Plant Circular RNA Database

Detail information of AT4G03090_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G03090_circ_g.1
					
						ID in PlantcircBase
						ath_circ_029526
					
						Alias
						Ath_circ_FC2529
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 1367185-1367892  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G03090						
					
						Parent gene annotation
						
							Nodulin homeobox
							
						Parent gene strand
						-
					
						Alternative splicing
						
							4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 ENSRNA049493837_circ_g.1 AT4G02980_circ_g.1 AT4G02980_circ_g.2 AT4G02980_circ_g.3 AT4G02990_circ_g.1 AT4G03000_circ_g.1 AT4G03020_circ_g.1 AT4G03020_circ_g.2 AT4G03020_circ_g.3 AT4G03020_circ_g.4 AT4G03050_circ_g.1 AT4G03080_circ_g.1 AT4G03080_circ_g.2 AT4G03080_circ_g.3 AT4G03080_circ_g.4 AT4G03080_circ_g.5 AT4G03080_circ_g.6 AT4G03080_circ_g.7 AT4G03080_circ_g.8 AT4G03080_circ_g.9 AT4G03080_circ_g.10 AT4G03080_circ_g.11 AT4G03080_circ_g.12 AT4G03090_circ_g.2 AT4G03110_circ_g.1 AT4G03110_circ_g.2 AT4G03115_circ_g.1 AT4G03120_circ_g.1 AT4G03180_circ_g.1 AT4G03190_circ_g.1 AT4G03200_circ_g.1 AT4G03200_circ_g.2 AT4G03200_circ_g.3 AT4G03200_circ_g.4 AT4G03200_circ_g.5 AT4G03200_circ_g.6 AT4G03200_circ_g.7 AT4G03200_circ_g.8 AT4G03200_circ_g.9 AT4G03200_circ_g.10 AT4G03210_circ_g.1 AT4G03210_circ_g.2 AT4G03210_circ_g.3 AT4G03230_circ_g.1 AT4G03240_circ_g.1 AT4G03250_circ_g.1 AT4G03250_circ_g.2 AT4G03250_circ_g.3 AT4G03260_circ_g.1 AT4G03270_circ_g.1 AT4G03280_circ_g.1 AT4G03280_circ_g.2 AT4G03280_circ_g.3 AT4G03280_circ_g.4 AT4G03280_circ_g.5 AT4G03290_circ_g.1 4_circ_igg.2 4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 ENSRNA049493832_circ_g.1 4_circ_ag.2 ENSRNA049493835_circ_g.1 ENSRNA049493835_circ_g.2 ENSRNA049493835_circ_g.3 ENSRNA049493835_circ_g.4 ENSRNA049493835_circ_g.5 ENSRNA049493835_circ_g.6 ENSRNA049493835_circ_g.7 ENSRNA049493835_circ_g.8 AT4G03390_circ_g.1 AT4G03390_circ_g.2 AT4G03390_circ_g.3 AT4G03390_circ_g.4 AT4G03400_circ_g.1 AT4G03400_circ_g.2 AT4G03400_circ_g.3 AT4G03400_circ_g.4 AT4G03410_circ_g.1 AT4G03410_circ_g.2 AT4G03410_circ_g.3 AT4G03410_circ_g.4 AT4G03420_circ_g.1 AT4G03420_circ_g.2 AT4G03420_circ_g.3 						
					
						Support reads
						15
					
						Tissues
						whole_plant
					
						Exon boundary  
						
							No-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-CA							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
						AT4G03090.2:2
AT4G03090.1:2
AT4G03090.4:2
AT4G03090.5:2
AT4G03090.3:2

General Information
CircRNA Name	AT4G03090_circ_g.1
ID in PlantcircBase	ath_circ_029526
Alias	Ath_circ_FC2529
Organism	Arabidpsis thaliana
Position	chr4: 1367185-1367892 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT4G03090
Parent gene annotation	Nodulin homeobox
Parent gene strand	-
Alternative splicing	4_circ_ag.6 4_circ_ag.7 4_circ_ag.8 4_circ_ag.9 ENSRNA049493837_circ_g.1 AT4G02980_circ_g.1 AT4G02980_circ_g.2 AT4G02980_circ_g.3 AT4G02990_circ_g.1 AT4G03000_circ_g.1 AT4G03020_circ_g.1 AT4G03020_circ_g.2 AT4G03020_circ_g.3 AT4G03020_circ_g.4 AT4G03050_circ_g.1 AT4G03080_circ_g.1 AT4G03080_circ_g.2 AT4G03080_circ_g.3 AT4G03080_circ_g.4 AT4G03080_circ_g.5 AT4G03080_circ_g.6 AT4G03080_circ_g.7 AT4G03080_circ_g.8 AT4G03080_circ_g.9 AT4G03080_circ_g.10 AT4G03080_circ_g.11 AT4G03080_circ_g.12 AT4G03090_circ_g.2 AT4G03110_circ_g.1 AT4G03110_circ_g.2 AT4G03115_circ_g.1 AT4G03120_circ_g.1 AT4G03180_circ_g.1 AT4G03190_circ_g.1 AT4G03200_circ_g.1 AT4G03200_circ_g.2 AT4G03200_circ_g.3 AT4G03200_circ_g.4 AT4G03200_circ_g.5 AT4G03200_circ_g.6 AT4G03200_circ_g.7 AT4G03200_circ_g.8 AT4G03200_circ_g.9 AT4G03200_circ_g.10 AT4G03210_circ_g.1 AT4G03210_circ_g.2 AT4G03210_circ_g.3 AT4G03230_circ_g.1 AT4G03240_circ_g.1 AT4G03250_circ_g.1 AT4G03250_circ_g.2 AT4G03250_circ_g.3 AT4G03260_circ_g.1 AT4G03270_circ_g.1 AT4G03280_circ_g.1 AT4G03280_circ_g.2 AT4G03280_circ_g.3 AT4G03280_circ_g.4 AT4G03280_circ_g.5 AT4G03290_circ_g.1 4_circ_igg.2 4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 ENSRNA049493832_circ_g.1 4_circ_ag.2 ENSRNA049493835_circ_g.1 ENSRNA049493835_circ_g.2 ENSRNA049493835_circ_g.3 ENSRNA049493835_circ_g.4 ENSRNA049493835_circ_g.5 ENSRNA049493835_circ_g.6 ENSRNA049493835_circ_g.7 ENSRNA049493835_circ_g.8 AT4G03390_circ_g.1 AT4G03390_circ_g.2 AT4G03390_circ_g.3 AT4G03390_circ_g.4 AT4G03400_circ_g.1 AT4G03400_circ_g.2 AT4G03400_circ_g.3 AT4G03400_circ_g.4 AT4G03410_circ_g.1 AT4G03410_circ_g.2 AT4G03410_circ_g.3 AT4G03410_circ_g.4 AT4G03420_circ_g.1 AT4G03420_circ_g.2 AT4G03420_circ_g.3
Support reads	15
Tissues	whole_plant
Exon boundary	No-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-CA 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	AT4G03090.2:2 AT4G03090.1:2 AT4G03090.4:2 AT4G03090.5:2 AT4G03090.3:2

