Plant Circular RNA Database

Detail information of 1_circ_ag.10

			
						 General Information
					
						CircRNA Name
						1_circ_ag.10
					
						ID in PlantcircBase
						ath_circ_004135
					
						Alias
						At_ciR230, Ath_circ_FC0499
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 8569515-8571877  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT1G24190_circ_g.6 AT1G24190_circ_g.7 AT1G24190_circ_g.8 AT1G24190_circ_g.9 AT1G24190_circ_g.11 						
					
						Support reads
						14/6
					
						Tissues
						leaf/inflorescences, whole_plant
					
						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
						NA

General Information
CircRNA Name	1_circ_ag.10
ID in PlantcircBase	ath_circ_004135
Alias	At_ciR230, Ath_circ_FC0499
Organism	Arabidpsis thaliana
Position	chr1: 8569515-8571877 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT1G24190_circ_g.6 AT1G24190_circ_g.7 AT1G24190_circ_g.8 AT1G24190_circ_g.9 AT1G24190_circ_g.11
Support reads	14/6
Tissues	leaf/inflorescences, whole_plant
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	NA

			
						 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  
						
							CCTCCCGGTAGACCGCGGTGATGGGCTTCCTATCCTTTCTGTACATGTTTAAAATGTCTAAAAC
TGATTTGTATACACGATCATCGCCCTGAAACCTTGTcttaatcttgttaacaaagctaatagct
tcctcaaactcaacacgtttcttcagtggaggttgtccatcctcaggttgaagtgtgatctcaa
aaccctta

									
								

					

						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
						
							CTTAATCTTGTTAACAAAGCTAATAGCTTCCTCAAACTCAACACGTTTCTTCAGTGGAGGTTGT
CCATCCTCAGGTTGAAGTGTGATCTCAAAACCCTTAGGCAAGAAAGTATTAAACCCCAAAATCA
ACTCTTGGTGTCCTTTGAAAAGTTCTTTTACCCTAGTTATCACACCAGCTGTATCAACTCTACA
ATGAAAAACACAATTAAGCAATCAGTTCTCAGATACCAAGTTTTTAACCTAAACATAACAAGGA
GAAGAAAAAAACTATACCTTTGAGATTTAAAATTCTTCATAACCTCGAGAAACTCGTCATATTT
TCCACGTTGATCCTGAAATTTGTCCTTCACGGCTTTAAGATATGCAAGAGCGTCGTTTGTAGTT
AGCTTCTGAGCACTTCCTCCTCCAACCATGGTGTTTGAAGTTGAACAGAGCTTCATTACCATTA
