Plant Circular RNA Database

Detail information of AT2G40280_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT2G40280_circ_g.1
					
						ID in PlantcircBase
						ath_circ_017600
					
						Alias
						2:16826096-16827669
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16826096-16827669  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G40280						
					
						Parent gene annotation
						
							Probable methyltransferase PMT23
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G40280_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						AT2G40280.1:6

General Information
CircRNA Name	AT2G40280_circ_g.1
ID in PlantcircBase	ath_circ_017600
Alias	2:16826096-16827669
Organism	Arabidpsis thaliana
Position	chr2: 16826096-16827669 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G40280
Parent gene annotation	Probable methyltransferase PMT23
Parent gene strand	-
Alternative splicing	AT2G40280_circ_g.2
Support reads	1
Tissues	root
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	AT2G40280.1:6

			
						 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  
						
							CTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTCCTTCTTGTATTC
AACAAGCTTGGGATGAGGAACATTGTCATACCAAATctttgtgtgagatcacctaggaggaaac
tggaatgtaacagatcgtatgttctagggtaagtgttgacggactcacaccaatcatggtaaac
tccgatca

									
								

					

						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: 1136
Transcript exons: 16826096-16826290,16826386-16826625,16826717-16826885,16
826973-16827083,16827164-16827434,16827520-16827669
CTTTGTGTGAGATCACCTAGGAGGAAACTGGAATGTAACAGATCGTATGTTCTAGGGTAAGTGT
TGACGGACTCACACCAATCATGGTAAACTCCGATCAAGCCTCGATCATAAACGACGGAGAGAGT
GTCAGGTTTATCCACAGGGACAACATTCATCACCCAGAGTGGTAGATTTATAAGTGCAGCAGCA
AAACCGCCAAAACCAGCATTCATGTCCATCACATTCCGCACAGTCGACCAGTTTACAGCTAGAT
GTTTGAGGTAAACATCAGAAACACTTGCTGACCATTTCTCTGTATCTTTCTTCAATGTTTCCGC
TTTAACTGAAATGCTTTGCGGTTTAACACTCACAAGCCGTTTAGGCCATAGTTCAGGCCAACTC
TGGACATTTCCACTAGGTAACTTGGAAAGGCATTTAGCGAGAGGAACATACCATGAACCATTTG
CTTCCTTTTTATCACAAAGTGGTGGATCTTGTGTGCTGCGTTTATTATAACAGGATTCTGATGT
TGGCTTTTGATAGATCACAAGTCCGATTCCAGAGGAATCAACCGTCTTTGTCACGACCTTCCAG
CAAATGGATTTAGTAAGAGAAACCATTTCATTCCAAATTCTGCTATCTCTGTCATTATCTCGAT
AGACTGGTGTTGCAGACCATATGAAGAAACCTCCTGGCCTAAGTACCCTATTGAGCTCCAACAA
CGGTTTCCCACCATCAGCATCCCAATGGACTCTGCACCGTGCACAATGTATAAGATCAAATGCA
TTGCTCGGAAACGTGAGCTGTTGTGTTCCAATAACAGAAAGTGTTGCAGGTATTCCTCGTTCTA
ACGCAAATTGAATCTGAGCTTCATGTTCATCTTTAGGAGCAAACGACATTGTAATGACATCTTT
ATCTAATAAAGATCCGCCAAAGCTAGCAACACCACAACCAACATCTAATACAACCCTTATGTTT
TTCCCCCATTTGATACTCGGTAACGCCTTTTCGATGAACTCAACGTAATGAGTAACCCCGAATT
TGAATTGAGTACCTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTC
CTTCTTGTATTCAACAAGCTTGGGATGAGGAACATTGTCATACCAAAT
						
					

