Plant Circular RNA Database

Detail information of AT3G55440_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G55440_circ_g.5
					
						ID in PlantcircBase
						ath_circ_027644
					
						Alias
						3:20554160-20555767
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20554160-20555767  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G55440						
					
						Parent gene annotation
						
							Triosephosphate isomerase, cytosolic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G55440_circ_g.2 AT3G55440_circ_g.3 AT3G55440_circ_g.4 AT3G55440_circ_g.6 AT3G55440_circ_g.7 AT3G55440_circ_g.8 AT3G55440_circ_g.9 AT3G55440_circ_g.10 AT3G55440_circ_g.11 AT3G55440_circ_g.12 AT3G55440_circ_g.13 AT3G55440_circ_g.14 AT3G55440_circ_g.15 3_circ_ag.16 AT3G55440_circ_g.17 AT3G55440_circ_g.18 AT3G55440_circ_g.19 AT3G55450_circ_g.1 AT3G55450_circ_g.2 AT3G55450_circ_g.3 AT3G55460_circ_g.1 AT3G55460_circ_g.2 AT3G55460_circ_g.3 AT3G55460_circ_g.4 AT3G55460_circ_g.5 AT3G55460_circ_g.6 AT3G55460_circ_g.7 AT3G55470_circ_g.1 AT3G55470_circ_g.2 AT3G55480_circ_g.1 AT3G55480_circ_g.2 AT3G55480_circ_g.3 AT3G55480_circ_g.4 ENSRNA049493723_circ_g.1 AT3G55490_circ_g.1 AT3G55510_circ_g.1 AT3G55510_circ_g.2 AT3G55530_circ_g.1 AT3G55530_circ_g.2 AT3G55530_circ_g.3 AT3G55580_circ_g.1 AT3G55580_circ_g.2 AT3G55600_circ_g.1 AT3G55610_circ_g.1 AT3G55610_circ_g.2 AT3G55610_circ_g.3 AT3G55610_circ_g.4 AT3G55610_circ_g.5 AT3G55610_circ_g.6 AT3G55610_circ_g.7 AT3G55610_circ_g.8 AT3G55610_circ_g.9 AT3G55610_circ_g.10 AT3G55610_circ_g.11 AT3G55610_circ_g.12 AT3G55610_circ_g.13 AT3G55610_circ_g.14 AT3G55620_circ_g.1 AT3G55620_circ_g.2 AT3G55620_circ_g.3 AT3G55630_circ_g.1 AT3G55630_circ_g.2 AT3G55630_circ_g.3 AT3G55630_circ_g.4 AT3G55630_circ_g.5 AT3G55630_circ_g.6 AT3G55630_circ_g.7 AT3G55630_circ_g.8 AT3G55630_circ_g.9 AT3G55630_circ_g.10 AT3G55630_circ_g.11 AT3G55630_circ_g.12 AT3G55630_circ_g.13 AT3G55630_circ_g.14 AT3G55640_circ_g.1 AT3G55640_circ_g.2 AT3G55660_circ_g.1 AT3G55660_circ_g.2 AT3G55660_circ_g.3 						
					
						Support reads
						1/1
					
						Tissues
						seedling
					
						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  
						
							GT-AG							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
						AT3G55440.1:6

General Information
CircRNA Name	AT3G55440_circ_g.5
ID in PlantcircBase	ath_circ_027644
Alias	3:20554160-20555767
Organism	Arabidpsis thaliana
Position	chr3: 20554160-20555767 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G55440
Parent gene annotation	Triosephosphate isomerase, cytosolic
Parent gene strand	+
Alternative splicing	AT3G55440_circ_g.2 AT3G55440_circ_g.3 AT3G55440_circ_g.4 AT3G55440_circ_g.6 AT3G55440_circ_g.7 AT3G55440_circ_g.8 AT3G55440_circ_g.9 AT3G55440_circ_g.10 AT3G55440_circ_g.11 AT3G55440_circ_g.12 AT3G55440_circ_g.13 AT3G55440_circ_g.14 AT3G55440_circ_g.15 3_circ_ag.16 AT3G55440_circ_g.17 AT3G55440_circ_g.18 AT3G55440_circ_g.19 AT3G55450_circ_g.1 AT3G55450_circ_g.2 AT3G55450_circ_g.3 AT3G55460_circ_g.1 AT3G55460_circ_g.2 AT3G55460_circ_g.3 AT3G55460_circ_g.4 AT3G55460_circ_g.5 AT3G55460_circ_g.6 AT3G55460_circ_g.7 AT3G55470_circ_g.1 AT3G55470_circ_g.2 AT3G55480_circ_g.1 AT3G55480_circ_g.2 AT3G55480_circ_g.3 AT3G55480_circ_g.4 ENSRNA049493723_circ_g.1 AT3G55490_circ_g.1 AT3G55510_circ_g.1 AT3G55510_circ_g.2 AT3G55530_circ_g.1 AT3G55530_circ_g.2 AT3G55530_circ_g.3 AT3G55580_circ_g.1 AT3G55580_circ_g.2 AT3G55600_circ_g.1 AT3G55610_circ_g.1 AT3G55610_circ_g.2 AT3G55610_circ_g.3 AT3G55610_circ_g.4 AT3G55610_circ_g.5 AT3G55610_circ_g.6 AT3G55610_circ_g.7 AT3G55610_circ_g.8 AT3G55610_circ_g.9 AT3G55610_circ_g.10 AT3G55610_circ_g.11 AT3G55610_circ_g.12 AT3G55610_circ_g.13 AT3G55610_circ_g.14 AT3G55620_circ_g.1 AT3G55620_circ_g.2 AT3G55620_circ_g.3 AT3G55630_circ_g.1 AT3G55630_circ_g.2 AT3G55630_circ_g.3 AT3G55630_circ_g.4 AT3G55630_circ_g.5 AT3G55630_circ_g.6 AT3G55630_circ_g.7 AT3G55630_circ_g.8 AT3G55630_circ_g.9 AT3G55630_circ_g.10 AT3G55630_circ_g.11 AT3G55630_circ_g.12 AT3G55630_circ_g.13 AT3G55630_circ_g.14 AT3G55640_circ_g.1 AT3G55640_circ_g.2 AT3G55660_circ_g.1 AT3G55660_circ_g.2 AT3G55660_circ_g.3
Support reads	1/1
Tissues	seedling
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	GT-AG 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	AT3G55440.1:6

