Plant Circular RNA Database

Detail information of AT4G00180_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G00180_circ_g.1
					
						ID in PlantcircBase
						ath_circ_029044
					
						Alias
						AT4G00180_C1, AT4G00180_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 72990-74427  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							AT4G00180						
					
						Parent gene annotation
						
							Axial regulator YABBY 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G00180_circ_g.2 AT4G00180_circ_g.3 AT4G00180_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						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
						AT4G00180.2:4
AT4G00180.1:4

General Information
CircRNA Name	AT4G00180_circ_g.1
ID in PlantcircBase	ath_circ_029044
Alias	AT4G00180_C1, AT4G00180_C1
Organism	Arabidpsis thaliana
Position	chr4: 72990-74427 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	AT4G00180
Parent gene annotation	Axial regulator YABBY 3
Parent gene strand	-
Alternative splicing	AT4G00180_circ_g.2 AT4G00180_circ_g.3 AT4G00180_circ_g.4
Support reads	NA
Tissues	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	AT4G00180.2:4 AT4G00180.1:4

			
						 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  
						
							GAGTCGCCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCATCATGTT
CATGTTTATATTCTGCCCTCCGCTTCGCATTTCCTCctgttggcgcacgttagccttcttcgtg
ggaggatggtcagccatgagtccaaagtgtatgtgagggaaatgagcccactgtttcatacata
ttacatca

									
								

					

						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: 363
Transcript exons: 72990-73067,73448-73523,73659-73707,74268-74427
CTGTTGGCGCACGTTAGCCTTCTTCGTGGGAGGATGGTCAGCCATGAGTCCAAAGTGTATGTGA
GGGAAATGAGCCCAGTTTTTGGCAGCAGCACTGAAGGCTTCTCTGTGGCTGATATCAGGGTTGC
CTGCCTTTATACGTTGGATCTCCTCTTTGATGAATCGGTTGTATGCAGATGGTACTCTTTGTCG
CTTCTCTGGGGGTCTATTGGCTGGTGGTGGCCGAGGCATCTCTTGTAGATGATCCACTGATCTT
CCGTTGCGAGTCGCCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCA
TCATGTTCATGTTTATATTCTGCCCTCCGCTTCGCATTTCCTC
						
					

						Genomic sequence
						
							CTGTTGGCGCACGTTAGCCTTCTTCGTGGGAGGATGGTCAGCCATGAGTCCAAAGTGTATGTGA
GGGAAATGAGCCCACTGTTTCATACATATTACATCATATACTTAGCTCTTTTAACATTAATGTG
TATTTATCTTATACATAACATAAAAACTTGGTCAAAAATATACGAATACAAAGCCAGACTAAAA
TATCTGCTAGGGAACTTTACTGAAACCCTAGATCGTAGATCCTAAGGCTAGTCCTAGCTAATGT
ATGCTGGATAAAGCTTATGAATTATGGATTATTACGGTAACTATTTTGTTTTATGTTTTTAATT
TAAAGCAATGTGAGTATCAATGTAGCTCCACAATAATCTAGCTAGGTTCAATTCATAAAGACTA
AAATGAGATTGTATGATTATGGATATAATGCAATATAGAAAATTAGTTTTATATATTAAAAAAA
GAAATGGTACGTTTTTGGCAGCAGCACTGAAGGCTTCTCTGTGGCTGATATCAGGGTTGCCTGC
CTTTATACGTTGGATCTCCTCTCTGTCAACATTTTTATTTTTATATCATATAATGAAATCAAAT
CTGTCACATCTATCGACCCTTAATTATATGAGTAAAATGGTTAATTAGGGAAATTTAATTATGC
CATTTTAAGCAAAGGAATAAACTTATTACTTGATGAATCGGTTGTATGCAGATGGTACTCTTTG
TCGCTTCTCTGGGGCTGCTTTTCCACAAACAAACAAACAGAACATATTCAATTTTAATTCCAAA
TCAAACCCTTTTGTTAAAAAAAACATTATTGGTTTTTATTGTGCCTCCCCAAAAAATCTAAAAA
TTCACCAAAAAAAAACAATTAAAAAAAAAAAAACAATCACTCTTCGACTCTTCCTCCTTTCTCT
CTCTCCCTCTCCCTCTCACTTTGCTCGTTATCATCATCACTTCATCATTATCTTTCTTACGATC
TACCCCCAAAACTATATCAGTTGGCATCTATAGGTTTAGCTAGATTTCCGGGGGATAAACACAT
CACTTATTAATTTTCCTTTTGTTGTCGAAATTGTTTTCTGACCAAAAAAAAAGTGCATGCGAGA
AGTCACATACCGAGGGAACAAAAATGAAATCAAAACTTATAAATTCATTATAAACAAACGAGAT
TCTTTGGAGTGTATATATAAAAGGTTGAAGAAATGAATGGATAAGGTTTTGTGAATTAGGGTTT
TTGTTTTCTTATATATATATATATGAAGATGTTGAAATAAAGAGTAGAAGATGGAAGGTTACGT
CTATTGGCTGGTGGTGGCCGAGGCATCTCTTGTAGATGATCCACTGATCTTCCGTTGCGAGTCG
CCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCATCATGTTCATGTT
TATATTCTGCCCTCCGCTTCGCATTTCCTC
						
