT3G57300
Parent gene annotation	DNA helicase INO80-like protein
Parent gene strand	+
Alternative splicing	AT3G57300_circ_g.1 AT3G57300_circ_g.3 AT3G57300_circ_g.4 AT3G57300_circ_g.5 AT3G57300_circ_g.6 AT3G57300_circ_g.7 AT3G57300_circ_g.8
Support reads	1
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	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	AT3G57300.2:5 AT3G57300.1:5 AT3G57300.3:5 AT3G57300.4:5

			
						 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  
						
							GGTGGGTAGATCATACAAAATCCCAAGAACTGCACCAATTCGCACTAGGAAGATATCCAGAGAC
ATGCTGCTATTCTGGAAGCGATATGACAAGCAGATGccgttgatgaagtttagaattccgaaac
ctgaagatgaagttgattattatgggagtagtagccaggatgaaagtagaagcactcaaggtac
agttttta

									
								

					

						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
						
							CCGTTGATGAAGTTTAGAATTCCGAAACCTGAAGATGAAGTTGATTATTATGGGAGTAGTAGCC
AGGATGAAAGTAGAAGCACTCAAGGTACAGTTTTTAATTGGTTTTATGGAATTACTTTTGCCAC
CTACTGTGATAGTTTTAAGTGACGTTTATCTGTGTTCTGTCTATATGGTTGGTAATGGTTAAAG
GTGGGGTAGTGGCAAACTACAGCAATGGGTCTAAATCGAGAATGAATGCGAGCTCCAAGAAGAG
AAAGCGGTGGACAGAAGCTGAGGATGCAGAGGACGATGATGATCTCTACAATCAACATGTTACT
GAGGAGCACTACCGATCAATGCTTGGGGAGCATGTACAAAAATTCAAAAATAGGTCCAAGGAGA
CTCAAGGGAATCCTCCTCATCTGATGGGTTTTCCGGTGCTAAAGAGCAATGTGGGCAGTTACAG
AGGTAGGAAACCAGGGAATGATTACCATGGGAGGTTCTATGACATGGACAACTCTCCAAATTTT
GCAGCTGATGTGACCCCACATAGGCGAGGAAGCTACCATGATCGTGATATTACACCCAAGTATG
TTGATCATATGTTTTTTCATGTTCCATGGGATCCGTGTAACCCTGTGTAATCCGCTTAGATAAC
TTACGGTGTTGGGTTTCCTAGATTGACACGTTGAATTTTGCATCATTTGCAGGATAGCATATGA
ACCTTCGTATTTGGACATTGGTGATGGTGTCATCTACAAAATCCCCCCAAGTTATGACAAGCTG
GTGGCATCATTAAACTTACCGAGCTTTTCAGACATTCATGTGGAAGAATTTTACTTGAAAGGAA
CTCTGGATCTGAGATCATTAGCAGAACTGATGGCAAGTGATAAAAGGTCTGGAGTAAGAAGCCG
TAATGGAATGGGTGAGCCTCGACCTCAATATGAATCTCTTCAAGCTAGAATGAAGGCCCTGTCA
CCTTCAAACTCCACCCCAAATTTTAGCCTCAAGGTGTCAGAAGCTGCAATGAATTCTGCCATTC
CAGAAGGATCTGCTGGAAGTACTGCACGGACAATTCTGTCTGAGGGTGGTGTTTTACAGGTCCA
TTACGTGAAGATTCTGGAGAAGGGGGATACATACGAGGTTTGGATTCTGTGGCAGTATTTTATG
AATCATAGTTTTGAATCCTTCATGGCTCATTCATGGCTCATTCATGGCTTTATTAACAACATTA
TCTTTTTGTTCCGACATTGTTTTATGTATCCTTTCTTCAGATTGTTAAACGAAGTCTACCGAAG
AAGCTGAAAGCAAAGAATGATCCTGCAGTCATTGAGAAAACAGAAAGGGATAAAATTAGAAAAG
CCTGGATCAATATTGTCAGAAGAGATATAGCAAAACACCATAGAATTTTCACTACTTTTCATCG
TAAACTATCAATTGATGCCAAGAGGTTTGCAGATGGTTGCCAAAGAGAGGTAATTGAAATTGAC
TCTCATATTAGTCTTTATTATATTTCCTTTCCTAGACGGATATTCTCTTTCCTTTCATTTTAGA
TTTTTTTTGGTCATCTGGTAGAAATTTTATAAAAGAAGAACCAAATTACATGTCGGCGATTAAC
AACATAATCCCGAAAACTAAGTTGTTAATCGCGGACTTAGATTTCATTTTTGATTAGATCTCTC
ATTTGATTACTTTGAGTTCACAGGTGAGAATGAAGGTGGGTAGATCATACAAAATCCCAAGAAC
TGCACCAATTCGCACTAGGAAGATATCCAGAGACATGCTGCTATTCTGGAAGCGATATGACAAG
CAGATG
						
