Plant Circular RNA Database

Detail information of AT1G07670_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G07670_circ_g.2
					
						ID in PlantcircBase
						ath_circ_001178
					
						Alias
						Chr1:2374242|2374456
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2374242-2374456  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT1G07670						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 4, endoplasmic reticulum-type
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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  
						
							AG-GT							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
						AT1G07670.2:1
AT1G07670.1:1

General Information
CircRNA Name	AT1G07670_circ_g.2
ID in PlantcircBase	ath_circ_001178
Alias	Chr1:2374242\|2374456
Organism	Arabidpsis thaliana
Position	chr1: 2374242-2374456 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT1G07670
Parent gene annotation	Calcium-transporting ATPase 4, endoplasmic reticulum-type
Parent gene strand	-
Alternative splicing	NA
Support reads	3
Tissues	seedling
Exon boundary	No-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	AG-GT 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	AT1G07670.2:1 AT1G07670.1:1

			
						 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  
						
							GTGTCAAAGCAACATATAATATACGAAGAATCCAAAAACACTCAAATTCCGAGAAAGCGAAGAA
CACGGACAACGAGATCGGCAAAAAAAAAAACTCACCcagcttcaagttacactatgagaaaaca
gagattgaaaacaaacgacgaatcttcgaataaaacaacgatcaaatttcaaaaatcgagtagc
cgcataaa

						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
						
							CAGCTTCAAGTTACACTATGAGAAAACAGAGATTGAAAACAAACGACGAATCTTCGAATAAAAC
AACGATCAAATTTCAAAAATCGAGTAGCCGCATAAATCAAATCAGAGATCAGTGTCAAAGCAAC
ATATAATATACGAAGAATCCAAAAACACTCAAATTCCGAGAAAGCGAAGAACACGGACAACGAG
ATCGGCAAAAAAAAAAACTCACC

Sequences
Splice junction sequence	GTGTCAAAGCAACATATAATATACGAAGAATCCAAAAACACTCAAATTCCGAGAAAGCGAAGAA CACGGACAACGAGATCGGCAAAAAAAAAAACTCACCcagcttcaagttacactatgagaaaaca gagattgaaaacaaacgacgaatcttcgaataaaacaacgatcaaatttcaaaaatcgagtagc cgcataaa
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	CAGCTTCAAGTTACACTATGAGAAAACAGAGATTGAAAACAAACGACGAATCTTCGAATAAAAC AACGATCAAATTTCAAAAATCGAGTAGCCGCATAAATCAAATCAGAGATCAGTGTCAAAGCAAC ATATAATATACGAAGAATCCAAAAACACTCAAATTCCGAGAAAGCGAAGAACACGGACAACGAG ATCGGCAAAAAAAAAAACTCACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.122868217

Conservation Information
Conserved circRNAs	NA
PMCS	0.122868217

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to methyl jasmonate

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT1G07670_circ_g.2

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