Plant Circular RNA Database

Detail information of AT4G08470_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G08470_circ_g.1
					
						ID in PlantcircBase
						ath_circ_029958
					
						Alias
						4:5384659-5385845
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 5384659-5385845  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G08470						
					
						Parent gene annotation
						
							Mitogen-activated protein kinase kinase kinase 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							4_circ_ag.2 4_circ_ag.2 AT4G08470_circ_g.3 4_circ_ag.4 AT4G08470_circ_g.5 4_circ_ag.6 4_circ_ag.7 AT4G08470_circ_g.8 AT4G08470_circ_g.9 4_circ_ag.10 4_circ_ag.11 						
					
						Support reads
						1/1/1/2/1
					
						Tissues
						root;leaf
					
						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
						AT4G08470.1:6
AT4G08470.3:5
AT4G08470.2:6

General Information
CircRNA Name	AT4G08470_circ_g.1
ID in PlantcircBase	ath_circ_029958
Alias	4:5384659-5385845
Organism	Arabidpsis thaliana
Position	chr4: 5384659-5385845 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G08470
Parent gene annotation	Mitogen-activated protein kinase kinase kinase 3
Parent gene strand	-
Alternative splicing	4_circ_ag.2 4_circ_ag.2 AT4G08470_circ_g.3 4_circ_ag.4 AT4G08470_circ_g.5 4_circ_ag.6 4_circ_ag.7 AT4G08470_circ_g.8 AT4G08470_circ_g.9 4_circ_ag.10 4_circ_ag.11
Support reads	1/1/1/2/1
Tissues	root;leaf
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	AT4G08470.1:6 AT4G08470.3:5 AT4G08470.2:6

			
						 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  
						
							ACCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATAGAAGGCGTC
ATCAAGGAACAAGTCGACTCGGAACCAACAGAGGAActccggagccatccaaaataatgttccc
ttgcaagacataatgtcgttgaactttgacgcctatataacaaaatgacacaggtaccatgtca
gtgggata

									
								

					

						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: 685
Transcript exons: 5384659-5384718,5384820-5384892,5384983-5385140,5385217-
5385279,5385417-5385501,5385600-5385845
CTCCGGAGCCATCCAAAATAATGTTCCCTTGCAAGACATAATGTCGTTGAACTTTGACGCCTCT
GCCAATCCAAAATCTGCAAGTTTGACGGTGCCATTAGCGTCCACCAACATATTTGCACATTTAA
TGTCCCTGTGAACAAAGCCTTTATCGTGGAGATAATTCAACCCAGCAAGAATTTGTCTTGTATA
CAAGGAGACTACTGTGTAGCTAAGTTGGTATCTTTCGTAGAGTTTTTGAACGGATCCTTGGGTT
ACAAGCTCAAGAAAGATGTACAATTTTGACACGTCCTTGGCTGTGCCACGATATCGCACAATAT
TCTGATGCTGAAGCTGACTAAGTAGTGCAATCTCCCCCTCAAGTTGTTGAATGCATTCTTGTGC
CTGAATTCCCTTATCAAGAAGTGAAACTTCCTTGACAGCAAAGAAGTCCCCATCTTCTGAAATG
GCTTCATACACAGAGGCATATGATCCTCGTCCTAGAAGTTGACCCTTCAGCCAAGACGTGATAT
CCTCAGGCTTACGAAAATTCTCAATCAACTTGTTACGCATCAATTTACGCTTTTCCTTAACACG
TCCACTAGGACCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATA
GAAGGCGTCATCAAGGAACAAGTCGACTCGGAACCAACAGAGGAA
						
					

						Genomic sequence
						
							CTCCGGAGCCATCCAAAATAATGTTCCCTTGCAAGACATAATGTCGTTGAACTTTGACGCCTAT
ATAACAAAATGACACAGGTACCATGTCAGTGGGATAAGCGATGTACCATATTATTAATTAGTAA
TAAAACTACAAACATCTATTAATGGAAAAGAACCTCTGCCAATCCAAAATCTGCAAGTTTGACG
GTGCCATTAGCGTCCACCAACATATTTGCACATTTAATGTCCCTTTGTCGCATCAGATGAGAAA
AGTAAGTAACACATGAAAGAAATCAGATTTTTAAGAAATACTATGACAAGAGAGTTTACTAGTC
AAACCTGTGAACAAAGCCTTTATCGTGGAGATAATTCAACCCAGCAAGAATTTGTCTTGTATAC
AAGGAGACTACTGTGTAGCTAAGTTGGTATCTTTCGTAGAGTTTTTGAACGGATCCTTGGGTTA
CAAGCTCAAGAAAGATGTACAATTTTGACACGTCCTGTAAACAGTGAAAGGAGTTACCAATTGC
ACAACAAAATGCAACTGAGAACAAGAAAGAGAGAACAAGACTACACCTTGGCTGTGCCACGATA
TCGCACAATATTCTGATGCTGAAGCTGACTAAGTAGTGCAATCTCCTGTAGAAAAATAAAAAAT
GAAAAATGTGGCAAATGTAAGGTCGATTAGCAACCTACTTTTGACCGATCAATGCAATAATGCT
ACAATGAAAGAAGTGATAAATGCTACGGATAACTGATGTATATGACTTTCATACCCCCTCAAGT
TGTTGAATGCATTCTTGTGCCTGAATTCCCTTATCAAGAAGTGAAACTTCCTTGACAGCAAAGA
AGTCCCCATCTCTACATTTAACATAAACCACCAGCCAAAAAAGCATATGTTGGCTCAACCAAGT
ATCTTACTTTAAGGTCAACAAACGTAAGCAACCAGTAAGACTTACTCTGAAATGGCTTCATACA
CAGAGGCATATGATCCTCGTCCTAGAAGTTGACCCTTCAGCCAAGACGTGATATCCTCAGGCTT
ACGAAAATTCTCAATCAACTTGTTACGCATCAATTTACGCTTTTCCTTAACACGTCCACTAGGA
CCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATAGAAGGCGTCA
TCAAGGAACAAGTCGACTCGGAACCAACAGAGGAA
						
