Plant Circular RNA Database

Detail information of AT5G54090_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G54090_circ_g.2
					
						ID in PlantcircBase
						ath_circ_044026
					
						Alias
						5:21950145-21951346
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 21950145-21951346  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G54090						
					
						Parent gene annotation
						
							DNA mismatch repair protein MutS, type 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							ENSRNA049493778_circ_g.1 ENSRNA049493778_circ_g.2 AT5G53740_circ_g.1 5_circ_ag.2 5_circ_ag.3 AT5G53740_circ_g.4 AT5G53740_circ_g.5 5_circ_ag.6 AT5G53760_circ_g.1 AT5G53770_circ_g.1 AT5G53770_circ_g.2 5_circ_ig.3 AT5G53850_circ_g.1 AT5G53850_circ_g.2 AT5G53850_circ_g.3 AT5G53850_circ_g.4 AT5G53850_circ_g.5 AT5G53860_circ_g.1 AT5G53860_circ_g.2 AT5G53860_circ_g.3 AT5G53860_circ_g.4 AT5G53860_circ_g.5 AT5G53860_circ_g.6 AT5G53860_circ_g.7 AT5G53860_circ_g.8 AT5G53860_circ_g.9 AT5G53860_circ_g.10 AT5G53860_circ_g.11 AT5G53880_circ_g.1 AT5G53905_circ_g.1 5_circ_ag.2 AT5G53905_circ_g.3 5_circ_ag.4 AT5G53920_circ_g.1 AT5G53940_circ_g.1 AT5G53940_circ_g.2 AT5G53970_circ_g.1 AT5G53970_circ_g.2 AT5G54000_circ_g.1 AT5G54060_circ_g.1 ENSRNA049493776_circ_g.1 ENSRNA049493776_circ_g.2 ENSRNA049493776_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 AT5G54080_circ_g.1 AT5G54080_circ_g.2 AT5G54080_circ_g.3 AT5G54080_circ_g.4 AT5G54090_circ_g.1 AT5G54090_circ_g.3 AT5G54090_circ_g.4 AT5G54100_circ_g.1 AT5G54130_circ_g.1 AT5G54130_circ_g.2 AT5G54130_circ_g.3 AT5G54130_circ_g.4 AT5G54130_circ_g.5 AT5G54160_circ_g.1 AT5G54160_circ_g.2 AT5G54170_circ_g.1 ENSRNA049493783_circ_g.1 ENSRNA049493783_circ_g.2 ENSRNA049493783_circ_g.3 ENSRNA049493783_circ_g.4 						
					
						Support reads
						1/1
					
						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
						AT5G54090.1:5

General Information
CircRNA Name	AT5G54090_circ_g.2
ID in PlantcircBase	ath_circ_044026
Alias	5:21950145-21951346
Organism	Arabidpsis thaliana
Position	chr5: 21950145-21951346 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G54090
Parent gene annotation	DNA mismatch repair protein MutS, type 2
Parent gene strand	-
Alternative splicing	ENSRNA049493778_circ_g.1 ENSRNA049493778_circ_g.2 AT5G53740_circ_g.1 5_circ_ag.2 5_circ_ag.3 AT5G53740_circ_g.4 AT5G53740_circ_g.5 5_circ_ag.6 AT5G53760_circ_g.1 AT5G53770_circ_g.1 AT5G53770_circ_g.2 5_circ_ig.3 AT5G53850_circ_g.1 AT5G53850_circ_g.2 AT5G53850_circ_g.3 AT5G53850_circ_g.4 AT5G53850_circ_g.5 AT5G53860_circ_g.1 AT5G53860_circ_g.2 AT5G53860_circ_g.3 AT5G53860_circ_g.4 AT5G53860_circ_g.5 AT5G53860_circ_g.6 AT5G53860_circ_g.7 AT5G53860_circ_g.8 AT5G53860_circ_g.9 AT5G53860_circ_g.10 AT5G53860_circ_g.11 AT5G53880_circ_g.1 AT5G53905_circ_g.1 5_circ_ag.2 AT5G53905_circ_g.3 5_circ_ag.4 AT5G53920_circ_g.1 AT5G53940_circ_g.1 AT5G53940_circ_g.2 AT5G53970_circ_g.1 AT5G53970_circ_g.2 AT5G54000_circ_g.1 AT5G54060_circ_g.1 ENSRNA049493776_circ_g.1 ENSRNA049493776_circ_g.2 ENSRNA049493776_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 AT5G54080_circ_g.1 AT5G54080_circ_g.2 AT5G54080_circ_g.3 AT5G54080_circ_g.4 AT5G54090_circ_g.1 AT5G54090_circ_g.3 AT5G54090_circ_g.4 AT5G54100_circ_g.1 AT5G54130_circ_g.1 AT5G54130_circ_g.2 AT5G54130_circ_g.3 AT5G54130_circ_g.4 AT5G54130_circ_g.5 AT5G54160_circ_g.1 AT5G54160_circ_g.2 AT5G54170_circ_g.1 ENSRNA049493783_circ_g.1 ENSRNA049493783_circ_g.2 ENSRNA049493783_circ_g.3 ENSRNA049493783_circ_g.4
Support reads	1/1
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	AT5G54090.1:5

