Plant Circular RNA Database

Detail information of AT3G04340_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G04340_circ_g.3
					
						ID in PlantcircBase
						ath_circ_019637
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 1147138-1147951  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G04340						
					
						Parent gene annotation
						
							Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, ch
loroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.3 AT3G03330_circ_g.1 AT3G03330_circ_g.2 AT3G03340_circ_g.1 AT3G03340_circ_g.2 AT3G03340_circ_g.3 AT3G03340_circ_g.4 AT3G03340_circ_g.5 AT3G03340_circ_g.6 AT3G03350_circ_g.1 AT3G03350_circ_g.2 3_circ_ag.3 AT3G03350_circ_g.4 3_circ_ag.5 AT3G03380_circ_g.1 AT3G03380_circ_g.2 AT3G03380_circ_g.3 AT3G03380_circ_g.4 AT3G03380_circ_g.5 AT3G03380_circ_g.6 AT3G03380_circ_g.7 AT3G03380_circ_g.8 AT3G03380_circ_g.9 AT3G03380_circ_g.10 AT3G03380_circ_g.11 AT3G03380_circ_g.12 AT3G03380_circ_g.13 AT3G03380_circ_g.14 AT3G03380_circ_g.15 AT3G03380_circ_g.16 AT3G03380_circ_g.17 AT3G03380_circ_g.18 AT3G03420_circ_g.1 AT3G03420_circ_g.2 AT3G03420_circ_g.3 AT3G03470_circ_g.1 AT3G03520_circ_g.1 AT3G03520_circ_g.2 AT3G03520_circ_g.3 AT3G03550_circ_g.1 AT3G03560_circ_g.1 AT3G03560_circ_g.2 AT3G03560_circ_g.3 AT3G03560_circ_g.4 AT3G03560_circ_g.5 AT3G03560_circ_g.6 AT3G03560_circ_g.7 AT3G03560_circ_g.8 AT3G03560_circ_g.9 AT3G03560_circ_g.10 AT3G03560_circ_g.11 AT3G03560_circ_g.12 AT3G03560_circ_g.13 AT3G03570_circ_g.1 AT3G03610_circ_g.1 AT3G03610_circ_g.2 AT3G03610_circ_g.3 AT3G03630_circ_g.1 AT3G03640_circ_g.1 AT3G03640_circ_g.2 AT3G03680_circ_g.1 AT3G03680_circ_g.2 AT3G03690_circ_g.1 AT3G03690_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 AT3G03710_circ_g.1 AT3G03710_circ_g.2 AT3G03710_circ_g.3 3_circ_ag.4 AT3G03710_circ_g.5 AT3G03710_circ_g.6 AT3G03710_circ_g.7 AT3G03710_circ_g.8 AT3G03720_circ_g.1 AT3G03720_circ_g.2 AT3G03720_circ_g.3 AT3G03720_circ_g.4 AT3G03720_circ_g.5 AT3G03720_circ_g.6 AT3G03770_circ_g.1 AT3G03770_circ_g.2 AT3G03770_circ_g.3 AT3G03770_circ_g.4 AT3G03773_circ_g.1 AT3G03773_circ_g.2 AT3G03773_circ_g.3 AT3G03780_circ_g.1 AT3G03780_circ_g.2 AT3G03780_circ_g.3 AT3G03780_circ_g.4 AT3G03780_circ_g.5 AT3G03780_circ_g.6 AT3G03780_circ_g.7 AT3G03780_circ_g.8 AT3G03790_circ_g.1 AT3G03790_circ_g.2 AT3G03790_circ_g.3 AT3G03790_circ_g.4 AT3G03790_circ_g.5 AT3G03790_circ_g.6 AT3G03790_circ_g.7 AT3G03810_circ_g.1 AT3G03810_circ_g.2 AT3G03810_circ_g.3 AT3G03860_circ_g.1 AT3G03900_circ_g.1 AT3G03900_circ_g.2 AT3G03920_circ_g.1 AT3G03920_circ_g.2 AT3G03920_circ_g.3 AT3G03920_circ_g.4 AT3G03920_circ_g.5 AT3G03940_circ_g.1 AT3G03940_circ_g.2 AT3G03940_circ_g.3 AT3G03940_circ_g.4 AT3G03940_circ_g.5 AT3G03940_circ_g.6 AT3G03940_circ_g.7 AT3G03940_circ_g.8 AT3G03940_circ_g.9 AT3G03940_circ_g.10 AT3G03940_circ_g.11 AT3G03950_circ_g.1 AT3G03950_circ_g.2 AT3G03950_circ_g.3 AT3G03960_circ_g.1 AT3G03960_circ_g.2 AT3G03960_circ_g.3 AT3G03960_circ_g.4 AT3G03960_circ_g.5 AT3G03960_circ_g.6 AT3G03960_circ_g.7 AT3G03960_circ_g.8 AT3G03960_circ_g.9 AT3G04020_circ_g.1 AT3G04020_circ_g.2 AT3G04020_circ_g.3 AT3G04080_circ_g.1 AT3G04080_circ_g.2 AT3G04080_circ_g.3 AT3G04080_circ_g.4 AT3G04080_circ_g.5 AT3G04090_circ_g.1 AT3G04120_circ_g.1 AT3G04120_circ_g.2 AT3G04120_circ_g.3 AT3G04120_circ_g.4 AT3G04120_circ_g.5 AT3G04120_circ_g.6 AT3G04120_circ_g.7 AT3G04120_circ_g.8 AT3G04120_circ_g.9 AT3G04120_circ_g.10 AT3G04120_circ_g.11 AT3G04120_circ_g.12 AT3G04120_circ_g.13 AT3G04120_circ_g.14 AT3G04120_circ_g.15 AT3G04120_circ_g.16 AT3G04160_circ_g.1 AT3G04220_circ_g.1 AT3G04240_circ_g.1 AT3G04240_circ_g.2 AT3G04240_circ_g.3 AT3G04240_circ_g.4 AT3G04240_circ_g.5 AT3G04240_circ_g.6 AT3G04240_circ_g.7 AT3G04240_circ_g.8 AT3G04240_circ_g.9 AT3G04240_circ_g.10 AT3G04240_circ_g.11 AT3G04240_circ_g.12 AT3G04240_circ_g.13 AT3G04240_circ_g.14 AT3G04240_circ_g.15 AT3G04260_circ_g.1 AT3G04260_circ_g.2 AT3G04260_circ_g.3 AT3G04260_circ_g.4 AT3G04290_circ_g.1 AT3G04290_circ_g.2 AT3G04340_circ_g.1 AT3G04340_circ_g.2 AT3G04340_circ_g.4 AT3G04340_circ_g.5 AT3G04340_circ_g.6 AT3G04340_circ_g.7 AT3G04340_circ_g.8 AT3G04340_circ_g.9 AT3G04380_circ_g.1 AT3G04400_circ_g.1 AT3G04400_circ_g.2 AT3G04400_circ_g.3 AT3G04400_circ_g.4 AT3G04420_circ_g.1 AT3G04420_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						inflorescences
					
