Plant Circular RNA Database

Detail information of AT5G40270_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G40270_circ_g.1
					
						ID in PlantcircBase
						ath_circ_041680
					
						Alias
						Chr5:16093397|16096079
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 16093397-16096079  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT5G40270						
					
						Parent gene annotation
						
							AT5g40270/MSN9_170
							
						Parent gene strand
						-
					
						Alternative splicing
						
							5_circ_ag.2 5_circ_ag.3 AT5G40270_circ_g.4 5_circ_ag.5 AT5G40270_circ_g.6 AT5G40270_circ_g.7 AT5G40270_circ_g.8 AT5G40270_circ_g.9 AT5G40270_circ_g.10 5_circ_ag.11 5_circ_ag.12 AT5G40270_circ_g.13 5_circ_ag.14 AT5G40270_circ_g.15 5_circ_ag.16 5_circ_ag.17 5_circ_ag.18 AT5G40270_circ_g.19 5_circ_ag.20 AT5G40280_circ_g.1 AT5G40280_circ_g.2 AT5G40280_circ_g.3 						
					
						Support reads
						3
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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-TA							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
						AT5G40270.2:15
AT5G40270.1:16

General Information
CircRNA Name	AT5G40270_circ_g.1
ID in PlantcircBase	ath_circ_041680
Alias	Chr5:16093397\|16096079
Organism	Arabidpsis thaliana
Position	chr5: 16093397-16096079 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT5G40270
Parent gene annotation	AT5g40270/MSN9_170
Parent gene strand	-
Alternative splicing	5_circ_ag.2 5_circ_ag.3 AT5G40270_circ_g.4 5_circ_ag.5 AT5G40270_circ_g.6 AT5G40270_circ_g.7 AT5G40270_circ_g.8 AT5G40270_circ_g.9 AT5G40270_circ_g.10 5_circ_ag.11 5_circ_ag.12 AT5G40270_circ_g.13 5_circ_ag.14 AT5G40270_circ_g.15 5_circ_ag.16 5_circ_ag.17 5_circ_ag.18 AT5G40270_circ_g.19 5_circ_ag.20 AT5G40280_circ_g.1 AT5G40280_circ_g.2 AT5G40280_circ_g.3
Support reads	3
Tissues	seedling
Exon boundary	No-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-TA 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	AT5G40270.2:15 AT5G40270.1:16

			
						 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  
						
							TTTTTTAGCCTCTGAGCAGTTTCGCCTGCAAGCCAATACACGCCTAGAGAGTGCTCAAATCTCG
AATGTACAGCTCCTGGATATACCATGTTTGTCACTCcatcacacgccttttctttttctcaggt
gttgcgtgtacttgagctttgattccatacgttctcatttggaagttttcaaatgcctcagaaa
ctgcttct

									
								

					