			
						 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  
						
							TAAAAATTCAAGTTTACCTGGAAAGCAGAAGACCATTAACAGAAGTTAGCTGATTTGAGCTCAT
TTGTATACACCATCTTCCATCAATTTCAGCCGCTAAccgattttgccatcatcgcagcgagccc
aactgatttcaagcaaatggttttacctcctgtgtttggaccggtaataaccaaaactctagtg
cccttaga

									
								

					

						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: 667
Transcript exons: 21950145-21950295,21950380-21950628,21950751-21950810,21
950965-21951088,21951264-21951346
CCGATTTTGCCATCATCGCAGCGAGCCCAACTGATTTCAAGCAAATGGTTTTACCTCCTGTGTT
TGGACCGGTAATAACCAAAACTCTAGTGCCCTTAGAGATCTGGAAATCAGCCGGAATTGGTGGA
GCTCCTGATAATACAGTGTCTGCTGTTTTATGAAATTTTACCGTCTCCCGCGTCTTTCTTATGC
CTTTCTTGTGTTGGTAAAGCAATAGAGGATGATAACATCTAGGTAGATACAGCAACCATTCTTT
TTTAGAAAGCGGTTTCTCACTCGGTAAGTTAATATCCGGCGAGTTTTCTCCAGCAGACAAAGAT
TCAACCTCATCTTCAGGTGGCAAGTATATATCAGGATGTGCACCACCATATGCACGACTGTAAG
TTGCTCGAGCGTTTATCACATCCAGCTGAATCGAGTAGCTCAACACCACCTCGATTTGACAAAG
ACCATCTTGCATCTTTTCAGTTAACATTGAAAGAATCTCTGCCTCAGCCTTTGCAACTGATGCT
CTCGCACTTTGAAGGTCATCATTCATAGACACCGCAGCTATTGGCTCCGCCGCAGTCCCTCCAC
CTGAACCACTGGAAAGCAGAAGACCATTAACAGAAGTTAGCTGATTTGAGCTCATTTGTATACA
CCATCTTCCATCAATTTCAGCCGCTAA
						
					

						Genomic sequence
						
							CCGATTTTGCCATCATCGCAGCGAGCCCAACTGATTTCAAGCAAATGGTTTTACCTCCTGTGTT
TGGACCGGTAATAACCAAAACTCTAGTGCCCTTAGAGATCTGGAAATCAGCCGGAATTGGTGGA
GCTCCTGATAATACAGTGTCTGCCTATAAATATAACCATGTATATATTAACTTCAGCTAAAATG
CATCATCAATCGACTCTATGATCATAACATCTGACGAACTTACTGTTTTATGAAATTTTACCGT
CTCCCGCGTCTTTCTTATGCCTTTCTTGTGTTGGTAAAGCAATAGAGGATGATAACATCTAGGT
AGATACAGCAACCATTCTTTTTTAGAAAGCGGTTTCTCACTCGGTAAGTTAATATCCGGCGAGT
TTTCTCCAGCAGACAAAGATTCAACCTCATCTTCAGGTGGCAAGTATATATCAGGATGTGCACC
ACCATATGCACGACTGTAAGTTGCTCGAGCGTTTATCTAGCCAGAAAAGAAAAAAAAAAACTGT
AAACCACATGTTTGGAAGCTCATGTTGCTGAGATTTGTTTTACTGAGTTTTGCTTTAATAGAAA
GAGAAATGATTGGTATTAAAGTATAATTACCACATCCAGCTGAATCGAGTAGCTCAACACCACC
TCGATTTGACAAAGACCATCTTGCATCTGTTTTGCTTGCATCAAAATGAACAAAAATGTCAACA
AGCAGAAAACAATAAGAAGGAAAGTTACAGAATTCTAACTTTAAAAATTAATACACTTTTCATC
AAAATGAACAAAAATGTCAACAAGCAGAAAACAATAAGCAGAAAACAATTACCTTTTCAGTTAA
CATTGAAAGAATCTCTGCCTCAGCCTTTGCAACTGATGCTCTCGCACTTTGAAGGTCATCATTC
ATAGACACCGCAGCTATTGGCTCCGCCGCAGTCCCTCCACCTGAACCACTGAAACACATATTAT
CTTCAAGAGATAGAACTTGAAAATAAACACTAAAAGAGAAGCATAACTTCTCAATAACTTGGAA
AATGGTAATGAACTCTTGTTAATAAATCATTGATAAATTGCAAACCAAAATTCTGAATCTTCTT
TGGTAACTTAAATCTAAAAATTCAAGTTTACCTGGAAAGCAGAAGACCATTAACAGAAGTTAGC
TGATTTGAGCTCATTTGTATACACCATCTTCCATCAATTTCAGCCGCTAA
						