						Genomic sequence
						
							CTTTGTGTGAGATCACCTAGGAGGAAACTGGAATGTAACAGATCGTATGTTCTAGGGTAAGTGT
TGACGGACTCACACCAATCATGGTAAACTCCGATCAAGCCTCGATCATAAACGACGGAGAGAGT
GTCAGGTTTATCCACAGGGACAACATTCATCACCCAGAGTGGTAGATTTATAAGTGCAGCAGCA
AAACTATACCAAAAAGAAGAAAAGAAGAAAAACTTGTGTCAAGTTTCAGTTTGGGATAAACCGG
ATTCTGGTTAAAGTTTCAGAGATTGTAAATGTACCCGCCAAAACCAGCATTCATGTCCATCACA
TTCCGCACAGTCGACCAGTTTACAGCTAGATGTTTGAGGTAAACATCAGAAACACTTGCTGACC
ATTTCTCTGTATCTTTCTTCAATGTTTCCGCTTTAACTGAAATGCTTTGCGGTTTAACACTCAC
AAGCCGTTTAGGCCATAGTTCAGGCCAACTCTGGACATTTCCACTAGGTAACTTGGAAAGGCAT
TTAGCGAGAGGAACATACCTAAAATTAATCAGAAGGAAATGTTACAAAAAATAGTGGACATTAC
TTATATGTGAATGTAAAGCATCATTTTGTGTAATAGTTTTTTTACCATGAACCATTTGCTTCCT
TTTTATCACAAAGTGGTGGATCTTGTGTGCTGCGTTTATTATAACAGGATTCTGATGTTGGCTT
TTGATAGATCACAAGTCCGATTCCAGAGGAATCAACCGTCTTTGTCACGACCTTCCAGCAAATG
GATTTAGTAAGAGAAACCATTTCTGCAAAACAGAATTGTAACAGTTAAAACCATAGAGATCAAC
ATCAGTGTTGAATGATCAAATAAAAAAAACATGATTGTTGCGAACCATTCCAAATTCTGCTATC
TCTGTCATTATCTCGATAGACTGGTGTTGCAGACCATATGAAGAAACCTCCTGGCCTAAGTACC
CTATTGAGCTCCAACAACGGTTTCCCACCTAACAAATTAAACCATAATGATCATTGGAACCTTG
AAGCAAATGGGCTAAGAGGAAAAAGAATGGAACAAAAGAAATACCATCAGCATCCCAATGGACT
CTGCACCGTGCACAATGTATAAGATCAAATGCATTGCTCGGAAACGTGAGCTGTTGTGTTCCAA
TAACAGAAAGTGTTGCAGGTATTCCTCGTTCTAACGCAAATTGAATCTGAGCTTCATGTTCATC
TTTAGGAGCAAACGACATTGTAATGACATCTTTATCTAATAAAGATCCGCCAAAGCTAGCAACA
CCACAACCAACATCTAATACAACCCTTATGTTTTTCCCCCATTTGATACTCGGTAACGCCTGTG
AATATGAAATGATTTCAACACAAAGATAGATGCTTTCTATTCAAGAAAAACAGGGGAAACAGAG
CTAAGAAAGTGCTGACCTTTTCGATGAACTCAACGTAATGAGTAACCCCGAATTTGAATTGAGT
ACCTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTCCTTCTTGTAT
TCAACAAGCTTGGGATGAGGAACATTGTCATACCAAAT
						
					

			
		

