Plant Circular RNA Database

Detail information of AT5G56010_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G56010_circ_g.3
					
						ID in PlantcircBase
						ath_circ_044298
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 22681533-22681806  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							i-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup
					
						Parent gene
						
							AT5G56010						
					
						Parent gene annotation
						
							Heat shock protein 90-3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							5_circ_ag.2 5_circ_ag.3 5_circ_ag.4 AT5G56010_circ_g.1 AT5G56010_circ_g.2 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 AT5G56010_circ_g.12 5_circ_ag.13 AT5G56010_circ_g.14 AT5G56010_circ_g.15 AT5G56010_circ_g.16 AT5G56010_circ_g.17 AT5G56010_circ_g.18 AT5G56010_circ_g.19 AT5G56010_circ_g.20 5_circ_ag.21 AT5G56030_circ_g.1 AT5G56030_circ_g.2 AT5G56030_circ_g.3 AT5G56030_circ_g.4 AT5G56030_circ_g.5 AT5G56030_circ_g.6 AT5G56030_circ_g.7 AT5G56030_circ_g.8 AT5G56030_circ_g.9 AT5G56030_circ_g.10 AT5G56030_circ_g.11 AT5G56030_circ_g.12 AT5G56030_circ_g.13 AT5G56030_circ_g.14 AT5G56030_circ_g.15 AT5G56030_circ_g.16 						
					
						Support reads
						1/3
					
						Tissues
						root/seedlings
					
						Exon boundary  
						
							No-No							"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  
						
							CG-AT							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
						0

General Information
CircRNA Name	AT5G56010_circ_g.3
ID in PlantcircBase	ath_circ_044298
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 22681533-22681806 JBrowse»
Reference genome	TAIR10.38
Type	i-circRNA
Identification method	CIRCexplorer, circseq_cup
Parent gene	AT5G56010
Parent gene annotation	Heat shock protein 90-3
Parent gene strand	+
Alternative splicing	5_circ_ag.2 5_circ_ag.3 5_circ_ag.4 AT5G56010_circ_g.1 AT5G56010_circ_g.2 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 AT5G56010_circ_g.12 5_circ_ag.13 AT5G56010_circ_g.14 AT5G56010_circ_g.15 AT5G56010_circ_g.16 AT5G56010_circ_g.17 AT5G56010_circ_g.18 AT5G56010_circ_g.19 AT5G56010_circ_g.20 5_circ_ag.21 AT5G56030_circ_g.1 AT5G56030_circ_g.2 AT5G56030_circ_g.3 AT5G56030_circ_g.4 AT5G56030_circ_g.5 AT5G56030_circ_g.6 AT5G56030_circ_g.7 AT5G56030_circ_g.8 AT5G56030_circ_g.9 AT5G56030_circ_g.10 AT5G56030_circ_g.11 AT5G56030_circ_g.12 AT5G56030_circ_g.13 AT5G56030_circ_g.14 AT5G56030_circ_g.15 AT5G56030_circ_g.16
Support reads	1/3
Tissues	root/seedlings
Exon boundary	No-No "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	CG-AT 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	0

			
						 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  
						
							TTTAGTGTTGATACCAACGATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAA
TTTGTATATACGTTCTGTGTATTGGTTGGTTACTTAgtacgatctctatctctctacaccttat
tttatacttgtctgtctcgtttgattgatctggctgttcgatctgtagatttaggattgattag
ggtttagt

						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: 274
Transcript exons: 22681533-22681806
GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG
TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG
GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC
GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT
GTATTGGTTGGTTACTTA
Transcript length: 274
Transcript exons: 22681533-22681806
GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG
TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG
GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC
GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT
GTATTGGTTGGTTACTTT
						
						Genomic sequence
						
							GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG
TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG
GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC
GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT
GTATTGGTTGGTTACTTA

Sequences
Splice junction sequence	TTTAGTGTTGATACCAACGATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAA TTTGTATATACGTTCTGTGTATTGGTTGGTTACTTAgtacgatctctatctctctacaccttat tttatacttgtctgtctcgtttgattgatctggctgttcgatctgtagatttaggattgattag ggtttagt
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: 274 Transcript exons: 22681533-22681806 GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT GTATTGGTTGGTTACTTA Transcript length: 274 Transcript exons: 22681533-22681806 GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT GTATTGGTTGGTTACTTT
Genomic sequence	GTACGATCTCTATCTCTCTACACCTTATTTTATACTTGTCTGTCTCGTTTGATTGATCTGGCTG TTCGATCTGTAGATTTAGGATTGATTAGGGTTTAGTGTTCTAGCCGATTTTAGAATTTTGGTTG GTAATTGAAGTTGCGAAGCTGTTTGTGTTCAAATCTGTTGATTAGTTTTAGTGTTGATACCAAC GATTAAGCAGACTCTTGTTAGATTTACAAAGTTTGCTTATATGTAATTTGTATATACGTTCTGT GTATTGGTTGGTTACTTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.19692792

Conservation Information
Conserved circRNAs	NA
PMCS	0.19692792

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

			
						 Other Information
					
						References
						Chu et al., 2017;Pan et al., 2017

circRNA

Detail information of AT5G56010_circ_g.3

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