Plant Circular RNA Database

Detail information of AT3G24870_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G24870_circ_g.4
					
						ID in PlantcircBase
						ath_circ_023678
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 9079019-9079099  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G24870						
					
						Parent gene annotation
						
							Chromatin modification-related protein EAF1 B
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 AT3G24870_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G24870_circ_g.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 3_circ_ag.12 3_circ_ag.13 3_circ_ag.14 3_circ_ag.15 AT3G24870_circ_g.16 3_circ_ag.17 3_circ_ag.18 3_circ_ag.19 3_circ_ag.20 3_circ_ag.21 3_circ_ag.22 3_circ_ag.23 AT3G24880_circ_g.1 AT3G24880_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						aerial
					
						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
						AT3G24870.4:1
AT3G24870.2:1
AT3G24870.3:1
AT3G24870.1:1

General Information
CircRNA Name	AT3G24870_circ_g.4
ID in PlantcircBase	ath_circ_023678
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 9079019-9079099 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G24870
Parent gene annotation	Chromatin modification-related protein EAF1 B
Parent gene strand	-
Alternative splicing	3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 AT3G24870_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 AT3G24870_circ_g.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 3_circ_ag.12 3_circ_ag.13 3_circ_ag.14 3_circ_ag.15 AT3G24870_circ_g.16 3_circ_ag.17 3_circ_ag.18 3_circ_ag.19 3_circ_ag.20 3_circ_ag.21 3_circ_ag.22 3_circ_ag.23 AT3G24880_circ_g.1 AT3G24880_circ_g.2
Support reads	1
Tissues	aerial
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	AT3G24870.4:1 AT3G24870.2:1 AT3G24870.3:1 AT3G24870.1:1

			
						 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  
						
							CCCAGTTAGGCCCCATATCATGCACCAGGACAACAAGCGCcttaattttaagagtgctgttcat
tgcatcactaatgagct

						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
						
							CTTAATTTTAAGAGTGCTGTTCATTGCATCACTAATGAGCTCCCAGTTAGGCCCCATATCATGC
ACCAGGACAACAAGCGC

Sequences
Splice junction sequence	CCCAGTTAGGCCCCATATCATGCACCAGGACAACAAGCGCcttaattttaagagtgctgttcat tgcatcactaatgagct
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	CTTAATTTTAAGAGTGCTGTTCATTGCATCACTAATGAGCTCCCAGTTAGGCCCCATATCATGC ACCAGGACAACAAGCGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.232509259

Conservation Information
Conserved circRNAs	NA
PMCS	0.232509259

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9079076-9079021(-)
9079079-9079096(+)
9079053-9079096(+)
						
						Potential amino acid sequence
						
							MGPNWELISDAMNSTLKIKALVVLVHDMGPNWELISDAMNSTLKIKALVVLVHDMGPNWELISD
AMNSTLKIKALVVLVHDMGPNWELISDAMNSTLKIK(-)
MHQDNKRLNFKSAVHCITNELPVRPHIMHQDNKRLNFKSAVHCITNELPVRPHIMHQDNKRLNF
KSAVHCITNELPVRPHIMHQDNKR(+)
MSSQLGPISCTRTTSALILRVLFIASLMSSQLGPISCTRTTSALILRVLFIASLMSSQLGPISC
TRTTSALILRVLFIASLMSSQLGPISCTRTTS(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9079076-9079021(-) 9079079-9079096(+) 9079053-9079096(+)
Potential amino acid sequence	MGPNWELISDAMNSTLKIKALVVLVHDMGPNWELISDAMNSTLKIKALVVLVHDMGPNWELISD AMNSTLKIKALVVLVHDMGPNWELISDAMNSTLKIK(-) MHQDNKRLNFKSAVHCITNELPVRPHIMHQDNKRLNFKSAVHCITNELPVRPHIMHQDNKRLNF KSAVHCITNELPVRPHIMHQDNKR(+) MSSQLGPISCTRTTSALILRVLFIASLMSSQLGPISCTRTTSALILRVLFIASLMSSQLGPISC TRTTSALILRVLFIASLMSSQLGPISCTRTTS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G24870_circ_g.4

Address

Any questions?

Supported by