AAAAAAACAGATCATTTAGAAAGCTATTCAACATCTCATAAGACCAAAGAACGTTTCTTTAGAG
AATTCAAGTAAAATTTGGGATTCAGCAAAAGAACAAAAGCTGAAAACAACTTTCTTCATGTTCA
TCTACAAATCAAAACCTAGTAAAACTCAAAATCAATCACATAAACAAGGAAAATTCAAAGAACC
GAACTTGAATTTCATCCCAATAAGCAACACCTGTAGATCTAGCAGCTACAGAAACAATTTATGA
AGAAAAAACAAAAGGAGACGGACCAGAAAAAATCGATCTTAACTTAATCCTCAGATTATTTCAC
ATTCAGTTCACGATTAAAATTGTAATACCCAAAAATCAAACAGAAAGGATAAAAAACGAAAGAA
GATCATCATCGTTTATGTGTTAGAGAGTTTACCGAAGAAATTCAGAGAAGACGAAGAAGAAGAA
GAAGAAGAAGTCTAGAAGAAGAAGCTTCCTCCGACGAAACAGCTGAGAAGACAAAAACTATTCA
ACAATTTTCAGACAGAAAGAAAAGACTCACTGAGCAAACGAGAGTTTTATGTTTTTATGAAGAA
AGGATTGAGATTTCTCTCAAAGGAGTTTTACGTCTTCTTAAGTAAATTAAAATCTACATATTTA
ATACACTTTCTCGTTCGCTAAATTTTTCGTTTACTTACTTATTTCATTTTTCTGTTGACAAAAA
ATAAAATAAAAATCAAAGTTGTATTTTCTTGTTTTTATTACTTCCTTTTGTTGGTTGTATCATT
TTAGGAGACTTATAATTTATCTTCTTCTTTTATTATTTTTAACATTTTTTTTCTTTTGGAAGTT
TTTATCTCCTTTGGTATGTGAGAGAGACATACTTAATTTTGAAAATTTTTGATATAAAATAAAT
TATTCATTTTTTTTGGAAATAATTTTGTAATTAAAAAGTTTTAGATGATTAATCATATTATTAA
TAGATGTTTTTTTTCTCTTTATTTTGGTCAACATAGATGTTTTTTCTTAAAATTTCTAAGTTAA
TTACTTAATGCAAAACCTATCAAAATTATTAATGGGGAAAAAATGTTCTAAAATCATTGATGTA
AATGGAATCTATATTACATTACACGGTTAGATTTTGCTTAAATCTAAAAAATAATATTTGGCTA
ACATTAATAGAAGAATAATTTAACTCTAACTTGATTAAAACCATAAAAACGGAACATATTATTC
GCCTTTTAAATTCATTTTTTTTTTATCGGCATTACTATCTTTCCGGTAGACCGAAAACTTTGTC
ACCTTGTTCGTAGAATAATTCCGATAACCCTTATCCTCATGTTACACATAGTAAACTCATAGGT
AAGCATTGAAATAACTAGGTAAAAAAAAAAGCATTGAATAACTATAGATGATGGTAATTTTGAA
TTTTGATAGTGGCTATAATTTATAGGGAAAAGAAAGCTATTAATCATGCATATTAAAAAGAAAA
AACCTCTACTATTATCTCTGACTTGTAACTTTAAAAAAAAAAAACTACTTATATGTGAAGCGAT
TGAAGTAACATAGCAATCCTTTCGTCACAAAAAACTCTGAGAAATAGTTGGCAGAAAGCAATCC
AACTCTTCAAGCAAATCAGGATGATCTATGCAAAACTGTGAATGCAACAAGGCTGTTGCTGGAG
TAGCTGGAGTAGCAGGCAGAAAGTGAGTAAACTCCACAAGCAAATTGTTATGATCTAGAAATAG
GATGGCAACCTGATAAGATAAACGTGTGAAACTAAGTAAAATATTAGCAATAAAAAAAAAAAAA
CTTAGTATGAATCAATGAGCCTACCTCCCGGTAGACCGCGGTGATGGGCTTCCTATCCTTTCTG
TACATGTTTAAAATGTCTAAAACTGATTTGTATACACGATCATCGCCCTGAAACCTTGT
						