Sequences
Splice junction sequence	CTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTCCTTCTTGTATTC AACAAGCTTGGGATGAGGAACATTGTCATACCAAATctttgtgtgagatcacctaggaggaaac tggaatgtaacagatcgtatgttctagggtaagtgttgacggactcacaccaatcatggtaaac tccgatca
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: 1136 Transcript exons: 16826096-16826290,16826386-16826625,16826717-16826885,16 826973-16827083,16827164-16827434,16827520-16827669 CTTTGTGTGAGATCACCTAGGAGGAAACTGGAATGTAACAGATCGTATGTTCTAGGGTAAGTGT TGACGGACTCACACCAATCATGGTAAACTCCGATCAAGCCTCGATCATAAACGACGGAGAGAGT GTCAGGTTTATCCACAGGGACAACATTCATCACCCAGAGTGGTAGATTTATAAGTGCAGCAGCA AAACCGCCAAAACCAGCATTCATGTCCATCACATTCCGCACAGTCGACCAGTTTACAGCTAGAT GTTTGAGGTAAACATCAGAAACACTTGCTGACCATTTCTCTGTATCTTTCTTCAATGTTTCCGC TTTAACTGAAATGCTTTGCGGTTTAACACTCACAAGCCGTTTAGGCCATAGTTCAGGCCAACTC TGGACATTTCCACTAGGTAACTTGGAAAGGCATTTAGCGAGAGGAACATACCATGAACCATTTG CTTCCTTTTTATCACAAAGTGGTGGATCTTGTGTGCTGCGTTTATTATAACAGGATTCTGATGT TGGCTTTTGATAGATCACAAGTCCGATTCCAGAGGAATCAACCGTCTTTGTCACGACCTTCCAG CAAATGGATTTAGTAAGAGAAACCATTTCATTCCAAATTCTGCTATCTCTGTCATTATCTCGAT AGACTGGTGTTGCAGACCATATGAAGAAACCTCCTGGCCTAAGTACCCTATTGAGCTCCAACAA CGGTTTCCCACCATCAGCATCCCAATGGACTCTGCACCGTGCACAATGTATAAGATCAAATGCA TTGCTCGGAAACGTGAGCTGTTGTGTTCCAATAACAGAAAGTGTTGCAGGTATTCCTCGTTCTA ACGCAAATTGAATCTGAGCTTCATGTTCATCTTTAGGAGCAAACGACATTGTAATGACATCTTT ATCTAATAAAGATCCGCCAAAGCTAGCAACACCACAACCAACATCTAATACAACCCTTATGTTT TTCCCCCATTTGATACTCGGTAACGCCTTTTCGATGAACTCAACGTAATGAGTAACCCCGAATT TGAATTGAGTACCTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTC CTTCTTGTATTCAACAAGCTTGGGATGAGGAACATTGTCATACCAAAT
Genomic sequence	CTTTGTGTGAGATCACCTAGGAGGAAACTGGAATGTAACAGATCGTATGTTCTAGGGTAAGTGT TGACGGACTCACACCAATCATGGTAAACTCCGATCAAGCCTCGATCATAAACGACGGAGAGAGT GTCAGGTTTATCCACAGGGACAACATTCATCACCCAGAGTGGTAGATTTATAAGTGCAGCAGCA AAACTATACCAAAAAGAAGAAAAGAAGAAAAACTTGTGTCAAGTTTCAGTTTGGGATAAACCGG ATTCTGGTTAAAGTTTCAGAGATTGTAAATGTACCCGCCAAAACCAGCATTCATGTCCATCACA TTCCGCACAGTCGACCAGTTTACAGCTAGATGTTTGAGGTAAACATCAGAAACACTTGCTGACC ATTTCTCTGTATCTTTCTTCAATGTTTCCGCTTTAACTGAAATGCTTTGCGGTTTAACACTCAC AAGCCGTTTAGGCCATAGTTCAGGCCAACTCTGGACATTTCCACTAGGTAACTTGGAAAGGCAT TTAGCGAGAGGAACATACCTAAAATTAATCAGAAGGAAATGTTACAAAAAATAGTGGACATTAC TTATATGTGAATGTAAAGCATCATTTTGTGTAATAGTTTTTTTACCATGAACCATTTGCTTCCT TTTTATCACAAAGTGGTGGATCTTGTGTGCTGCGTTTATTATAACAGGATTCTGATGTTGGCTT TTGATAGATCACAAGTCCGATTCCAGAGGAATCAACCGTCTTTGTCACGACCTTCCAGCAAATG GATTTAGTAAGAGAAACCATTTCTGCAAAACAGAATTGTAACAGTTAAAACCATAGAGATCAAC ATCAGTGTTGAATGATCAAATAAAAAAAACATGATTGTTGCGAACCATTCCAAATTCTGCTATC TCTGTCATTATCTCGATAGACTGGTGTTGCAGACCATATGAAGAAACCTCCTGGCCTAAGTACC CTATTGAGCTCCAACAACGGTTTCCCACCTAACAAATTAAACCATAATGATCATTGGAACCTTG AAGCAAATGGGCTAAGAGGAAAAAGAATGGAACAAAAGAAATACCATCAGCATCCCAATGGACT CTGCACCGTGCACAATGTATAAGATCAAATGCATTGCTCGGAAACGTGAGCTGTTGTGTTCCAA TAACAGAAAGTGTTGCAGGTATTCCTCGTTCTAACGCAAATTGAATCTGAGCTTCATGTTCATC TTTAGGAGCAAACGACATTGTAATGACATCTTTATCTAATAAAGATCCGCCAAAGCTAGCAACA CCACAACCAACATCTAATACAACCCTTATGTTTTTCCCCCATTTGATACTCGGTAACGCCTGTG AATATGAAATGATTTCAACACAAAGATAGATGCTTTCTATTCAAGAAAAACAGGGGAAACAGAG CTAAGAAAGTGCTGACCTTTTCGATGAACTCAACGTAATGAGTAACCCCGAATTTGAATTGAGT ACCTCCTCCAGGAAAAACTAGAAATTCACCCTCTTTTTTAACCCAATTTTGTTCCTTCTTGTAT TCAACAAGCTTGGGATGAGGAACATTGTCATACCAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.346408084

Conservation Information
Conserved circRNAs	NA
PMCS	0.346408084

			
						 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 AT2G40280_circ_g.1

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