					

			
		

Sequences
Splice junction sequence	TAAAAATTCAAGTTTACCTGGAAAGCAGAAGACCATTAACAGAAGTTAGCTGATTTGAGCTCAT TTGTATACACCATCTTCCATCAATTTCAGCCGCTAAccgattttgccatcatcgcagcgagccc aactgatttcaagcaaatggttttacctcctgtgtttggaccggtaataaccaaaactctagtg cccttaga
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: 667 Transcript exons: 21950145-21950295,21950380-21950628,21950751-21950810,21 950965-21951088,21951264-21951346 CCGATTTTGCCATCATCGCAGCGAGCCCAACTGATTTCAAGCAAATGGTTTTACCTCCTGTGTT TGGACCGGTAATAACCAAAACTCTAGTGCCCTTAGAGATCTGGAAATCAGCCGGAATTGGTGGA GCTCCTGATAATACAGTGTCTGCTGTTTTATGAAATTTTACCGTCTCCCGCGTCTTTCTTATGC CTTTCTTGTGTTGGTAAAGCAATAGAGGATGATAACATCTAGGTAGATACAGCAACCATTCTTT TTTAGAAAGCGGTTTCTCACTCGGTAAGTTAATATCCGGCGAGTTTTCTCCAGCAGACAAAGAT TCAACCTCATCTTCAGGTGGCAAGTATATATCAGGATGTGCACCACCATATGCACGACTGTAAG TTGCTCGAGCGTTTATCACATCCAGCTGAATCGAGTAGCTCAACACCACCTCGATTTGACAAAG ACCATCTTGCATCTTTTCAGTTAACATTGAAAGAATCTCTGCCTCAGCCTTTGCAACTGATGCT CTCGCACTTTGAAGGTCATCATTCATAGACACCGCAGCTATTGGCTCCGCCGCAGTCCCTCCAC CTGAACCACTGGAAAGCAGAAGACCATTAACAGAAGTTAGCTGATTTGAGCTCATTTGTATACA CCATCTTCCATCAATTTCAGCCGCTAA
Genomic sequence	CCGATTTTGCCATCATCGCAGCGAGCCCAACTGATTTCAAGCAAATGGTTTTACCTCCTGTGTT TGGACCGGTAATAACCAAAACTCTAGTGCCCTTAGAGATCTGGAAATCAGCCGGAATTGGTGGA GCTCCTGATAATACAGTGTCTGCCTATAAATATAACCATGTATATATTAACTTCAGCTAAAATG CATCATCAATCGACTCTATGATCATAACATCTGACGAACTTACTGTTTTATGAAATTTTACCGT CTCCCGCGTCTTTCTTATGCCTTTCTTGTGTTGGTAAAGCAATAGAGGATGATAACATCTAGGT AGATACAGCAACCATTCTTTTTTAGAAAGCGGTTTCTCACTCGGTAAGTTAATATCCGGCGAGT TTTCTCCAGCAGACAAAGATTCAACCTCATCTTCAGGTGGCAAGTATATATCAGGATGTGCACC ACCATATGCACGACTGTAAGTTGCTCGAGCGTTTATCTAGCCAGAAAAGAAAAAAAAAAACTGT AAACCACATGTTTGGAAGCTCATGTTGCTGAGATTTGTTTTACTGAGTTTTGCTTTAATAGAAA GAGAAATGATTGGTATTAAAGTATAATTACCACATCCAGCTGAATCGAGTAGCTCAACACCACC TCGATTTGACAAAGACCATCTTGCATCTGTTTTGCTTGCATCAAAATGAACAAAAATGTCAACA AGCAGAAAACAATAAGAAGGAAAGTTACAGAATTCTAACTTTAAAAATTAATACACTTTTCATC AAAATGAACAAAAATGTCAACAAGCAGAAAACAATAAGCAGAAAACAATTACCTTTTCAGTTAA CATTGAAAGAATCTCTGCCTCAGCCTTTGCAACTGATGCTCTCGCACTTTGAAGGTCATCATTC ATAGACACCGCAGCTATTGGCTCCGCCGCAGTCCCTCCACCTGAACCACTGAAACACATATTAT CTTCAAGAGATAGAACTTGAAAATAAACACTAAAAGAGAAGCATAACTTCTCAATAACTTGGAA AATGGTAATGAACTCTTGTTAATAAATCATTGATAAATTGCAAACCAAAATTCTGAATCTTCTT TGGTAACTTAAATCTAAAAATTCAAGTTTACCTGGAAAGCAGAAGACCATTAACAGAAGTTAGC TGATTTGAGCTCATTTGTATACACCATCTTCCATCAATTTCAGCCGCTAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.195421608

Conservation Information
Conserved circRNAs	NA
PMCS	0.195421608

			
						 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 AT5G54090_circ_g.2

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