						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-GC							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
						AT3G04340.1:4

General Information
CircRNA Name	AT3G04340_circ_g.3
ID in PlantcircBase	ath_circ_019637
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 1147138-1147951 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G04340
Parent gene annotation	Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, ch loroplastic
Parent gene strand	-
Alternative splicing	3_circ_ag.3 AT3G03330_circ_g.1 AT3G03330_circ_g.2 AT3G03340_circ_g.1 AT3G03340_circ_g.2 AT3G03340_circ_g.3 AT3G03340_circ_g.4 AT3G03340_circ_g.5 AT3G03340_circ_g.6 AT3G03350_circ_g.1 AT3G03350_circ_g.2 3_circ_ag.3 AT3G03350_circ_g.4 3_circ_ag.5 AT3G03380_circ_g.1 AT3G03380_circ_g.2 AT3G03380_circ_g.3 AT3G03380_circ_g.4 AT3G03380_circ_g.5 AT3G03380_circ_g.6 AT3G03380_circ_g.7 AT3G03380_circ_g.8 AT3G03380_circ_g.9 AT3G03380_circ_g.10 AT3G03380_circ_g.11 AT3G03380_circ_g.12 AT3G03380_circ_g.13 AT3G03380_circ_g.14 AT3G03380_circ_g.15 AT3G03380_circ_g.16 AT3G03380_circ_g.17 AT3G03380_circ_g.18 AT3G03420_circ_g.1 AT3G03420_circ_g.2 AT3G03420_circ_g.3 AT3G03470_circ_g.1 AT3G03520_circ_g.1 AT3G03520_circ_g.2 AT3G03520_circ_g.3 AT3G03550_circ_g.1 AT3G03560_circ_g.1 AT3G03560_circ_g.2 AT3G03560_circ_g.3 AT3G03560_circ_g.4 AT3G03560_circ_g.5 AT3G03560_circ_g.6 AT3G03560_circ_g.7 AT3G03560_circ_g.8 AT3G03560_circ_g.9 AT3G03560_circ_g.10 AT3G03560_circ_g.11 AT3G03560_circ_g.12 AT3G03560_circ_g.13 AT3G03570_circ_g.1 AT3G03610_circ_g.1 AT3G03610_circ_g.2 AT3G03610_circ_g.3 AT3G03630_circ_g.1 AT3G03640_circ_g.1 AT3G03640_circ_g.2 AT3G03680_circ_g.1 AT3G03680_circ_g.2 AT3G03690_circ_g.1 AT3G03690_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 AT3G03710_circ_g.1 AT3G03710_circ_g.2 AT3G03710_circ_g.3 3_circ_ag.4 AT3G03710_circ_g.5 AT3G03710_circ_g.6 AT3G03710_circ_g.7 AT3G03710_circ_g.8 AT3G03720_circ_g.1 AT3G03720_circ_g.2 AT3G03720_circ_g.3 AT3G03720_circ_g.4 AT3G03720_circ_g.5 AT3G03720_circ_g.6 AT3G03770_circ_g.1 AT3G03770_circ_g.2 AT3G03770_circ_g.3 AT3G03770_circ_g.4 AT3G03773_circ_g.1 AT3G03773_circ_g.2 AT3G03773_circ_g.3 AT3G03780_circ_g.1 AT3G03780_circ_g.2 AT3G03780_circ_g.3 AT3G03780_circ_g.4 