Plant Circular RNA Database

Detail information of AT5G58140_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G58140_circ_g.4
					
						ID in PlantcircBase
						ath_circ_044683
					
						Alias
						At_ciR3356
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 23525403-23525758  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT5G58140						
					
						Parent gene annotation
						
							Phototropin-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 AT5G58060_circ_g.1 AT5G58060_circ_g.2 AT5G58060_circ_g.3 AT5G58060_circ_g.4 AT5G58060_circ_g.5 AT5G58060_circ_g.6 5_circ_ag.7 AT5G58070_circ_g.1 AT5G58070_circ_g.2 AT5G58100_circ_g.1 AT5G58100_circ_g.2 AT5G58100_circ_g.3 AT5G58100_circ_g.4 AT5G58100_circ_g.5 AT5G58100_circ_g.6 AT5G58100_circ_g.7 AT5G58100_circ_g.8 AT5G58100_circ_g.9 AT5G58100_circ_g.10 AT5G58110_circ_g.1 AT5G58130_circ_g.1 AT5G58130_circ_g.2 AT5G58140_circ_g.1 AT5G58140_circ_g.2 AT5G58140_circ_g.3 AT5G58140_circ_g.5 AT5G58140_circ_g.6 AT5G58140_circ_g.7 AT5G58140_circ_g.8 AT5G58140_circ_g.9 AT5G58140_circ_g.10 AT5G58140_circ_g.11 AT5G58140_circ_g.12 AT5G58140_circ_g.13 AT5G58140_circ_g.14 AT5G58140_circ_g.15 AT5G58140_circ_g.16 AT5G58140_circ_g.17 AT5G58140_circ_g.18 AT5G58140_circ_g.19 AT5G58140_circ_g.20 AT5G58140_circ_g.21 AT5G58140_circ_g.22 AT5G58140_circ_g.23 AT5G58160_circ_g.1 AT5G58160_circ_g.2 						
					
						Support reads
						2/36
					
						Tissues
						leaf/whole_plant
					
						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
						AT5G58140.5:2
AT5G58140.6:2
AT5G58140.7:2
AT5G58140.4:2
AT5G58140.3:2
AT5G58140.2:2
AT5G58140.1:2

General Information
CircRNA Name	AT5G58140_circ_g.4
ID in PlantcircBase	ath_circ_044683
Alias	At_ciR3356
Organism	Arabidpsis thaliana
Position	chr5: 23525403-23525758 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ, CIRI-full
Parent gene	AT5G58140
Parent gene annotation	Phototropin-2
Parent gene strand	+
Alternative splicing	5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 AT5G58060_circ_g.1 AT5G58060_circ_g.2 AT5G58060_circ_g.3 AT5G58060_circ_g.4 AT5G58060_circ_g.5 AT5G58060_circ_g.6 5_circ_ag.7 AT5G58070_circ_g.1 AT5G58070_circ_g.2 AT5G58100_circ_g.1 AT5G58100_circ_g.2 AT5G58100_circ_g.3 AT5G58100_circ_g.4 AT5G58100_circ_g.5 AT5G58100_circ_g.6 AT5G58100_circ_g.7 AT5G58100_circ_g.8 AT5G58100_circ_g.9 AT5G58100_circ_g.10 AT5G58110_circ_g.1 AT5G58130_circ_g.1 AT5G58130_circ_g.2 AT5G58140_circ_g.1 AT5G58140_circ_g.2 AT5G58140_circ_g.3 AT5G58140_circ_g.5 AT5G58140_circ_g.6 AT5G58140_circ_g.7 AT5G58140_circ_g.8 AT5G58140_circ_g.9 AT5G58140_circ_g.10 AT5G58140_circ_g.11 AT5G58140_circ_g.12 AT5G58140_circ_g.13 AT5G58140_circ_g.14 AT5G58140_circ_g.15 AT5G58140_circ_g.16 AT5G58140_circ_g.17 AT5G58140_circ_g.18 AT5G58140_circ_g.19 AT5G58140_circ_g.20 AT5G58140_circ_g.21 AT5G58140_circ_g.22 AT5G58140_circ_g.23 AT5G58160_circ_g.1 AT5G58160_circ_g.2
Support reads	2/36
Tissues	leaf/whole_plant
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	AT5G58140.5:2 AT5G58140.6:2 AT5G58140.7:2 AT5G58140.4:2 AT5G58140.3:2 AT5G58140.2:2 AT5G58140.1:2