					

			
		

Sequences
Splice junction sequence	ACCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATAGAAGGCGTC ATCAAGGAACAAGTCGACTCGGAACCAACAGAGGAActccggagccatccaaaataatgttccc ttgcaagacataatgtcgttgaactttgacgcctatataacaaaatgacacaggtaccatgtca gtgggata
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: 685 Transcript exons: 5384659-5384718,5384820-5384892,5384983-5385140,5385217- 5385279,5385417-5385501,5385600-5385845 CTCCGGAGCCATCCAAAATAATGTTCCCTTGCAAGACATAATGTCGTTGAACTTTGACGCCTCT GCCAATCCAAAATCTGCAAGTTTGACGGTGCCATTAGCGTCCACCAACATATTTGCACATTTAA TGTCCCTGTGAACAAAGCCTTTATCGTGGAGATAATTCAACCCAGCAAGAATTTGTCTTGTATA CAAGGAGACTACTGTGTAGCTAAGTTGGTATCTTTCGTAGAGTTTTTGAACGGATCCTTGGGTT ACAAGCTCAAGAAAGATGTACAATTTTGACACGTCCTTGGCTGTGCCACGATATCGCACAATAT TCTGATGCTGAAGCTGACTAAGTAGTGCAATCTCCCCCTCAAGTTGTTGAATGCATTCTTGTGC CTGAATTCCCTTATCAAGAAGTGAAACTTCCTTGACAGCAAAGAAGTCCCCATCTTCTGAAATG GCTTCATACACAGAGGCATATGATCCTCGTCCTAGAAGTTGACCCTTCAGCCAAGACGTGATAT CCTCAGGCTTACGAAAATTCTCAATCAACTTGTTACGCATCAATTTACGCTTTTCCTTAACACG TCCACTAGGACCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATA GAAGGCGTCATCAAGGAACAAGTCGACTCGGAACCAACAGAGGAA
Genomic sequence	CTCCGGAGCCATCCAAAATAATGTTCCCTTGCAAGACATAATGTCGTTGAACTTTGACGCCTAT ATAACAAAATGACACAGGTACCATGTCAGTGGGATAAGCGATGTACCATATTATTAATTAGTAA TAAAACTACAAACATCTATTAATGGAAAAGAACCTCTGCCAATCCAAAATCTGCAAGTTTGACG GTGCCATTAGCGTCCACCAACATATTTGCACATTTAATGTCCCTTTGTCGCATCAGATGAGAAA AGTAAGTAACACATGAAAGAAATCAGATTTTTAAGAAATACTATGACAAGAGAGTTTACTAGTC AAACCTGTGAACAAAGCCTTTATCGTGGAGATAATTCAACCCAGCAAGAATTTGTCTTGTATAC AAGGAGACTACTGTGTAGCTAAGTTGGTATCTTTCGTAGAGTTTTTGAACGGATCCTTGGGTTA CAAGCTCAAGAAAGATGTACAATTTTGACACGTCCTGTAAACAGTGAAAGGAGTTACCAATTGC ACAACAAAATGCAACTGAGAACAAGAAAGAGAGAACAAGACTACACCTTGGCTGTGCCACGATA TCGCACAATATTCTGATGCTGAAGCTGACTAAGTAGTGCAATCTCCTGTAGAAAAATAAAAAAT GAAAAATGTGGCAAATGTAAGGTCGATTAGCAACCTACTTTTGACCGATCAATGCAATAATGCT ACAATGAAAGAAGTGATAAATGCTACGGATAACTGATGTATATGACTTTCATACCCCCTCAAGT TGTTGAATGCATTCTTGTGCCTGAATTCCCTTATCAAGAAGTGAAACTTCCTTGACAGCAAAGA AGTCCCCATCTCTACATTTAACATAAACCACCAGCCAAAAAAGCATATGTTGGCTCAACCAAGT ATCTTACTTTAAGGTCAACAAACGTAAGCAACCAGTAAGACTTACTCTGAAATGGCTTCATACA CAGAGGCATATGATCCTCGTCCTAGAAGTTGACCCTTCAGCCAAGACGTGATATCCTCAGGCTT ACGAAAATTCTCAATCAACTTGTTACGCATCAATTTACGCTTTTCCTTAACACGTCCACTAGGA CCTTCTTCGCTGAAATCCCTTTTTCGGAAACTGATGCGATCCGGGAACTCCATAGAAGGCGTCA TCAAGGAACAAGTCGACTCGGAACCAACAGAGGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.25776371

Conservation Information
Conserved circRNAs	NA
PMCS	0.25776371

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT4G08470_circ_g.1

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