AT3G03780_circ_g.5 AT3G03780_circ_g.6 AT3G03780_circ_g.7 AT3G03780_circ_g.8 AT3G03790_circ_g.1 AT3G03790_circ_g.2 AT3G03790_circ_g.3 AT3G03790_circ_g.4 AT3G03790_circ_g.5 AT3G03790_circ_g.6 AT3G03790_circ_g.7 AT3G03810_circ_g.1 AT3G03810_circ_g.2 AT3G03810_circ_g.3 AT3G03860_circ_g.1 AT3G03900_circ_g.1 AT3G03900_circ_g.2 AT3G03920_circ_g.1 AT3G03920_circ_g.2 AT3G03920_circ_g.3 AT3G03920_circ_g.4 AT3G03920_circ_g.5 AT3G03940_circ_g.1 AT3G03940_circ_g.2 AT3G03940_circ_g.3 AT3G03940_circ_g.4 AT3G03940_circ_g.5 AT3G03940_circ_g.6 AT3G03940_circ_g.7 AT3G03940_circ_g.8 AT3G03940_circ_g.9 AT3G03940_circ_g.10 AT3G03940_circ_g.11 AT3G03950_circ_g.1 AT3G03950_circ_g.2 AT3G03950_circ_g.3 AT3G03960_circ_g.1 AT3G03960_circ_g.2 AT3G03960_circ_g.3 AT3G03960_circ_g.4 AT3G03960_circ_g.5 AT3G03960_circ_g.6 AT3G03960_circ_g.7 AT3G03960_circ_g.8 AT3G03960_circ_g.9 AT3G04020_circ_g.1 AT3G04020_circ_g.2 AT3G04020_circ_g.3 AT3G04080_circ_g.1 AT3G04080_circ_g.2 AT3G04080_circ_g.3 AT3G04080_circ_g.4 AT3G04080_circ_g.5 AT3G04090_circ_g.1 AT3G04120_circ_g.1 AT3G04120_circ_g.2 AT3G04120_circ_g.3 AT3G04120_circ_g.4 AT3G04120_circ_g.5 AT3G04120_circ_g.6 AT3G04120_circ_g.7 AT3G04120_circ_g.8 AT3G04120_circ_g.9 AT3G04120_circ_g.10 AT3G04120_circ_g.11 AT3G04120_circ_g.12 AT3G04120_circ_g.13 AT3G04120_circ_g.14 AT3G04120_circ_g.15 AT3G04120_circ_g.16 AT3G04160_circ_g.1 AT3G04220_circ_g.1 AT3G04240_circ_g.1 AT3G04240_circ_g.2 AT3G04240_circ_g.3 AT3G04240_circ_g.4 AT3G04240_circ_g.5 AT3G04240_circ_g.6 AT3G04240_circ_g.7 AT3G04240_circ_g.8 AT3G04240_circ_g.9 AT3G04240_circ_g.10 AT3G04240_circ_g.11 AT3G04240_circ_g.12 AT3G04240_circ_g.13 AT3G04240_circ_g.14 AT3G04240_circ_g.15 AT3G04260_circ_g.1 AT3G04260_circ_g.2 AT3G04260_circ_g.3 AT3G04260_circ_g.4 AT3G04290_circ_g.1 AT3G04290_circ_g.2 AT3G04340_circ_g.1 AT3G04340_circ_g.2 AT3G04340_circ_g.4 AT3G04340_circ_g.5 AT3G04340_circ_g.6 AT3G04340_circ_g.7 AT3G04340_circ_g.8 AT3G04340_circ_g.9 AT3G04380_circ_g.1 AT3G04400_circ_g.1 AT3G04400_circ_g.2 AT3G04400_circ_g.3 AT3G04400_circ_g.4 AT3G04420_circ_g.1 AT3G04420_circ_g.2
Support reads	2
Tissues	inflorescences
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-GC 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	AT3G04340.1:4