						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
						
							CATCACACGCCTTTTCTTTTTCTCAGGTGTTGCGTGTACTTGAGCTTTGATTCCATACGTTCTC
ATTTGGAAGTTTTCAAATGCCTCAGAAACTGCTTCTACCTGTTGATCAATTTTGCAAACCAAAA
ATAAAAACGTTACTTCGTGTGCATCACTAGAAACCATAATGTATTAAAGATTAATGAGGGTTAA
TAATAATCACTTACCAATTCTGGTTTTTTGGCATATACTCTCACTATCATGTCTTGATATGTTG
TTGGTAACAAGTGACTGACTCTGTCCTCAGGTATCACAAACTTCTCTGCACTATCATAATCCTG
TAAACACCATATAAATCAATTTATTGAGATTCTGTGTTATTTTCCTCTTTACACATTTACAGAA
GCAAATCTCAAAAACAAGACCAAAGACTTTTCTGTATGTACCTTATAGAAGTTGATGCTGAAGG
AGCCAGATCCAACACAAAGGTAAGTTGGTTAGAATTTTAATGAGGGAAACTGAGAAAACAAAGA
AGCTAAACTGTACTTTTTTTACCATTCAAGCGGATTTTCTCTCCCACGAGCCAAGTCAATCTTG
ACGTTTGTAACAGCTATATCTTCTTCTTTTAGTGTCAAGCTTGTGTGCTTCTGTTAAATCAGAA
AGCAATATAAGTATGGTAATGGACTGTACAATATACTTTTCCTCTATTTAAGTGCTAAAGATTG
TACAAACCTGAGAACAGATGATATCTTGAGGAGTGACAGCTTTGAAATGATCGATTTTGTCCTT
TGGAACCGCATATTCGTTACAGAACTGAAAGTCAAAATTCATACAGGTCAATCTTCTGAAGGGA
AATTCTTAACCTAATTAAGCATAAAAGAAAAAGAAGAAACTGGGTGAAAATTTTATATACTTGG
TACAACTGCCTTCTGCGAACACGGAGTATCAGCTCTTTCGCTTCTGCAAGTTCTGGATCTGGAG
CTATTTCGATAGTTTTGAGGATTGTGTCGTCTAACTGCATTTGTTTATGGAGAACAAAAACTAT
GTAAACAAGCAGAAAGGTAATATTTGTCTTCTGAGGAAGAACTGTACCTTCCAGTATTCAGATG
GGTCATTAATCATAGAAGAAATTTCCAAATGATTGTTGGCTTTGACCATGGCATCTACTATCAT
CAGCTCTATCGCCTGCAAATGAATGGAACGAGACAAGTGGGAAAGAGAGAAAGAATAGTCAAGG
TACAGAGAGAATGATAATGGTATAATACCTTTACTTTCGAATGCGTGTAGACGGTTCGATAAAG
ATCAGCTCGAGTTGCAAATAACTTGTGGACACTAAGATCTGAAAAATTAACCGGGTTTAAAATG
GGATAGAAGCAAACGCAAATAGAGAATTTAGGTGGGCAAAACTTACACTCCTTGGCGCGGAAGC
AGATTTCATTGTCCAGGACTCTCATCGTCTCTGTCAGTCTAGAAAGTTCTAATAATTAGCAATT
TCCTTATTAGAAACCAGTGAAATGACTATAGAATAGAATGAAGACCTTTGGAATTGAAAATTGG
ATCCCAGTCCACAAGCTCGAGAATCACGGACAAGGTAGTCAAACCTATAAATATTTGCAGACAT
TAAAAGTTGATGTTGTAAGATAAAGGTTCAAATTTACGCACCATGATGAGTGAAAAGGGAAAGA
AAGAAACTGCAGACAAGTATACAGGTAAAGAATTACTTGTCCACATCAATCCCATTTCGACCAT
TAGCAACAATATCATACAAGAAACGCTTCTCTGCATTGCCCTGCAAATTATGAAAAAGGGAAAA
TATATACAAAGCTTAAGTAGTTGTTCATGTTTGATTAGAATAGAGAACATACTTGTTATAAAAC
TTACTTTCAGCTGTGAAAATTCAGTACTAGCTAGTATCATGTCCTGGTCAGTTAACATTAGAGA
AAATCATCAGCAAAGAGACAAAGGAAGCAATAAATATTAAATTGGATTTGTAAAGACTGGAAAT
AATGTCACAATTTCCAGTTTCAAATAATAGAGGCCATTTGAGGGAAGCAAAACAGTCTTAAGAA
AGAAAGTTACCTTCACTCTTTTCAGCATTTGAGCATCAATATCGATGTGATGTGTATCAACCAT
ATGGTCAATCATGTTTACAGACATTAACTCATGAGACCTGCATCGAAGAATTGGCATATAAAGA
GCTAGAGATAATCCATAGAAGCCAACTACTAAAAGTTAAGGCATAGTTCTTATAATATCAAGTA
ACACCATGGCATTGATCTTTTCAAGGAATGTGCAAACATACCACTGACAGTCACTTATGACCTT
TGGAAGGAATTCACGCTCAAACATATGACTGAAAGGCCCATGGCCAATATCATGGAGAAGTCCT
ACACATACAAACAGATCAGAAATTGTATCAAGGAATAATGTAGTCATTGAGCTAATAATAGTTA
CCACTTACCAGCAAGTCTCACAGTCTGAAGATCATAATTGTCAATACCAAGCTCCATTCCCTAT
AGAAAGTTAAGCACGTACATTACAAACCTTACCATACTTAAATCAAAATGTGACTGCACCACTG
AAATCCAAATTAAAACCTGGAAATTTTTTAGCCTCTGAGCAGTTTCGCCTGCAAGCCAATACAC
GCCTAGAGAGTGCTCAAATCTCGAATGTACAGCTCCTGGATATACCATGTTTGTCACTC
						
					

			
		

