Plant Circular RNA Database

Detail information of AT3G55020_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT3G55020_circ_g.9
					
						ID in PlantcircBase
						ath_circ_027595
					
						Alias
						3:20390983-20393082
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20390983-20393082  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G55020						
					
						Parent gene annotation
						
							Ypt/Rab-GAP domain of gyp1p superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G55020_circ_g.5 AT3G55020_circ_g.6 AT3G55020_circ_g.7 AT3G55020_circ_g.8 AT3G55020_circ_g.10 AT3G55020_circ_g.11 AT3G55020_circ_g.12 AT3G55020_circ_g.13 						
					
						Support reads
						1/1
					
						Tissues
						root;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
						AT3G55020.2:8
AT3G55020.3:8
AT3G55020.1:8

General Information
CircRNA Name	AT3G55020_circ_g.9
ID in PlantcircBase	ath_circ_027595
Alias	3:20390983-20393082
Organism	Arabidpsis thaliana
Position	chr3: 20390983-20393082 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G55020
Parent gene annotation	Ypt/Rab-GAP domain of gyp1p superfamily protein
Parent gene strand	-
Alternative splicing	AT3G55020_circ_g.5 AT3G55020_circ_g.6 AT3G55020_circ_g.7 AT3G55020_circ_g.8 AT3G55020_circ_g.10 AT3G55020_circ_g.11 AT3G55020_circ_g.12 AT3G55020_circ_g.13
Support reads	1/1
Tissues	root;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	AT3G55020.2:8 AT3G55020.3:8 AT3G55020.1:8

			
						 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  
						
							CCTCTTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTTGATAATAATCCTTGCA
TCGTCGTTTCCTCACGCCCACGAATGCTTGCCATAActgcgcttgaagatcttgaacagaatct
acctccccatccccagttaggctaaccaacacttcatctgcattacttgatcctgactcagatc
gagacaaa

									
								

					

						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: 1056
Transcript exons: 20390983-20391389,20391503-20391586,20391747-20391839,20
391923-20391974,20392065-20392131,20392506-20392564,2039
2682-20392795,20392903-20393082
CTGCGCTTGAAGATCTTGAACAGAATCTACCTCCCCATCCCCAGTTAGGCTAACCAACACTTCA
TCTGCATTACTTGATCCTGACTCAGATCGAGACAAACTCCCATTTGACAATGAGGCTTTGCTAT
CCACCAAAACAGATTTTGGGTCTTGCTTAAAATTATATAATTTGGAGGCAAGTCCCTTAGAATC
TCTCCACGCTTGAAGCCCCTTTGACCTTTCCTCAAGTGCAGCGATCACAGCTGGCCTATGCTTG
CTTCGCAATTCTTGCAATCTAATTTCATGTACATTTTGGTAACCCATGCAAGCAGTTAAAACTA
GCTGGCTGCTATCAAATGTTGATCCAGTCAGTGATTGTAGCAAAGTAACAGCGTCTCCAGCATC
CTTCGTAGTAACTAATGCAGGACCATATAGTTCCATCAATGCGAGTGCTGTTCTGAAAAGCATA
ACACGAGTTCCTTCAAAGAGAAGCACATCCCAGACTCTAAGAACACTTTCCCATGGAAGCATAT
TCATGAAGATGGAAAGAAACCATGGCCCTGTAACCCAAGCCACTTGCACTCCAAGATAATCCAG
ATGATGAACCAATTTAGGAAATCTTTCTCGAACTAACTCCTCCAGAACTAGTTGATCAACCTGA
GACTCTATCATTTCTTCTGAATAATAACCATTGAAGTAGTCATCAATGAGTCCTATCAGTGCCC
AAAAGGCATTTTCTTCTGGCATCAAAAGCAATAAAAGCGCAGCAAAGAAATTCATAGCCTGACA
GTATCCTACAGAAGGATTATGCCTAGCATAAGCAGTAAGCAAACGCCGTAGAGCATTTCTACCA
TCATCATCTAGAGCAGGATGACCAGGAAATGTCCGAGGTAAGTCCTTTTCTATCTGTCCTTTCC
ATTTTTCCACAACAGCAATAGATTCTGTACTTGAACCTTTATCATCAACATGCTGCATATCCTC
TTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTTGATAATAATCCTTGCATCGT
CGTTTCCTCACGCCCACGAATGCTTGCCATAA
						
