Plant Circular RNA Database

Detail information of AT3G15380_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G15380_circ_g.6
					
						ID in PlantcircBase
						ath_circ_021915
					
						Alias
						At_ciR1975, AT3G15380_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5195567-5195827  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT3G15380						
					
						Parent gene annotation
						
							Choline transporter protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G15380_circ_g.1 AT3G15380_circ_g.2 AT3G15380_circ_g.3 AT3G15380_circ_g.4 AT3G15380_circ_g.5 AT3G15380_circ_g.7 AT3G15380_circ_g.8 						
					
						Support reads
						4/15/8
					
						Tissues
						leaf/root, leaf, aerial, inflorescences, whole_plant/seedlings
					
						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
						AT3G15380.1:1

General Information
CircRNA Name	AT3G15380_circ_g.6
ID in PlantcircBase	ath_circ_021915
Alias	At_ciR1975, AT3G15380_C2
Organism	Arabidpsis thaliana
Position	chr3: 5195567-5195827 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
Parent gene	AT3G15380
Parent gene annotation	Choline transporter protein 1
Parent gene strand	+
Alternative splicing	AT3G15380_circ_g.1 AT3G15380_circ_g.2 AT3G15380_circ_g.3 AT3G15380_circ_g.4 AT3G15380_circ_g.5 AT3G15380_circ_g.7 AT3G15380_circ_g.8
Support reads	4/15/8
Tissues	leaf/root, leaf, aerial, inflorescences, whole_plant/seedlings
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	AT3G15380.1:1

			
						 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  
						
							TGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGG
ACCATCAAATCGGTTAACCGTAATGCCTACATAATGccagagataccgtttcttcctgttttcg
catcaatgaagcggcttgcacgctacaacctaggatccgtggctcttggttcactcattgtctc
ttttgttg

									
								

					

						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: 153
Transcript exons: 5195567-5195595,5195704-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCAACAAAAGTAAGCGGGACCATACCTGATCACTGGT
TTTGGAGAATGGCTCATTACACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATC
GGTTAACCGTAATGCCTACATAATG
Transcript length: 182
Transcript exons: 5195567-5195636,5195716-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTTGT
CTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 184
Transcript exons: 5195567-5195650,5195728-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTT
GTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 189
Transcript exons: 5195567-5195680,5195753-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCCATTACACTTCACG
TGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 251
Transcript exons: 5195567-5195648,5195653-5195770,5195777-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTCGT
CGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTT
CACGTGGTAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 251
Transcript exons: 5195567-5195726,5195737-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACGTTTTGGAGAATGGCTCATTACACTTCACGTG
GTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 253
Transcript exons: 5195567-5195636,5195645-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTCGTCGTA
AAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACG
TGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 255
Transcript exons: 5195567-5195719,5195726-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGCCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCA
CGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG
Transcript length: 259
Transcript exons: 5195567-5195648,5195651-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTC
GTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACAC
TTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATA
ATG
Transcript length: 261
Transcript exons: 5195567-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC
ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA
TAATG
Transcript length: 261
Transcript exons: 5195567-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCTTTAC
ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA
TAATG
Transcript length: 261
Transcript exons: 5195567-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGTTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC
ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA
TAATG
Transcript length: 261
Transcript exons: 5195567-5195827
CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCATGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC
ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA
TAATG
						
					

						Genomic sequence
						
							CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT
CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT
TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC
ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA
TAATG
						
					

			
		

Sequences
Splice junction sequence	TGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGG ACCATCAAATCGGTTAACCGTAATGCCTACATAATGccagagataccgtttcttcctgttttcg catcaatgaagcggcttgcacgctacaacctaggatccgtggctcttggttcactcattgtctc ttttgttg
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: 153 Transcript exons: 5195567-5195595,5195704-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCAACAAAAGTAAGCGGGACCATACCTGATCACTGGT TTTGGAGAATGGCTCATTACACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATC GGTTAACCGTAATGCCTACATAATG Transcript length: 182 Transcript exons: 5195567-5195636,5195716-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTTGT CTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 184 Transcript exons: 5195567-5195650,5195728-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACGTGGTT GTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 189 Transcript exons: 5195567-5195680,5195753-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCCATTACACTTCACG TGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 251 Transcript exons: 5195567-5195648,5195653-5195770,5195777-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTCGT CGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTT CACGTGGTAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 251 Transcript exons: 5195567-5195726,5195737-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACGTTTTGGAGAATGGCTCATTACACTTCACGTG GTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 253 Transcript exons: 5195567-5195636,5195645-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTCGTCGTA AAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCACG TGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 255 Transcript exons: 5195567-5195719,5195726-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGCCTGATCACTGGTTTTGGAGAATGGCTCATTACACTTCA CGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATAATG Transcript length: 259 Transcript exons: 5195567-5195648,5195651-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAATTC GTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTACAC TTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACATA ATG Transcript length: 261 Transcript exons: 5195567-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA TAATG Transcript length: 261 Transcript exons: 5195567-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCTTTAC ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA TAATG Transcript length: 261 Transcript exons: 5195567-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGTTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA TAATG Transcript length: 261 Transcript exons: 5195567-5195827 CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCATGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA TAATG
Genomic sequence	CCAGAGATACCGTTTCTTCCTGTTTTCGCATCAATGAAGCGGCTTGCACGCTACAACCTAGGAT CCGTGGCTCTTGGTTCACTCATTGTCTCTTTTGTTGAGTCTGTTCGGTTCATTCTCGAAGCAAT TCGTCGTAAAACAAAAGTAAGCGGGACCATACCTGATCACTGGTTTTGGAGAATGGCTCATTAC ACTTCACGTGGTTGTCTCAAAAGTGTGGAGTGGACCATCAAATCGGTTAACCGTAATGCCTACA TAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.633397158

Conservation Information
Conserved circRNAs	NA
PMCS	0.633397158

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5195600-5195824(+)
						
						Potential amino acid sequence
						
							MKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCLKSVEW
TIKSVNRNAYIMPEIPFLPVFASMKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGT
IPDHWFWRMAHYTSRGCLKSVEWTIKSVNRNAYIMPEIPFLPVFASMKRLARYNLGSVALGSLI
VSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCLKSVEWTIKSVNRNAYIMPEIPFL
PVFASMKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCL
KSVEWTIKSVNRNAYIM(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress; responsive to heat stress

Functional Information
Coding potential	Y
Potential coding position	5195600-5195824(+)
Potential amino acid sequence	MKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCLKSVEW TIKSVNRNAYIMPEIPFLPVFASMKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGT IPDHWFWRMAHYTSRGCLKSVEWTIKSVNRNAYIMPEIPFLPVFASMKRLARYNLGSVALGSLI VSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCLKSVEWTIKSVNRNAYIMPEIPFL PVFASMKRLARYNLGSVALGSLIVSFVESVRFILEAIRRKTKVSGTIPDHWFWRMAHYTSRGCL KSVEWTIKSVNRNAYIM(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	response to drought stress; responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT3G15380_circ_g.6

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