Plant Circular RNA Database

Detail information of AT1G80640_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G80640_circ_g.3
					
						ID in PlantcircBase
						ath_circ_011330
					
						Alias
						At_ciR338, AT1G80640_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 30312632-30313101  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI2
					
						Parent gene
						
							AT1G80640						
					
						Parent gene annotation
						
							Probable receptor-like protein kinase At1g80640
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G80640_circ_g.1 AT1G80640_circ_g.2 AT1G80640_circ_g.4 AT1G80640_circ_g.5 AT1G80640_circ_g.6 AT1G80640_circ_g.7 AT1G80640_circ_g.8 AT1G80640_circ_g.9 AT1G80640_circ_g.10 						
					
						Support reads
						14/26/5
					
						Tissues
						leaf/root, leaf, whole_plant/seedlings
					
						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
						AT1G80640.2:2
AT1G80640.1:2

General Information
CircRNA Name	AT1G80640_circ_g.3
ID in PlantcircBase	ath_circ_011330
Alias	At_ciR338, AT1G80640_C2
Organism	Arabidpsis thaliana
Position	chr1: 30312632-30313101 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, circseq_cup, CIRI2
Parent gene	AT1G80640
Parent gene annotation	Probable receptor-like protein kinase At1g80640
Parent gene strand	+
Alternative splicing	AT1G80640_circ_g.1 AT1G80640_circ_g.2 AT1G80640_circ_g.4 AT1G80640_circ_g.5 AT1G80640_circ_g.6 AT1G80640_circ_g.7 AT1G80640_circ_g.8 AT1G80640_circ_g.9 AT1G80640_circ_g.10
Support reads	14/26/5
Tissues	leaf/root, leaf, whole_plant/seedlings
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	AT1G80640.2:2 AT1G80640.1:2

			
						 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  
						
							CAGAACATAGTTTCCTTATTGGGGTTTTGCGTATATCGGCAAACGAGTTGTATTGTGTATGAGT
TGATGCAGAATGGATCTTTGGAGAGTCAGTTACATGattcggtgaagagtgtaaccacgaaacc
gactgtacacaagattgattctgtgaggaaaggaaccatccctgtgtatgaatatcaattgctg
gaatctgc

						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: 375
Transcript exons: 30312632-30312873,30312969-30313101
ATTCGGTGAAGAGTGTAACCACGAAACCGACTGTACACAAGATTGATTCTGTGAGGAAAGGAAC
CATCCCTGTGTATGAATATCAATTGCTGGAATCTGCAACAAACAAGTTTAGTGATAGTAATGTG
TTGAGCCGAGGTGGTCGTGGATGCCTTTACAGAGCTTGTCTCGATGAAAAATCCTCAGTCACTG
TGAAGAAACTTGATGGCGGTGGGGAGACAGACATTGAAAAACAGTTTGAGACTGAAGTAGATTG
GTTGGCTAAGATCAGGCATCAGAACATAGTTTCCTTATTGGGGTTTTGCGTATATCGGCAAACG
AGTTGTATTGTGTATGAGTTGATGCAGAATGGATCTTTGGAGAGTCAGTTACATG
						
						Genomic sequence
						
							ATTCGGTGAAGAGTGTAACCACGAAACCGACTGTACACAAGATTGATTCTGTGAGGAAAGGAAC
CATCCCTGTGTATGAATATCAATTGCTGGAATCTGCAACAAACAAGTTTAGTGATAGTAATGTG
TTGAGCCGAGGTGGTCGTGGATGCCTTTACAGAGCTTGTCTCGATGAAAAATCCTCAGTCACTG
TGAAGAAACTTGATGGCGGTGGGGAGACAGACATTGAAAAACAGTTTGAGGTTTGACCCCTAAG
ATGATTATACAGAATCGCACCATCTCATTCGATAAACCATAACTCGGTTTTTTGCTTTCTCTTG
TTGATTTTCTAATGCAGACTGAAGTAGATTGGTTGGCTAAGATCAGGCATCAGAACATAGTTTC
CTTATTGGGGTTTTGCGTATATCGGCAAACGAGTTGTATTGTGTATGAGTTGATGCAGAATGGA
TCTTTGGAGAGTCAGTTACATG

Sequences
Splice junction sequence	CAGAACATAGTTTCCTTATTGGGGTTTTGCGTATATCGGCAAACGAGTTGTATTGTGTATGAGT TGATGCAGAATGGATCTTTGGAGAGTCAGTTACATGattcggtgaagagtgtaaccacgaaacc gactgtacacaagattgattctgtgaggaaaggaaccatccctgtgtatgaatatcaattgctg gaatctgc
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: 375 Transcript exons: 30312632-30312873,30312969-30313101 ATTCGGTGAAGAGTGTAACCACGAAACCGACTGTACACAAGATTGATTCTGTGAGGAAAGGAAC CATCCCTGTGTATGAATATCAATTGCTGGAATCTGCAACAAACAAGTTTAGTGATAGTAATGTG TTGAGCCGAGGTGGTCGTGGATGCCTTTACAGAGCTTGTCTCGATGAAAAATCCTCAGTCACTG TGAAGAAACTTGATGGCGGTGGGGAGACAGACATTGAAAAACAGTTTGAGACTGAAGTAGATTG GTTGGCTAAGATCAGGCATCAGAACATAGTTTCCTTATTGGGGTTTTGCGTATATCGGCAAACG AGTTGTATTGTGTATGAGTTGATGCAGAATGGATCTTTGGAGAGTCAGTTACATG
Genomic sequence	ATTCGGTGAAGAGTGTAACCACGAAACCGACTGTACACAAGATTGATTCTGTGAGGAAAGGAAC CATCCCTGTGTATGAATATCAATTGCTGGAATCTGCAACAAACAAGTTTAGTGATAGTAATGTG TTGAGCCGAGGTGGTCGTGGATGCCTTTACAGAGCTTGTCTCGATGAAAAATCCTCAGTCACTG TGAAGAAACTTGATGGCGGTGGGGAGACAGACATTGAAAAACAGTTTGAGGTTTGACCCCTAAG ATGATTATACAGAATCGCACCATCTCATTCGATAAACCATAACTCGGTTTTTTGCTTTCTCTTG TTGATTTTCTAATGCAGACTGAAGTAGATTGGTTGGCTAAGATCAGGCATCAGAACATAGTTTC CTTATTGGGGTTTTGCGTATATCGGCAAACGAGTTGTATTGTGTATGAGTTGATGCAGAATGGA TCTTTGGAGAGTCAGTTACATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.616685373

Conservation Information
Conserved circRNAs	NA
PMCS	0.616685373

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30313068-30313098(+)
						
						Potential amino acid sequence
						
							MQNGSLESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLY
RACLDEKSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQN
GSLESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLYRAC
LDEKSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQNGSL
ESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLYRACLDE
KSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQNGSLESQ
LH(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	30313068-30313098(+)
Potential amino acid sequence	MQNGSLESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLY RACLDEKSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQN GSLESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLYRAC LDEKSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQNGSL ESQLHDSVKSVTTKPTVHKIDSVRKGTIPVYEYQLLESATNKFSDSNVLSRGGRGCLYRACLDE KSSVTVKKLDGGGETDIEKQFETEVDWLAKIRHQNIVSLLGFCVYRQTSCIVYELMQNGSLESQ LH(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT1G80640_circ_g.3

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