					

			
		

Sequences
Splice junction sequence	GGTGGGTAGATCATACAAAATCCCAAGAACTGCACCAATTCGCACTAGGAAGATATCCAGAGAC ATGCTGCTATTCTGGAAGCGATATGACAAGCAGATGccgttgatgaagtttagaattccgaaac ctgaagatgaagttgattattatgggagtagtagccaggatgaaagtagaagcactcaaggtac agttttta
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	CCGTTGATGAAGTTTAGAATTCCGAAACCTGAAGATGAAGTTGATTATTATGGGAGTAGTAGCC AGGATGAAAGTAGAAGCACTCAAGGTACAGTTTTTAATTGGTTTTATGGAATTACTTTTGCCAC CTACTGTGATAGTTTTAAGTGACGTTTATCTGTGTTCTGTCTATATGGTTGGTAATGGTTAAAG GTGGGGTAGTGGCAAACTACAGCAATGGGTCTAAATCGAGAATGAATGCGAGCTCCAAGAAGAG AAAGCGGTGGACAGAAGCTGAGGATGCAGAGGACGATGATGATCTCTACAATCAACATGTTACT GAGGAGCACTACCGATCAATGCTTGGGGAGCATGTACAAAAATTCAAAAATAGGTCCAAGGAGA CTCAAGGGAATCCTCCTCATCTGATGGGTTTTCCGGTGCTAAAGAGCAATGTGGGCAGTTACAG AGGTAGGAAACCAGGGAATGATTACCATGGGAGGTTCTATGACATGGACAACTCTCCAAATTTT GCAGCTGATGTGACCCCACATAGGCGAGGAAGCTACCATGATCGTGATATTACACCCAAGTATG TTGATCATATGTTTTTTCATGTTCCATGGGATCCGTGTAACCCTGTGTAATCCGCTTAGATAAC TTACGGTGTTGGGTTTCCTAGATTGACACGTTGAATTTTGCATCATTTGCAGGATAGCATATGA ACCTTCGTATTTGGACATTGGTGATGGTGTCATCTACAAAATCCCCCCAAGTTATGACAAGCTG GTGGCATCATTAAACTTACCGAGCTTTTCAGACATTCATGTGGAAGAATTTTACTTGAAAGGAA CTCTGGATCTGAGATCATTAGCAGAACTGATGGCAAGTGATAAAAGGTCTGGAGTAAGAAGCCG TAATGGAATGGGTGAGCCTCGACCTCAATATGAATCTCTTCAAGCTAGAATGAAGGCCCTGTCA CCTTCAAACTCCACCCCAAATTTTAGCCTCAAGGTGTCAGAAGCTGCAATGAATTCTGCCATTC CAGAAGGATCTGCTGGAAGTACTGCACGGACAATTCTGTCTGAGGGTGGTGTTTTACAGGTCCA TTACGTGAAGATTCTGGAGAAGGGGGATACATACGAGGTTTGGATTCTGTGGCAGTATTTTATG AATCATAGTTTTGAATCCTTCATGGCTCATTCATGGCTCATTCATGGCTTTATTAACAACATTA TCTTTTTGTTCCGACATTGTTTTATGTATCCTTTCTTCAGATTGTTAAACGAAGTCTACCGAAG AAGCTGAAAGCAAAGAATGATCCTGCAGTCATTGAGAAAACAGAAAGGGATAAAATTAGAAAAG CCTGGATCAATATTGTCAGAAGAGATATAGCAAAACACCATAGAATTTTCACTACTTTTCATCG TAAACTATCAATTGATGCCAAGAGGTTTGCAGATGGTTGCCAAAGAGAGGTAATTGAAATTGAC TCTCATATTAGTCTTTATTATATTTCCTTTCCTAGACGGATATTCTCTTTCCTTTCATTTTAGA TTTTTTTTGGTCATCTGGTAGAAATTTTATAAAAGAAGAACCAAATTACATGTCGGCGATTAAC AACATAATCCCGAAAACTAAGTTGTTAATCGCGGACTTAGATTTCATTTTTGATTAGATCTCTC ATTTGATTACTTTGAGTTCACAGGTGAGAATGAAGGTGGGTAGATCATACAAAATCCCAAGAAC TGCACCAATTCGCACTAGGAAGATATCCAGAGACATGCTGCTATTCTGGAAGCGATATGACAAG CAGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.128886499