			
						 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  
						
							TTTCAAGTAAAACAATGAAGGTTACCGCGTTAGTAGCATAGTATACTGCAGGACTGTCATCGGG
TCCCCAGCCATATTGAAGCACCATACGTGTTGCAATctcattgtaattggttcctgatagaaag
aaaggttccttctcccgaatcccaccattctcatgaacaattctttccaaatcctgcaaaccat
tacgagga

						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
						
							CTCATTGTAATTGGTTCCTGATAGAAAGAAAGGTTCCTTCTCCCGAATCCCACCATTCTCATGA
ACAATTCTTTCCAAATCCTGCAAACCATTACGAGGAAACAAAATTGATGATATTTTATATGCAG
AGAGGTTGTTTGGAACATCCTTCACTCTAAGTTGATCCAAACTTCGTACCTTATGAGTTAAAAT
CTCAAATTCGAGTAGCTCCTCTGTGATTTTCTCAAGGACACGTCGATTTTTAAGGAGCATTCCC
TTTGCCTTTTCGTACGCTAAGTCATAAATCTGTAAAGGAATAAGATGACATTAGAGACTGTAGA
GGAACAAGATGACATTAGAGAGGTTATGTATTTTAGCCTTGGACAATGCTTGAACCAACTGAAA
AGCGAAGCTGAAGATAGAAAATTGCGAACACTAGAGAGGCACCAATGACACTGGCAGATATTAA
GAACGTATTGGAAACTAGAGAGCAAAACAAACCTTTTCAACTTTACCCGCCATTTCATATTCGT
GATTGTTCCCCATACTCAAAGCTGAAACCTGCTCATTCGAATCAAATAAACCAAACAGAAAGAA
AAAAAAGTATAAGGTCAATCAACTGACCAGATGAGACATCAGAATGAATGCAAACTGTATGTAA
GATCGAATCATCATGTTCAGTATTCAACATGTTGGTTCAGTGGTATCAGACATTTAGTCTTGGA
ATGGAACCAATTTCAAGTAAAACAATGAAGGTTACCGCGTTAGTAGCATAGTATACTGCAGGAC
TGTCATCGGGTCCCCAGCCATATTGAAGCACCATACGTGTTGCAAT