					

						Genomic sequence
						
							CTGCGCTTGAAGATCTTGAACAGAATCTACCTCCCCATCCCCAGTTAGGCTAACCAACACTTCA
TCTGCATTACTTGATCCTGACTCAGATCGAGACAAACTCCCATTTGACAATGAGGCTTTGCTAT
CCACCAAAACAGATTTTGGGTCTTGCTTAAAATTATATAATTTGGAGGCAAGTCCCTTAGAATC
TCTCCACGCTTGAAGCCCCTTTGACCTTTCCTCAAGTGCAGCGATCACAGCTGGCCTATGCTTG
CTTCGCAATTCTTGCAATCTAATTTCATGTACATTTTGGTAACCCATGCAAGCAGTTAAAACTA
GCTGGCTGCTATCAAATGTTGATCCAGTCAGTGATTGTAGCAAAGTAACAGCGTCTCCAGCATC
CTTCGTAGTAACTAATGCAGGACCTGAAGTGAATTAAACCATAAGTTAGAGCAGTCTCGATGAT
GACGCCACTGCGTTCAGAAGGTCCACAAACCATCTCACTTAAATTGAAAGACCAGCAGTTTCAA
TCAAGTACCATATAGTTCCATCAATGCGAGTGCTGTTCTGAAAAGCATAACACGAGTTCCTTCA
AAGAGAAGCACATCCCAGACTCTAAGAACTGTGATCAAGAAGACGAACATTTAGAAAGAAAATG
GGTTCTCAGTCCCAAATCTCAAAGAGAAAGATGATCAAATTTTAACAGATTGCCAGCATAATTT
ACTAGTTACTCAATTCTATTTCAAACAAGACAGCTTTAATTCCAATGTTTAAAACCTGACCACT
TTCCCATGGAAGCATATTCATGAAGATGGAAAGAAACCATGGCCCTGTAACCCAAGCCACTTGC
ACTCCAAGATAATCCAGATGATGAACTGTAGACATAGAAAAGTTGCAGAGCTTAGTACTAACTG
TGAACATTCTACAAGATGAAACAAAAAACTTTGAGGGAACTCACCCAATTTAGGAAATCTTTCT
CGAACTAACTCCTCCAGAACTAGTTGATCAACCTAAAATATGAAGGTACATGTTGTCATGATGC
TATCACCAGTCAGCCCAAAATTTTTGCAAATGTATAGAAAGGCAACTAATATTATCACCTGAGA
CTCTATCATTTCTTCTGAATAATAACCATTGAAGTAGTCATCAATGAGTCCTATCAGTGCCCTA
AAAATCACAAGTATTTAATTAGAAGGGGCATCAGTTTAGAAAGAAAAAAGGAGAAGATATAAGG
ATGCTTAATAACAGTTTGATCAACCATGAGAATATGAAAGTGATAGATATTAAAACTAAACACA
GAGCAAGGAGTTCATGTTTAGACAGAAAAATAAGATTAGGAATGAAAAAAGTAGATTAATCAAA
CAACATTGGTTAAATTAGAAATAAGGATACAGAGAATGACCCAAGAACAGTTAATGTTTGGAAG
AAGGAAGGCGATATAACACAAACTAAACAGTAAACACAGATCAAAAGAGTTCGATTTTCACAGG
AAATAATATTAGGACTTGGAGATGATAAATTCATCAAATTTGTGAACATACCAAAAGGCATTTT
CTTCTGGCATCAAAAGCAATAAAAGCGCAGCAAAGAAATTCATAGCCTGCAGAAAGTATATTGA
CAAAAGATATTAACTTGATATTAATGTTAATTTACTATGTCTCGGTACTAAAATAGAGGTACTA
CAATAAAGATCATGATATTGGTTAAGAACAAATACCTGACAGTATCCTACAGAAGGATTATGCC
TAGCATAAGCAGTAAGCAAACGCCGTAGAGCATTTCTACCATCATCATCTAGAGCAGGATGACC
AGGAAATGTCCGAGGTAAGTCCTGTACTTTAAACAAGCAACGGCATAAGAATCCTGATCAACTT
CAGCATAAGCCACGCTGCATCACTACATAGAGAGGGTCAAGGCTGAATAAATTTTGAGTACTAC
CTTTTCTATCTGTCCTTTCCATTTTTCCACAACAGCAATAGATTCTGTACTTGAACCTTTATCA
TCAACATGCTGCATATCCTCTTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTT
GATAATAATCCTTGCATCGTCGTTTCCTCACGCCCACGAATGCTTGCCATAA
						
