Plant Circular RNA Database

Detail information of AT1G80830_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G80830_circ_g.3
					
						ID in PlantcircBase
						ath_circ_011368
					
						Alias
						AT1G80830_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 30373643-30373879  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT1G80830						
					
						Parent gene annotation
						
							Metal transporter Nramp1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G80830_circ_g.1 AT1G80830_circ_g.2 AT1G80830_circ_g.4 AT1G80830_circ_g.5 AT1G80830_circ_g.6 						
					
						Support reads
						24
					
						Tissues
						root, whole_plant, 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  
						
							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
						AT1G80830.2:1
AT1G80830.1:1

General Information
CircRNA Name	AT1G80830_circ_g.3
ID in PlantcircBase	ath_circ_011368
Alias	AT1G80830_C1
Organism	Arabidpsis thaliana
Position	chr1: 30373643-30373879 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT1G80830
Parent gene annotation	Metal transporter Nramp1
Parent gene strand	-
Alternative splicing	AT1G80830_circ_g.1 AT1G80830_circ_g.2 AT1G80830_circ_g.4 AT1G80830_circ_g.5 AT1G80830_circ_g.6
Support reads	24
Tissues	root, whole_plant, 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	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	AT1G80830.2:1 AT1G80830.1:1

			
						 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  
						
							TTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCGAT
TGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTTcgaggcaatgatgattaactttccagct
ccagctgaaccaccgatgagagcaacaattagactcgggattatagctaaacatcttgttagta
agtttctg

									
								

					

						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: 184
Transcript exons: 30373643-30373806,30373860-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC
GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA
AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGCTCCATTTTCCCACAACGTT
Transcript length: 189
Transcript exons: 30373643-30373742,30373791-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC
GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGCCAGCATAAGTTCCGGTTATCGTCGAGC
TCTGACCAGAAGCAAGAAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
Transcript length: 213
Transcript exons: 30373643-30373667,30373692-30373879
CGAGGCAATGATGATTAACTTTCCAGCAACAATTAGACTCGGGATTATAGCTAAACATCTTGTT
AGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCCCTGCATTACATATTGTCCAG
CATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCGATTGCAAATAGCTTTGA
GCTCCATTTTCCCACAACGTT
Transcript length: 230
Transcript exons: 30373643-30373675,30373683-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCCCGATGAGAGCAACAATTAGACTCGGGATTA
TAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCCCTG
CATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCG
ATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
Transcript length: 233
Transcript exons: 30373643-30373727,30373732-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC
GGGATTATAGCTAAACATCTTGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCC
CTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGC
GCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
Transcript length: 234
Transcript exons: 30373643-30373701,30373705-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTATCGGG
ATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGC
CCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAG
CGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
Transcript length: 237
Transcript exons: 30373643-30373879
CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC
GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA
AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAG
AAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
						
					

						Genomic sequence
						
							CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC
GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA
AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAG
AAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
						
					

			
		

Sequences
Splice junction sequence	TTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCGAT TGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTTcgaggcaatgatgattaactttccagct ccagctgaaccaccgatgagagcaacaattagactcgggattatagctaaacatcttgttagta agtttctg
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: 184 Transcript exons: 30373643-30373806,30373860-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGCTCCATTTTCCCACAACGTT Transcript length: 189 Transcript exons: 30373643-30373742,30373791-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGCCAGCATAAGTTCCGGTTATCGTCGAGC TCTGACCAGAAGCAAGAAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT Transcript length: 213 Transcript exons: 30373643-30373667,30373692-30373879 CGAGGCAATGATGATTAACTTTCCAGCAACAATTAGACTCGGGATTATAGCTAAACATCTTGTT AGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCCCTGCATTACATATTGTCCAG CATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCGATTGCAAATAGCTTTGA GCTCCATTTTCCCACAACGTT Transcript length: 230 Transcript exons: 30373643-30373675,30373683-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCCCGATGAGAGCAACAATTAGACTCGGGATTA TAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCCCTG CATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGCGCG ATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT Transcript length: 233 Transcript exons: 30373643-30373727,30373732-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC GGGATTATAGCTAAACATCTTGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGCC CTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAGC GCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT Transcript length: 234 Transcript exons: 30373643-30373701,30373705-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTATCGGG ATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAAAGC CCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAGAAG CGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT Transcript length: 237 Transcript exons: 30373643-30373879 CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAG AAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT
Genomic sequence	CGAGGCAATGATGATTAACTTTCCAGCTCCAGCTGAACCACCGATGAGAGCAACAATTAGACTC GGGATTATAGCTAAACATCTTGTTAGTAAGTTTCTGAGCCATGGCTCGAGTCTGAGATCAAGAA AGCCCTGCATTACATATTGTCCAGCATAAGTTCCGGTTATCGTCGAGCTCTGACCAGAAGCAAG AAGCGCGATTGCAAATAGCTTTGAGCTCCATTTTCCCACAACGTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.75388871

Conservation Information
Conserved circRNAs	NA
PMCS	0.75388871

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30373781-30373645(-)
						
						Potential amino acid sequence
						
							MQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGGSAGAGKLIIIASNVVGKWSSKLFAIALLAS
GQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGGSAGAGKLIIIASNVV
GKWSSKLFAIALLASGQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGG
SAGAGKLIIIASNVVGKWSSKLFAIALLASGQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTR
CLAIIPSLIVALIGGSAGAGKLIIIAS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	30373781-30373645(-)
Potential amino acid sequence	MQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGGSAGAGKLIIIASNVVGKWSSKLFAIALLAS GQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGGSAGAGKLIIIASNVV GKWSSKLFAIALLASGQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTRCLAIIPSLIVALIGG SAGAGKLIIIASNVVGKWSSKLFAIALLASGQSSTITGTYAGQYVMQGFLDLRLEPWLRNLLTR CLAIIPSLIVALIGGSAGAGKLIIIAS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

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

circRNA

Detail information of AT1G80830_circ_g.3

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