Conservation Information
Conserved circRNAs	NA
PMCS	0.128886499

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							21199882-21201670(+)
						
					

						Potential amino acid sequence
						
							MKFRIPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDL
YNQHVTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDM
DNSPNFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIH
VEEFYLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVS
EAAMNSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKT
ERDKIRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRT
RKISRDMLLFWKRYDKQMPLMKFRIPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNA
SSKKRKRWTEAEDAEDDDDLYNQHVTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSN
VGSYRGRKPGNDYHGRFYDMDNSPNFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKI
PPSYDKLVASLNLPSFSDIHVEEFYLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQ
ARMKALSPSNSTPNFSLKVSEAAMNSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIV
KRSLPKKLKAKNDPAVIEKTERDKIRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQR
EVRMKVGRSYKIPRTAPIRTRKISRDMLLFWKRYDKQMPLMKFRIPKPEDEVDYYGSSSQDESR
STQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDLYNQHVTEEHYRSMLGEHVQKFKNR
SKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDMDNSPNFAADVTPHRRGSYHDRDIT
PKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIHVEEFYLKGTLDLRSLAELMASDKR
SGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVSEAAMNSAIPEGSAGSTARTILSEG
GVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKTERDKIRKAWINIVRRDIAKHHRIF
TTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRTRKISRDMLLFWKRYDKQMPLMKFR
IPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDLYNQH
VTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDMDNSP
NFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIHVEEF
YLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVSEAAM
NSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKTERDK
IRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRTRKIS
RDMLLFWKRYDKQM(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	21199882-21201670(+)
Potential amino acid sequence	MKFRIPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDL YNQHVTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDM DNSPNFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIH VEEFYLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVS EAAMNSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKT ERDKIRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRT RKISRDMLLFWKRYDKQMPLMKFRIPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNA SSKKRKRWTEAEDAEDDDDLYNQHVTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSN VGSYRGRKPGNDYHGRFYDMDNSPNFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKI PPSYDKLVASLNLPSFSDIHVEEFYLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQ ARMKALSPSNSTPNFSLKVSEAAMNSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIV KRSLPKKLKAKNDPAVIEKTERDKIRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQR EVRMKVGRSYKIPRTAPIRTRKISRDMLLFWKRYDKQMPLMKFRIPKPEDEVDYYGSSSQDESR STQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDLYNQHVTEEHYRSMLGEHVQKFKNR SKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDMDNSPNFAADVTPHRRGSYHDRDIT PKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIHVEEFYLKGTLDLRSLAELMASDKR SGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVSEAAMNSAIPEGSAGSTARTILSEG GVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKTERDKIRKAWINIVRRDIAKHHRIF TTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRTRKISRDMLLFWKRYDKQMPLMKFR IPKPEDEVDYYGSSSQDESRSTQGGVVANYSNGSKSRMNASSKKRKRWTEAEDAEDDDDLYNQH VTEEHYRSMLGEHVQKFKNRSKETQGNPPHLMGFPVLKSNVGSYRGRKPGNDYHGRFYDMDNSP NFAADVTPHRRGSYHDRDITPKIAYEPSYLDIGDGVIYKIPPSYDKLVASLNLPSFSDIHVEEF YLKGTLDLRSLAELMASDKRSGVRSRNGMGEPRPQYESLQARMKALSPSNSTPNFSLKVSEAAM NSAIPEGSAGSTARTILSEGGVLQVHYVKILEKGDTYEIVKRSLPKKLKAKNDPAVIEKTERDK IRKAWINIVRRDIAKHHRIFTTFHRKLSIDAKRFADGCQREVRMKVGRSYKIPRTAPIRTRKIS RDMLLFWKRYDKQM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G57300_circ_g.2

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