Sequences
Splice junction sequence	TTTCAAGTAAAACAATGAAGGTTACCGCGTTAGTAGCATAGTATACTGCAGGACTGTCATCGGG TCCCCAGCCATATTGAAGCACCATACGTGTTGCAATctcattgtaattggttcctgatagaaag aaaggttccttctcccgaatcccaccattctcatgaacaattctttccaaatcctgcaaaccat tacgagga
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	CTCATTGTAATTGGTTCCTGATAGAAAGAAAGGTTCCTTCTCCCGAATCCCACCATTCTCATGA ACAATTCTTTCCAAATCCTGCAAACCATTACGAGGAAACAAAATTGATGATATTTTATATGCAG AGAGGTTGTTTGGAACATCCTTCACTCTAAGTTGATCCAAACTTCGTACCTTATGAGTTAAAAT CTCAAATTCGAGTAGCTCCTCTGTGATTTTCTCAAGGACACGTCGATTTTTAAGGAGCATTCCC TTTGCCTTTTCGTACGCTAAGTCATAAATCTGTAAAGGAATAAGATGACATTAGAGACTGTAGA GGAACAAGATGACATTAGAGAGGTTATGTATTTTAGCCTTGGACAATGCTTGAACCAACTGAAA AGCGAAGCTGAAGATAGAAAATTGCGAACACTAGAGAGGCACCAATGACACTGGCAGATATTAA GAACGTATTGGAAACTAGAGAGCAAAACAAACCTTTTCAACTTTACCCGCCATTTCATATTCGT GATTGTTCCCCATACTCAAAGCTGAAACCTGCTCATTCGAATCAAATAAACCAAACAGAAAGAA AAAAAAGTATAAGGTCAATCAACTGACCAGATGAGACATCAGAATGAATGCAAACTGTATGTAA GATCGAATCATCATGTTCAGTATTCAACATGTTGGTTCAGTGGTATCAGACATTTAGTCTTGGA ATGGAACCAATTTCAAGTAAAACAATGAAGGTTACCGCGTTAGTAGCATAGTATACTGCAGGAC TGTCATCGGGTCCCCAGCCATATTGAAGCACCATACGTGTTGCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.156074887

Conservation Information
Conserved circRNAs	NA
PMCS	0.156074887

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1147940-1147140(-)
						
						Potential amino acid sequence
						
							MVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRVLEKI
TEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNEIATRMVLQYGWGPDDSPAVYYATN
AVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRVLEKITEELLEFEILTHKDLERIVH
ENGGIREKEPFFLSGTNYNEIATRMVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVE
KIYDLAYEKAKGMLLKNRRVLEKITEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNE
IATRMVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRV
LEKITEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1147940-1147140(-)
Potential amino acid sequence	MVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRVLEKI TEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNEIATRMVLQYGWGPDDSPAVYYATN AVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRVLEKITEELLEFEILTHKDLERIVH ENGGIREKEPFFLSGTNYNEIATRMVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVE KIYDLAYEKAKGMLLKNRRVLEKITEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNE IATRMVLQYGWGPDDSPAVYYATNAVSALSMGNNHEYEMAGKVEKIYDLAYEKAKGMLLKNRRV LEKITEELLEFEILTHKDLERIVHENGGIREKEPFFLSGTNYNE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G04340_circ_g.3

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