Plant Circular RNA Database

Detail information of AT3G14980_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G14980_circ_g.4
					
						ID in PlantcircBase
						ath_circ_021848
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5041800-5042317  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT3G14980						
					
						Parent gene annotation
						
							Increased DNA methylation 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G14980_circ_g.1 AT3G14980_circ_g.2 AT3G14980_circ_g.3 AT3G14980_circ_g.5 						
					
						Support reads
						3
					
						Tissues
						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  
						
							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
						AT3G14980.2:2
AT3G14980.5:2
AT3G14980.4:2
AT3G14980.3:2
AT3G14980.1:2
AT3G14980.6:2

General Information
CircRNA Name	AT3G14980_circ_g.4
ID in PlantcircBase	ath_circ_021848
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 5041800-5042317 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT3G14980
Parent gene annotation	Increased DNA methylation 1
Parent gene strand	-
Alternative splicing	AT3G14980_circ_g.1 AT3G14980_circ_g.2 AT3G14980_circ_g.3 AT3G14980_circ_g.5
Support reads	3
Tissues	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	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	AT3G14980.2:2 AT3G14980.5:2 AT3G14980.4:2 AT3G14980.3:2 AT3G14980.1:2 AT3G14980.6:2

			
						 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  
						
							AACATTTAAAGTCCTGAGAGCGTTCAGCATTATCACTAACCAACTCGCTGCATATCCAACATGT
GCAGCTCGAGCAATACCAACTTCCTTCAGGGAGCACcttctcgcaatttttaccacaaaagtag
gtctctggaaaaagctttctgcgtttacttatcccttgcaaacatgttccatgatctgataaca
taaaggta

						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: 201
Transcript exons: 5041800-5041882,5042200-5042317
CTTCTCGCAATTTTTACCACAAAAGTAGGTCTCTGGAAAAAGCTTTCTGCGTTTACTTATCCCT
TGCAAACATGTTCCATGATATTTATGCGCACACTGGGAACATTTAAAGTCCTGAGAGCGTTCAG
CATTATCACTAACCAACTCGCTGCATATCCAACATGTGCAGCTCGAGCAATACCAACTTCCTTC
AGGGAGCAC
						
						Genomic sequence
						
							CTTCTCGCAATTTTTACCACAAAAGTAGGTCTCTGGAAAAAGCTTTCTGCGTTTACTTATCCCT
TGCAAACATGTTCCATGATCTGATAACATAAAGGTAACAATCATCAGCCAAAGTGGATTTCATA
CCAAAATAACTAATGTGGGATCCAACTGTCGCGAGAGGCATAACTCCAAAAGTGAGTTTTACAA
AGTGTCAATTACTAAAGAAAGAAAATTGGAGAAGTGCTGAGCCTGGCAGAAAACCACCATCTAC
AACTGTTACTGATGAACAGTGACATCAATCGTGATAAAATCTCAGTGAGACATGATAGAAGAGA
ATTCAAATCAGGGGTTTCCTTTCATGTGATAAAGAAATAAATCATAGTTTCTAAGAGATTGCGA
GCTGTAAGATGATTACATTTATGCGCACACTGGGAACATTTAAAGTCCTGAGAGCGTTCAGCAT
TATCACTAACCAACTCGCTGCATATCCAACATGTGCAGCTCGAGCAATACCAACTTCCTTCAGG
GAGCAC

Sequences
Splice junction sequence	AACATTTAAAGTCCTGAGAGCGTTCAGCATTATCACTAACCAACTCGCTGCATATCCAACATGT GCAGCTCGAGCAATACCAACTTCCTTCAGGGAGCACcttctcgcaatttttaccacaaaagtag gtctctggaaaaagctttctgcgtttacttatcccttgcaaacatgttccatgatctgataaca taaaggta
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: 201 Transcript exons: 5041800-5041882,5042200-5042317 CTTCTCGCAATTTTTACCACAAAAGTAGGTCTCTGGAAAAAGCTTTCTGCGTTTACTTATCCCT TGCAAACATGTTCCATGATATTTATGCGCACACTGGGAACATTTAAAGTCCTGAGAGCGTTCAG CATTATCACTAACCAACTCGCTGCATATCCAACATGTGCAGCTCGAGCAATACCAACTTCCTTC AGGGAGCAC
Genomic sequence	CTTCTCGCAATTTTTACCACAAAAGTAGGTCTCTGGAAAAAGCTTTCTGCGTTTACTTATCCCT TGCAAACATGTTCCATGATCTGATAACATAAAGGTAACAATCATCAGCCAAAGTGGATTTCATA CCAAAATAACTAATGTGGGATCCAACTGTCGCGAGAGGCATAACTCCAAAAGTGAGTTTTACAA AGTGTCAATTACTAAAGAAAGAAAATTGGAGAAGTGCTGAGCCTGGCAGAAAACCACCATCTAC AACTGTTACTGATGAACAGTGACATCAATCGTGATAAAATCTCAGTGAGACATGATAGAAGAGA ATTCAAATCAGGGGTTTCCTTTCATGTGATAAAGAAATAAATCATAGTTTCTAAGAGATTGCGA GCTGTAAGATGATTACATTTATGCGCACACTGGGAACATTTAAAGTCCTGAGAGCGTTCAGCAT TATCACTAACCAACTCGCTGCATATCCAACATGTGCAGCTCGAGCAATACCAACTTCCTTCAGG GAGCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.240883355

Conservation Information
Conserved circRNAs	NA
PMCS	0.240883355

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5041878-5042314(+)
						
						Potential amino acid sequence
						
							MIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSAFTYPLQ
TCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSAFTY
PLQTCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSA
FTYPLQTCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREH(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5041878-5042314(+)
Potential amino acid sequence	MIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSAFTYPLQ TCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSAFTY PLQTCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREHLLAIFTTKVGLWKKLSA FTYPLQTCSMIFMRTLGTFKVLRAFSIITNQLAAYPTCAARAIPTSFREH(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Pan et al., 2017

circRNA

Detail information of AT3G14980_circ_g.4

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