			
						 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  
						
							ATCTGCAGGATGCAGGTTGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGC
CTAATGGACTCTCCAAATCCTTGATTCGATATGATGccggtttctgcaagggccagacaccgac
aagaatgaggttgccaaaatcagagattgtgtcaagaatggaaaaagttactgtggaaggctgt
taaactac

						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: 275
Transcript exons: 23525403-23525585,23525667-23525758
CCGGTTTCTGCAAGGGCCAGACACCGACAAGAATGAGGTTGCCAAAATCAGAGATTGTGTCAAG
AATGGAAAAAGTTACTGTGGAAGGCTGTTAAACTACAAAAAGGACGGAACTCCCTTCTGGAATC
TTCTCACAGTCACTCCTATCAAGGACGACCAGGGCAATACCATCAAGTTCATTGGGATGCAGGT
TGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGCCTAATGGACTCTCCAAA
TCCTTGATTCGATATGATG
						
						Genomic sequence
						
							CCGGTTTCTGCAAGGGCCAGACACCGACAAGAATGAGGTTGCCAAAATCAGAGATTGTGTCAAG
AATGGAAAAAGTTACTGTGGAAGGCTGTTAAACTACAAAAAGGACGGAACTCCCTTCTGGAATC
TTCTCACAGTCACTCCTATCAAGGACGACCAGGGCAATACCATCAAGTTCATTGGGTACGTCCC
TTAATTCCTCCCTGTTTTTCCCTAATTAATCGACTGTCCCTCGATCAATCATTTTCACATTTCC
ATCTGCAGGATGCAGGTTGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGC
CTAATGGACTCTCCAAATCCTTGATTCGATATGATG

Sequences
Splice junction sequence	ATCTGCAGGATGCAGGTTGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGC CTAATGGACTCTCCAAATCCTTGATTCGATATGATGccggtttctgcaagggccagacaccgac aagaatgaggttgccaaaatcagagattgtgtcaagaatggaaaaagttactgtggaaggctgt taaactac
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: 275 Transcript exons: 23525403-23525585,23525667-23525758 CCGGTTTCTGCAAGGGCCAGACACCGACAAGAATGAGGTTGCCAAAATCAGAGATTGTGTCAAG AATGGAAAAAGTTACTGTGGAAGGCTGTTAAACTACAAAAAGGACGGAACTCCCTTCTGGAATC TTCTCACAGTCACTCCTATCAAGGACGACCAGGGCAATACCATCAAGTTCATTGGGATGCAGGT TGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGCCTAATGGACTCTCCAAA TCCTTGATTCGATATGATG
Genomic sequence	CCGGTTTCTGCAAGGGCCAGACACCGACAAGAATGAGGTTGCCAAAATCAGAGATTGTGTCAAG AATGGAAAAAGTTACTGTGGAAGGCTGTTAAACTACAAAAAGGACGGAACTCCCTTCTGGAATC TTCTCACAGTCACTCCTATCAAGGACGACCAGGGCAATACCATCAAGTTCATTGGGTACGTCCC TTAATTCCTCCCTGTTTTTCCCTAATTAATCGACTGTCCCTCGATCAATCATTTTCACATTTCC ATCTGCAGGATGCAGGTTGAAGTTAGCAAATACACAGAAGGGGTAAATGATAAAGCATTGAGGC CTAATGGACTCTCCAAATCCTTGATTCGATATGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gma_circ_003993 						
					
						PMCS
						0.232012653

Conservation Information
Conserved circRNAs	gma_circ_003993
PMCS	0.232012653

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT5G58140_circ_g.4

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