			
						 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  
						
							ACCAATGTATAAGAGAGCAAAAAGCTTTTTCACCTTCACCTGTACTTGACTTTCCTCAAACTCG
GAATGGATTAACGGCTGTAACTGGTCACAAAACACCccttttgacttattttatcagcccataa
ctgtctcgaagctgaattccgctgcaaatcaggttcttcagcaagcgccttctcaatcatcccc
atttgatc

						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
						
							CCTTTTGACTTATTTTATCAGCCCATAACTGTCTCGAAGCTGAATTCCGCTGCAAATCAGGTTC
TTCAGCAAGCGCCTTCTCAATCATCCCCATTTGATCAGCATTCATAATACTACGCTTCCGTTTC
TTCTTCTGCTTCTCAAAGACAAGGAAGGTTTCAGATTTCTCATCCTCCTTCACCTCTCCTGATG
CACTGCCTTTAAATCGCTTGCTCATATTCTGAACCAACTCTCCCTCTTCAACCAGACCCTTCCC
TCTGTTAGAGCTTGTATCTGAACCACTGGTTTCAAGATTGCTAGCATCTGCATCGCTCTCTTTC
AACCTTTCAACTGTGTCTATCTCCTCGTTCACGCCTTGCTTTGTCATCACACCTTCAACTCGGA
CATCACAATCCTCTGAAGCTTCCTCATTGTTAAGATTCAGAAGCTCTTTTAGCTTACCAGATAA
ATTCCCGCCCCTACCTTCAATATCCTAGTACAACATAACATTTGAAGGTTAGCAAAAGATCTGT
CTTACGTAGAAATTTAACATACGATGGACATGAGTAAAACCTTGTTACACCTACTTGTATCAGT
GTAACTAAACAGATAAGCCAGAGAATTGTAAAACCAATGTATAAGAGAGCAAAAAGCTTTTTCA
CCTTCACCTGTACTTGACTTTCCTCAAACTCGGAATGGATTAACGGCTGTAACTGGTCACAAAA
CACC

Sequences
Splice junction sequence	ACCAATGTATAAGAGAGCAAAAAGCTTTTTCACCTTCACCTGTACTTGACTTTCCTCAAACTCG GAATGGATTAACGGCTGTAACTGGTCACAAAACACCccttttgacttattttatcagcccataa ctgtctcgaagctgaattccgctgcaaatcaggttcttcagcaagcgccttctcaatcatcccc atttgatc
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	CCTTTTGACTTATTTTATCAGCCCATAACTGTCTCGAAGCTGAATTCCGCTGCAAATCAGGTTC TTCAGCAAGCGCCTTCTCAATCATCCCCATTTGATCAGCATTCATAATACTACGCTTCCGTTTC TTCTTCTGCTTCTCAAAGACAAGGAAGGTTTCAGATTTCTCATCCTCCTTCACCTCTCCTGATG CACTGCCTTTAAATCGCTTGCTCATATTCTGAACCAACTCTCCCTCTTCAACCAGACCCTTCCC TCTGTTAGAGCTTGTATCTGAACCACTGGTTTCAAGATTGCTAGCATCTGCATCGCTCTCTTTC AACCTTTCAACTGTGTCTATCTCCTCGTTCACGCCTTGCTTTGTCATCACACCTTCAACTCGGA CATCACAATCCTCTGAAGCTTCCTCATTGTTAAGATTCAGAAGCTCTTTTAGCTTACCAGATAA ATTCCCGCCCCTACCTTCAATATCCTAGTACAACATAACATTTGAAGGTTAGCAAAAGATCTGT CTTACGTAGAAATTTAACATACGATGGACATGAGTAAAACCTTGTTACACCTACTTGTATCAGT GTAACTAAACAGATAAGCCAGAGAATTGTAAAACCAATGTATAAGAGAGCAAAAAGCTTTTTCA CCTTCACCTGTACTTGACTTTCCTCAAACTCGGAATGGATTAACGGCTGTAACTGGTCACAAAA CACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.105823823

Conservation Information
Conserved circRNAs	NA
PMCS	0.105823823

			
						 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
						Chen et al., 2017a

circRNA

Detail information of AT4G03090_circ_g.1

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