			
						 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  
						
							GCTTGTTTCGTTTATGAACAGGTACACGATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTG
CTGATGTCGCTGCTACAACCCGCATCATTTATGGAGaacggaactgctgaggaggtgaagaaga
ttgtgaacactcttaatgaagctcaggttccttcacaggatgttgtaggtatgtgtagcatctc
aattgctt

									
								

					

						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: 592
Transcript exons: 20554160-20554235,20554526-20554649,20554994-20555078,20
555173-20555305,20555484-20555578,20555689-20555767
AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC
AGGATGTTGTAGAGGTTGTGGTTAGCCCTCCATATGTTTTTCTTCCCCTGGTTAAGAGCACATT
GAGGTCTGACTTTTTTGTTGCGGCACAAAACTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGT
GAAGTGAGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAA
GGAGGGCAATCCTTAATGAATCAAGCGAGTTCGTCGGAGACAAGGTTGCCTATGCACTTGCTCA
AGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCATG
GATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGATCGGGTGACAAACTGGTCAAATGTTGTCA
TAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGA
AGTACACGATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTGCTGATGTCGCTGCTACAACC
CGCATCATTTATGGAG
						
					

						Genomic sequence
						
							AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC
AGGATGTTGTAGGTATGTGTAGCATCTCAATTGCTTTGACGACATTATGGCTTTTTTTTTAATT
TCCATGTCTATGAAATCTTAAGTAGTGACAAATATTTTGGGCATACAATTACAAACCTGTTTCA
ATGTACATCGATGTTCTATAGTGTTTATGCTTCTTAGGAACCATGGATAGATCTAGTGTTTGTT
GTTAGTTAAAATGTTCTTTATCATATACTTGTTATGGTTCTATCTTTGTTGATAGTTATAAGTA
TGTTTGTTCTTGTATTAATAATTTGATGAAATTTTACTAAATGCAGAGGTTGTGGTTAGCCCTC
CATATGTTTTTCTTCCCCTGGTTAAGAGCACATTGAGGTCTGACTTTTTTGTTGCGGCACAAAA
CTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGTGAAGTGAGGTGAGATTCTAACCATTGGTGT
ATACTTTAAGCTGTTTTACCATTATTGCTTCATGCAGTAAATATTTATGGTTTTGAAAATGAAT
ATGATTGTGTTTATAAACGAATCGATTTTTCCATCTGTTCTTCTTCTTTATCTTCTTTCCTATA
AGAATTGTGTAACCTAAGTGATTAAGAAAACAACTAGTAGTTGGTAGTAAGACCATGATTGGAT
TCGTGCCTGGTTAGACAAGTAGGTGTAATATGATTTACCTGTCTATGGAATGCTTTCATAGGAA
GAAAAGATATATTCTGTGGTGCCTGTATTTCCTGCTCTTATGCATTGTGTAATTTGTGTGTTTT
AGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAAGGAGGG
CAATCCTTAATGAATCAAGCGAGGTTGGTGACTTTACATGATAAAATAATTTTCTGGAGACTCA
AATAGCTTTTAAATTCATGATTTTGGTTTTTGACCTCTATCCTACATTTGTAGTTCGTCGGAGA
CAAGGTTGCCTATGCACTTGCTCAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAG
GAGCGGGAAGCTGGATCGACCATGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGGTATGT
ATATTGTCAAACATTTAATCTCTTTTTGCTATCTCAGTTCGTTCTCGTTTACAGTGAGACCTGT
TTTGATGATAGTGATGCCCGTTTCTACGCACTATACTCCCTTAGTGTGTGATTCAAACCCCACA
GAAATATTTGTTGGCTAAAAAACTCTTTTTGTTGGTAATGGCAGATCGGGTGACAAACTGGTCA
AATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCC
AAGCTCAAGAAGTAAGTGGTTCTCGATGCGCAGTTGCACTGTAACGTGTTGCATATGGTCATGA
TTTAATAGGAAAACCAATGCTGTTTTCCTTACGAGAGCTTGTTTCGTTTATGAACAGGTACACG
ATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTGCTGATGTCGCTGCTACAACCCGCATCAT
TTATGGAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGTTTCGTTTATGAACAGGTACACGATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTG CTGATGTCGCTGCTACAACCCGCATCATTTATGGAGaacggaactgctgaggaggtgaagaaga ttgtgaacactcttaatgaagctcaggttccttcacaggatgttgtaggtatgtgtagcatctc aattgctt
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: 592 Transcript exons: 20554160-20554235,20554526-20554649,20554994-20555078,20 555173-20555305,20555484-20555578,20555689-20555767 AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC AGGATGTTGTAGAGGTTGTGGTTAGCCCTCCATATGTTTTTCTTCCCCTGGTTAAGAGCACATT GAGGTCTGACTTTTTTGTTGCGGCACAAAACTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGT GAAGTGAGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAA GGAGGGCAATCCTTAATGAATCAAGCGAGTTCGTCGGAGACAAGGTTGCCTATGCACTTGCTCA AGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAGGAGCGGGAAGCTGGATCGACCATG GATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGATCGGGTGACAAACTGGTCAAATGTTGTCA TAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGA AGTACACGATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTGCTGATGTCGCTGCTACAACC CGCATCATTTATGGAG
Genomic sequence	AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCAC AGGATGTTGTAGGTATGTGTAGCATCTCAATTGCTTTGACGACATTATGGCTTTTTTTTTAATT TCCATGTCTATGAAATCTTAAGTAGTGACAAATATTTTGGGCATACAATTACAAACCTGTTTCA ATGTACATCGATGTTCTATAGTGTTTATGCTTCTTAGGAACCATGGATAGATCTAGTGTTTGTT GTTAGTTAAAATGTTCTTTATCATATACTTGTTATGGTTCTATCTTTGTTGATAGTTATAAGTA TGTTTGTTCTTGTATTAATAATTTGATGAAATTTTACTAAATGCAGAGGTTGTGGTTAGCCCTC CATATGTTTTTCTTCCCCTGGTTAAGAGCACATTGAGGTCTGACTTTTTTGTTGCGGCACAAAA CTGTTGGGTTAAGAAAGGAGGTGCTTTCACTGGTGAAGTGAGGTGAGATTCTAACCATTGGTGT ATACTTTAAGCTGTTTTACCATTATTGCTTCATGCAGTAAATATTTATGGTTTTGAAAATGAAT ATGATTGTGTTTATAAACGAATCGATTTTTCCATCTGTTCTTCTTCTTTATCTTCTTTCCTATA AGAATTGTGTAACCTAAGTGATTAAGAAAACAACTAGTAGTTGGTAGTAAGACCATGATTGGAT TCGTGCCTGGTTAGACAAGTAGGTGTAATATGATTTACCTGTCTATGGAATGCTTTCATAGGAA GAAAAGATATATTCTGTGGTGCCTGTATTTCCTGCTCTTATGCATTGTGTAATTTGTGTGTTTT AGTGCGGAGATGCTTGTGAACTTGGATATTCCATGGGTTATCCTTGGTCACTCTGAAAGGAGGG CAATCCTTAATGAATCAAGCGAGGTTGGTGACTTTACATGATAAAATAATTTTCTGGAGACTCA AATAGCTTTTAAATTCATGATTTTGGTTTTTGACCTCTATCCTACATTTGTAGTTCGTCGGAGA CAAGGTTGCCTATGCACTTGCTCAAGGTTTGAAAGTGATTGCTTGTGTTGGTGAGACTCTTGAG GAGCGGGAAGCTGGATCGACCATGGATGTTGTGGCTGCCCAGACCAAGGCTATTGCCGGTATGT ATATTGTCAAACATTTAATCTCTTTTTGCTATCTCAGTTCGTTCTCGTTTACAGTGAGACCTGT TTTGATGATAGTGATGCCCGTTTCTACGCACTATACTCCCTTAGTGTGTGATTCAAACCCCACA GAAATATTTGTTGGCTAAAAAACTCTTTTTGTTGGTAATGGCAGATCGGGTGACAAACTGGTCA AATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCC AAGCTCAAGAAGTAAGTGGTTCTCGATGCGCAGTTGCACTGTAACGTGTTGCATATGGTCATGA TTTAATAGGAAAACCAATGCTGTTTTCCTTACGAGAGCTTGTTTCGTTTATGAACAGGTACACG ATGAGCTGAGGAAATGGCTGGCCAAGAACGTGAGTGCTGATGTCGCTGCTACAACCCGCATCAT TTATGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.205828768

Conservation Information
Conserved circRNAs	NA
PMCS	0.205828768

			
						 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 AT3G55440_circ_g.5

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