					

			
		

Sequences
Splice junction sequence	CCTCTTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTTGATAATAATCCTTGCA TCGTCGTTTCCTCACGCCCACGAATGCTTGCCATAActgcgcttgaagatcttgaacagaatct acctccccatccccagttaggctaaccaacacttcatctgcattacttgatcctgactcagatc gagacaaa
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: 1056 Transcript exons: 20390983-20391389,20391503-20391586,20391747-20391839,20 391923-20391974,20392065-20392131,20392506-20392564,2039 2682-20392795,20392903-20393082 CTGCGCTTGAAGATCTTGAACAGAATCTACCTCCCCATCCCCAGTTAGGCTAACCAACACTTCA TCTGCATTACTTGATCCTGACTCAGATCGAGACAAACTCCCATTTGACAATGAGGCTTTGCTAT CCACCAAAACAGATTTTGGGTCTTGCTTAAAATTATATAATTTGGAGGCAAGTCCCTTAGAATC TCTCCACGCTTGAAGCCCCTTTGACCTTTCCTCAAGTGCAGCGATCACAGCTGGCCTATGCTTG CTTCGCAATTCTTGCAATCTAATTTCATGTACATTTTGGTAACCCATGCAAGCAGTTAAAACTA GCTGGCTGCTATCAAATGTTGATCCAGTCAGTGATTGTAGCAAAGTAACAGCGTCTCCAGCATC CTTCGTAGTAACTAATGCAGGACCATATAGTTCCATCAATGCGAGTGCTGTTCTGAAAAGCATA ACACGAGTTCCTTCAAAGAGAAGCACATCCCAGACTCTAAGAACACTTTCCCATGGAAGCATAT TCATGAAGATGGAAAGAAACCATGGCCCTGTAACCCAAGCCACTTGCACTCCAAGATAATCCAG ATGATGAACCAATTTAGGAAATCTTTCTCGAACTAACTCCTCCAGAACTAGTTGATCAACCTGA GACTCTATCATTTCTTCTGAATAATAACCATTGAAGTAGTCATCAATGAGTCCTATCAGTGCCC AAAAGGCATTTTCTTCTGGCATCAAAAGCAATAAAAGCGCAGCAAAGAAATTCATAGCCTGACA GTATCCTACAGAAGGATTATGCCTAGCATAAGCAGTAAGCAAACGCCGTAGAGCATTTCTACCA TCATCATCTAGAGCAGGATGACCAGGAAATGTCCGAGGTAAGTCCTTTTCTATCTGTCCTTTCC ATTTTTCCACAACAGCAATAGATTCTGTACTTGAACCTTTATCATCAACATGCTGCATATCCTC TTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTTGATAATAATCCTTGCATCGT CGTTTCCTCACGCCCACGAATGCTTGCCATAA
Genomic sequence	CTGCGCTTGAAGATCTTGAACAGAATCTACCTCCCCATCCCCAGTTAGGCTAACCAACACTTCA TCTGCATTACTTGATCCTGACTCAGATCGAGACAAACTCCCATTTGACAATGAGGCTTTGCTAT CCACCAAAACAGATTTTGGGTCTTGCTTAAAATTATATAATTTGGAGGCAAGTCCCTTAGAATC TCTCCACGCTTGAAGCCCCTTTGACCTTTCCTCAAGTGCAGCGATCACAGCTGGCCTATGCTTG CTTCGCAATTCTTGCAATCTAATTTCATGTACATTTTGGTAACCCATGCAAGCAGTTAAAACTA GCTGGCTGCTATCAAATGTTGATCCAGTCAGTGATTGTAGCAAAGTAACAGCGTCTCCAGCATC