Plant Circular RNA Database

Detail information of AT2G39470_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G39470_circ_g.3
					
						ID in PlantcircBase
						ath_circ_017406
					
						Alias
						2:16477002-16477283
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16477002-16477283  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G39470						
					
						Parent gene annotation
						
							Photosynthetic NDH subunit of lumenal location 1, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G39470_circ_g.4 						
					
						Support reads
						1/1/1/1
					
						Tissues
						seedling;flower
					
						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
						AT2G39470.1:2
AT2G39470.2:2
AT2G39470.3:2

General Information
CircRNA Name	AT2G39470_circ_g.3
ID in PlantcircBase	ath_circ_017406
Alias	2:16477002-16477283
Organism	Arabidpsis thaliana
Position	chr2: 16477002-16477283 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G39470
Parent gene annotation	Photosynthetic NDH subunit of lumenal location 1, chloroplastic
Parent gene strand	+
Alternative splicing	AT2G39470_circ_g.4
Support reads	1/1/1/1
Tissues	seedling;flower
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	AT2G39470.1:2 AT2G39470.2:2 AT2G39470.3:2

			
						 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  
						
							GTTCATCATTCTTATATATGTTCATCAGGTGGTTTATGATCTAGTGAAGCATAAGTTTGCAGCA
CCAAACCAAGTAGCTACCATCTACGATATGAAAGAGgaatttgacttcagggcacatgattcag
ccttcaaagatagatacttgcaactgcagaatgtgcgggtcaggttcataccaacggagaaaaa
cgacatcc

						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: 195
Transcript exons: 16477002-16477124,16477212-16477283
GAATTTGACTTCAGGGCACATGATTCAGCCTTCAAAGATAGATACTTGCAACTGCAGAATGTGC
GGGTCAGGTTCATACCAACGGAGAAAAACGACATCCATGAAGTAGGTCCTATGGAAGAGGTGGT
TTATGATCTAGTGAAGCATAAGTTTGCAGCACCAAACCAAGTAGCTACCATCTACGATATGAAA
GAG
						
						Genomic sequence
						
							GAATTTGACTTCAGGGCACATGATTCAGCCTTCAAAGATAGATACTTGCAACTGCAGAATGTGC
GGGTCAGGTTCATACCAACGGAGAAAAACGACATCCATGAAGTAGGTCCTATGGAAGAGGTATG
TATTACACACCTTACTTTCCCTCTACCATCTATGTCATTAGAGAATTCACATTGGTTCATCATT
CTTATATATGTTCATCAGGTGGTTTATGATCTAGTGAAGCATAAGTTTGCAGCACCAAACCAAG
TAGCTACCATCTACGATATGAAAGAG

Sequences
Splice junction sequence	GTTCATCATTCTTATATATGTTCATCAGGTGGTTTATGATCTAGTGAAGCATAAGTTTGCAGCA CCAAACCAAGTAGCTACCATCTACGATATGAAAGAGgaatttgacttcagggcacatgattcag ccttcaaagatagatacttgcaactgcagaatgtgcgggtcaggttcataccaacggagaaaaa cgacatcc
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: 195 Transcript exons: 16477002-16477124,16477212-16477283 GAATTTGACTTCAGGGCACATGATTCAGCCTTCAAAGATAGATACTTGCAACTGCAGAATGTGC GGGTCAGGTTCATACCAACGGAGAAAAACGACATCCATGAAGTAGGTCCTATGGAAGAGGTGGT TTATGATCTAGTGAAGCATAAGTTTGCAGCACCAAACCAAGTAGCTACCATCTACGATATGAAA GAG
Genomic sequence	GAATTTGACTTCAGGGCACATGATTCAGCCTTCAAAGATAGATACTTGCAACTGCAGAATGTGC GGGTCAGGTTCATACCAACGGAGAAAAACGACATCCATGAAGTAGGTCCTATGGAAGAGGTATG TATTACACACCTTACTTTCCCTCTACCATCTATGTCATTAGAGAATTCACATTGGTTCATCATT CTTATATATGTTCATCAGGTGGTTTATGATCTAGTGAAGCATAAGTTTGCAGCACCAAACCAAG TAGCTACCATCTACGATATGAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.252994504

Conservation Information
Conserved circRNAs	NA
PMCS	0.252994504

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT2G39470_circ_g.3

Address

Any questions?

Supported by