					

			
		

Sequences
Splice junction sequence	GAGTCGCCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCATCATGTT CATGTTTATATTCTGCCCTCCGCTTCGCATTTCCTCctgttggcgcacgttagccttcttcgtg ggaggatggtcagccatgagtccaaagtgtatgtgagggaaatgagcccactgtttcatacata ttacatca
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: 363 Transcript exons: 72990-73067,73448-73523,73659-73707,74268-74427 CTGTTGGCGCACGTTAGCCTTCTTCGTGGGAGGATGGTCAGCCATGAGTCCAAAGTGTATGTGA GGGAAATGAGCCCAGTTTTTGGCAGCAGCACTGAAGGCTTCTCTGTGGCTGATATCAGGGTTGC CTGCCTTTATACGTTGGATCTCCTCTTTGATGAATCGGTTGTATGCAGATGGTACTCTTTGTCG CTTCTCTGGGGGTCTATTGGCTGGTGGTGGCCGAGGCATCTCTTGTAGATGATCCACTGATCTT CCGTTGCGAGTCGCCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCA TCATGTTCATGTTTATATTCTGCCCTCCGCTTCGCATTTCCTC
Genomic sequence	CTGTTGGCGCACGTTAGCCTTCTTCGTGGGAGGATGGTCAGCCATGAGTCCAAAGTGTATGTGA GGGAAATGAGCCCACTGTTTCATACATATTACATCATATACTTAGCTCTTTTAACATTAATGTG TATTTATCTTATACATAACATAAAAACTTGGTCAAAAATATACGAATACAAAGCCAGACTAAAA TATCTGCTAGGGAACTTTACTGAAACCCTAGATCGTAGATCCTAAGGCTAGTCCTAGCTAATGT ATGCTGGATAAAGCTTATGAATTATGGATTATTACGGTAACTATTTTGTTTTATGTTTTTAATT TAAAGCAATGTGAGTATCAATGTAGCTCCACAATAATCTAGCTAGGTTCAATTCATAAAGACTA AAATGAGATTGTATGATTATGGATATAATGCAATATAGAAAATTAGTTTTATATATTAAAAAAA GAAATGGTACGTTTTTGGCAGCAGCACTGAAGGCTTCTCTGTGGCTGATATCAGGGTTGCCTGC CTTTATACGTTGGATCTCCTCTCTGTCAACATTTTTATTTTTATATCATATAATGAAATCAAAT CTGTCACATCTATCGACCCTTAATTATATGAGTAAAATGGTTAATTAGGGAAATTTAATTATGC CATTTTAAGCAAAGGAATAAACTTATTACTTGATGAATCGGTTGTATGCAGATGGTACTCTTTG TCGCTTCTCTGGGGCTGCTTTTCCACAAACAAACAAACAGAACATATTCAATTTTAATTCCAAA TCAAACCCTTTTGTTAAAAAAAACATTATTGGTTTTTATTGTGCCTCCCCAAAAAATCTAAAAA TTCACCAAAAAAAAACAATTAAAAAAAAAAAAACAATCACTCTTCGACTCTTCCTCCTTTCTCT CTCTCCCTCTCCCTCTCACTTTGCTCGTTATCATCATCACTTCATCATTATCTTTCTTACGATC TACCCCCAAAACTATATCAGTTGGCATCTATAGGTTTAGCTAGATTTCCGGGGGATAAACACAT CACTTATTAATTTTCCTTTTGTTGTCGAAATTGTTTTCTGACCAAAAAAAAAGTGCATGCGAGA AGTCACATACCGAGGGAACAAAAATGAAATCAAAACTTATAAATTCATTATAAACAAACGAGAT TCTTTGGAGTGTATATATAAAAGGTTGAAGAAATGAATGGATAAGGTTTTGTGAATTAGGGTTT TTGTTTTCTTATATATATATATATGAAGATGTTGAAATAAAGAGTAGAAGATGGAAGGTTACGT CTATTGGCTGGTGGTGGCCGAGGCATCTCTTGTAGATGATCCACTGATCTTCCGTTGCGAGTCG CCATAACCAAATGCTCGTTCGGGTGGTGAGCTGAAGCGTGATGGCTCATCATCATGTTCATGTT TATATTCTGCCCTCCGCTTCGCATTTCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.25662358

Conservation Information
Conserved circRNAs	NA
PMCS	0.25662358

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							74423-72992(-)
						
						Potential amino acid sequence
						
							MRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYN
RFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQN
INMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEI
QRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQNINMNMMM
SHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGN
PDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQNINMNMMMSHHASAH
HPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHRE
AFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQ
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	74423-72992(-)
Potential amino acid sequence	MRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYN RFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQN INMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEI QRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQNINMNMMM SHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGN PDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEEMRSGGQNINMNMMMSHHASAH HPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHRE AFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQ
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress

			
						 Other Information
					
						References
						Zhang et al., 2019

circRNA

Detail information of AT4G00180_circ_g.1

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