CTTCGTAGTAACTAATGCAGGACCTGAAGTGAATTAAACCATAAGTTAGAGCAGTCTCGATGAT GACGCCACTGCGTTCAGAAGGTCCACAAACCATCTCACTTAAATTGAAAGACCAGCAGTTTCAA TCAAGTACCATATAGTTCCATCAATGCGAGTGCTGTTCTGAAAAGCATAACACGAGTTCCTTCA AAGAGAAGCACATCCCAGACTCTAAGAACTGTGATCAAGAAGACGAACATTTAGAAAGAAAATG GGTTCTCAGTCCCAAATCTCAAAGAGAAAGATGATCAAATTTTAACAGATTGCCAGCATAATTT ACTAGTTACTCAATTCTATTTCAAACAAGACAGCTTTAATTCCAATGTTTAAAACCTGACCACT TTCCCATGGAAGCATATTCATGAAGATGGAAAGAAACCATGGCCCTGTAACCCAAGCCACTTGC ACTCCAAGATAATCCAGATGATGAACTGTAGACATAGAAAAGTTGCAGAGCTTAGTACTAACTG TGAACATTCTACAAGATGAAACAAAAAACTTTGAGGGAACTCACCCAATTTAGGAAATCTTTCT CGAACTAACTCCTCCAGAACTAGTTGATCAACCTAAAATATGAAGGTACATGTTGTCATGATGC TATCACCAGTCAGCCCAAAATTTTTGCAAATGTATAGAAAGGCAACTAATATTATCACCTGAGA CTCTATCATTTCTTCTGAATAATAACCATTGAAGTAGTCATCAATGAGTCCTATCAGTGCCCTA AAAATCACAAGTATTTAATTAGAAGGGGCATCAGTTTAGAAAGAAAAAAGGAGAAGATATAAGG ATGCTTAATAACAGTTTGATCAACCATGAGAATATGAAAGTGATAGATATTAAAACTAAACACA GAGCAAGGAGTTCATGTTTAGACAGAAAAATAAGATTAGGAATGAAAAAAGTAGATTAATCAAA CAACATTGGTTAAATTAGAAATAAGGATACAGAGAATGACCCAAGAACAGTTAATGTTTGGAAG AAGGAAGGCGATATAACACAAACTAAACAGTAAACACAGATCAAAAGAGTTCGATTTTCACAGG AAATAATATTAGGACTTGGAGATGATAAATTCATCAAATTTGTGAACATACCAAAAGGCATTTT CTTCTGGCATCAAAAGCAATAAAAGCGCAGCAAAGAAATTCATAGCCTGCAGAAAGTATATTGA CAAAAGATATTAACTTGATATTAATGTTAATTTACTATGTCTCGGTACTAAAATAGAGGTACTA CAATAAAGATCATGATATTGGTTAAGAACAAATACCTGACAGTATCCTACAGAAGGATTATGCC TAGCATAAGCAGTAAGCAAACGCCGTAGAGCATTTCTACCATCATCATCTAGAGCAGGATGACC AGGAAATGTCCGAGGTAAGTCCTGTACTTTAAACAAGCAACGGCATAAGAATCCTGATCAACTT CAGCATAAGCCACGCTGCATCACTACATAGAGAGGGTCAAGGCTGAATAAATTTTGAGTACTAC CTTTTCTATCTGTCCTTTCCATTTTTCCACAACAGCAATAGATTCTGTACTTGAACCTTTATCA TCAACATGCTGCATATCCTCTTGCTCTATGGTGTTTACAGAACCATCTGCTGCAAGAAGGTTTT GATAATAATCCTTGCATCGTCGTTTCCTCACGCCCACGAATGCTTGCCATAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.226369102

Conservation Information
Conserved circRNAs	NA
PMCS	0.226369102

			
						 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 AT3G55020_circ_g.9

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