Sequences
Splice junction sequence	TTTTTTAGCCTCTGAGCAGTTTCGCCTGCAAGCCAATACACGCCTAGAGAGTGCTCAAATCTCG AATGTACAGCTCCTGGATATACCATGTTTGTCACTCcatcacacgccttttctttttctcaggt gttgcgtgtacttgagctttgattccatacgttctcatttggaagttttcaaatgcctcagaaa ctgcttct
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	CATCACACGCCTTTTCTTTTTCTCAGGTGTTGCGTGTACTTGAGCTTTGATTCCATACGTTCTC ATTTGGAAGTTTTCAAATGCCTCAGAAACTGCTTCTACCTGTTGATCAATTTTGCAAACCAAAA ATAAAAACGTTACTTCGTGTGCATCACTAGAAACCATAATGTATTAAAGATTAATGAGGGTTAA TAATAATCACTTACCAATTCTGGTTTTTTGGCATATACTCTCACTATCATGTCTTGATATGTTG TTGGTAACAAGTGACTGACTCTGTCCTCAGGTATCACAAACTTCTCTGCACTATCATAATCCTG TAAACACCATATAAATCAATTTATTGAGATTCTGTGTTATTTTCCTCTTTACACATTTACAGAA GCAAATCTCAAAAACAAGACCAAAGACTTTTCTGTATGTACCTTATAGAAGTTGATGCTGAAGG AGCCAGATCCAACACAAAGGTAAGTTGGTTAGAATTTTAATGAGGGAAACTGAGAAAACAAAGA AGCTAAACTGTACTTTTTTTACCATTCAAGCGGATTTTCTCTCCCACGAGCCAAGTCAATCTTG ACGTTTGTAACAGCTATATCTTCTTCTTTTAGTGTCAAGCTTGTGTGCTTCTGTTAAATCAGAA AGCAATATAAGTATGGTAATGGACTGTACAATATACTTTTCCTCTATTTAAGTGCTAAAGATTG TACAAACCTGAGAACAGATGATATCTTGAGGAGTGACAGCTTTGAAATGATCGATTTTGTCCTT TGGAACCGCATATTCGTTACAGAACTGAAAGTCAAAATTCATACAGGTCAATCTTCTGAAGGGA AATTCTTAACCTAATTAAGCATAAAAGAAAAAGAAGAAACTGGGTGAAAATTTTATATACTTGG TACAACTGCCTTCTGCGAACACGGAGTATCAGCTCTTTCGCTTCTGCAAGTTCTGGATCTGGAG CTATTTCGATAGTTTTGAGGATTGTGTCGTCTAACTGCATTTGTTTATGGAGAACAAAAACTAT GTAAACAAGCAGAAAGGTAATATTTGTCTTCTGAGGAAGAACTGTACCTTCCAGTATTCAGATG GGTCATTAATCATAGAAGAAATTTCCAAATGATTGTTGGCTTTGACCATGGCATCTACTATCAT CAGCTCTATCGCCTGCAAATGAATGGAACGAGACAAGTGGGAAAGAGAGAAAGAATAGTCAAGG TACAGAGAGAATGATAATGGTATAATACCTTTACTTTCGAATGCGTGTAGACGGTTCGATAAAG ATCAGCTCGAGTTGCAAATAACTTGTGGACACTAAGATCTGAAAAATTAACCGGGTTTAAAATG GGATAGAAGCAAACGCAAATAGAGAATTTAGGTGGGCAAAACTTACACTCCTTGGCGCGGAAGC AGATTTCATTGTCCAGGACTCTCATCGTCTCTGTCAGTCTAGAAAGTTCTAATAATTAGCAATT TCCTTATTAGAAACCAGTGAAATGACTATAGAATAGAATGAAGACCTTTGGAATTGAAAATTGG ATCCCAGTCCACAAGCTCGAGAATCACGGACAAGGTAGTCAAACCTATAAATATTTGCAGACAT TAAAAGTTGATGTTGTAAGATAAAGGTTCAAATTTACGCACCATGATGAGTGAAAAGGGAAAGA AAGAAACTGCAGACAAGTATACAGGTAAAGAATTACTTGTCCACATCAATCCCATTTCGACCAT TAGCAACAATATCATACAAGAAACGCTTCTCTGCATTGCCCTGCAAATTATGAAAAAGGGAAAA TATATACAAAGCTTAAGTAGTTGTTCATGTTTGATTAGAATAGAGAACATACTTGTTATAAAAC TTACTTTCAGCTGTGAAAATTCAGTACTAGCTAGTATCATGTCCTGGTCAGTTAACATTAGAGA AAATCATCAGCAAAGAGACAAAGGAAGCAATAAATATTAAATTGGATTTGTAAAGACTGGAAAT AATGTCACAATTTCCAGTTTCAAATAATAGAGGCCATTTGAGGGAAGCAAAACAGTCTTAAGAA AGAAAGTTACCTTCACTCTTTTCAGCATTTGAGCATCAATATCGATGTGATGTGTATCAACCAT ATGGTCAATCATGTTTACAGACATTAACTCATGAGACCTGCATCGAAGAATTGGCATATAAAGA GCTAGAGATAATCCATAGAAGCCAACTACTAAAAGTTAAGGCATAGTTCTTATAATATCAAGTA ACACCATGGCATTGATCTTTTCAAGGAATGTGCAAACATACCACTGACAGTCACTTATGACCTT TGGAAGGAATTCACGCTCAAACATATGACTGAAAGGCCCATGGCCAATATCATGGAGAAGTCCT ACACATACAAACAGATCAGAAATTGTATCAAGGAATAATGTAGTCATTGAGCTAATAATAGTTA CCACTTACCAGCAAGTCTCACAGTCTGAAGATCATAATTGTCAATACCAAGCTCCATTCCCTAT AGAAAGTTAAGCACGTACATTACAAACCTTACCATACTTAAATCAAAATGTGACTGCACCACTG AAATCCAAATTAAAACCTGGAAATTTTTTAGCCTCTGAGCAGTTTCGCCTGCAAGCCAATACAC GCCTAGAGAGTGCTCAAATCTCGAATGTACAGCTCCTGGATATACCATGTTTGTCACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.137894834

Conservation Information
Conserved circRNAs	NA
PMCS	0.137894834

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							th-miR864-5p NA 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to methyl jasmonate

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	th-miR864-5p NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT5G40270_circ_g.1

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