					

			
		

Sequences
Splice junction sequence	CCTCCCGGTAGACCGCGGTGATGGGCTTCCTATCCTTTCTGTACATGTTTAAAATGTCTAAAAC TGATTTGTATACACGATCATCGCCCTGAAACCTTGTcttaatcttgttaacaaagctaatagct tcctcaaactcaacacgtttcttcagtggaggttgtccatcctcaggttgaagtgtgatctcaa aaccctta
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	CTTAATCTTGTTAACAAAGCTAATAGCTTCCTCAAACTCAACACGTTTCTTCAGTGGAGGTTGT CCATCCTCAGGTTGAAGTGTGATCTCAAAACCCTTAGGCAAGAAAGTATTAAACCCCAAAATCA ACTCTTGGTGTCCTTTGAAAAGTTCTTTTACCCTAGTTATCACACCAGCTGTATCAACTCTACA ATGAAAAACACAATTAAGCAATCAGTTCTCAGATACCAAGTTTTTAACCTAAACATAACAAGGA GAAGAAAAAAACTATACCTTTGAGATTTAAAATTCTTCATAACCTCGAGAAACTCGTCATATTT TCCACGTTGATCCTGAAATTTGTCCTTCACGGCTTTAAGATATGCAAGAGCGTCGTTTGTAGTT AGCTTCTGAGCACTTCCTCCTCCAACCATGGTGTTTGAAGTTGAACAGAGCTTCATTACCATTA AAAAAAACAGATCATTTAGAAAGCTATTCAACATCTCATAAGACCAAAGAACGTTTCTTTAGAG AATTCAAGTAAAATTTGGGATTCAGCAAAAGAACAAAAGCTGAAAACAACTTTCTTCATGTTCA TCTACAAATCAAAACCTAGTAAAACTCAAAATCAATCACATAAACAAGGAAAATTCAAAGAACC GAACTTGAATTTCATCCCAATAAGCAACACCTGTAGATCTAGCAGCTACAGAAACAATTTATGA AGAAAAAACAAAAGGAGACGGACCAGAAAAAATCGATCTTAACTTAATCCTCAGATTATTTCAC ATTCAGTTCACGATTAAAATTGTAATACCCAAAAATCAAACAGAAAGGATAAAAAACGAAAGAA GATCATCATCGTTTATGTGTTAGAGAGTTTACCGAAGAAATTCAGAGAAGACGAAGAAGAAGAA GAAGAAGAAGTCTAGAAGAAGAAGCTTCCTCCGACGAAACAGCTGAGAAGACAAAAACTATTCA ACAATTTTCAGACAGAAAGAAAAGACTCACTGAGCAAACGAGAGTTTTATGTTTTTATGAAGAA AGGATTGAGATTTCTCTCAAAGGAGTTTTACGTCTTCTTAAGTAAATTAAAATCTACATATTTA ATACACTTTCTCGTTCGCTAAATTTTTCGTTTACTTACTTATTTCATTTTTCTGTTGACAAAAA ATAAAATAAAAATCAAAGTTGTATTTTCTTGTTTTTATTACTTCCTTTTGTTGGTTGTATCATT TTAGGAGACTTATAATTTATCTTCTTCTTTTATTATTTTTAACATTTTTTTTCTTTTGGAAGTT TTTATCTCCTTTGGTATGTGAGAGAGACATACTTAATTTTGAAAATTTTTGATATAAAATAAAT TATTCATTTTTTTTGGAAATAATTTTGTAATTAAAAAGTTTTAGATGATTAATCATATTATTAA TAGATGTTTTTTTTCTCTTTATTTTGGTCAACATAGATGTTTTTTCTTAAAATTTCTAAGTTAA TTACTTAATGCAAAACCTATCAAAATTATTAATGGGGAAAAAATGTTCTAAAATCATTGATGTA AATGGAATCTATATTACATTACACGGTTAGATTTTGCTTAAATCTAAAAAATAATATTTGGCTA ACATTAATAGAAGAATAATTTAACTCTAACTTGATTAAAACCATAAAAACGGAACATATTATTC GCCTTTTAAATTCATTTTTTTTTTATCGGCATTACTATCTTTCCGGTAGACCGAAAACTTTGTC ACCTTGTTCGTAGAATAATTCCGATAACCCTTATCCTCATGTTACACATAGTAAACTCATAGGT AAGCATTGAAATAACTAGGTAAAAAAAAAAGCATTGAATAACTATAGATGATGGTAATTTTGAA TTTTGATAGTGGCTATAATTTATAGGGAAAAGAAAGCTATTAATCATGCATATTAAAAAGAAAA AACCTCTACTATTATCTCTGACTTGTAACTTTAAAAAAAAAAAACTACTTATATGTGAAGCGAT TGAAGTAACATAGCAATCCTTTCGTCACAAAAAACTCTGAGAAATAGTTGGCAGAAAGCAATCC AACTCTTCAAGCAAATCAGGATGATCTATGCAAAACTGTGAATGCAACAAGGCTGTTGCTGGAG TAGCTGGAGTAGCAGGCAGAAAGTGAGTAAACTCCACAAGCAAATTGTTATGATCTAGAAATAG GATGGCAACCTGATAAGATAAACGTGTGAAACTAAGTAAAATATTAGCAATAAAAAAAAAAAAA CTTAGTATGAATCAATGAGCCTACCTCCCGGTAGACCGCGGTGATGGGCTTCCTATCCTTTCTG TACATGTTTAAAATGTCTAAAACTGATTTGTATACACGATCATCGCCCTGAAACCTTGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.739887727

Conservation Information
Conserved circRNAs	NA
PMCS	0.739887727

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5021 						
					
						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	ath-miR5021
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of 1_circ_ag.10

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