Plant Circular RNA Database

Detail information of AT5G18310_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G18310_circ_g.1
					
						ID in PlantcircBase
						ath_circ_038974
					
						Alias
						At_ciR3959, Ath_circ_FC3370
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6062150-6062718  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, circRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT5G18310						
					
						Parent gene annotation
						
							AT5G18310 protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G18310_circ_g.2 AT5G18310_circ_g.3 AT5G18310_circ_g.4 						
					
						Support reads
						9/2
					
						Tissues
						leaf/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  
						
							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
						AT5G18310.3:2
AT5G18310.4:3
AT5G18310.1:3
AT5G18310.2:2

General Information
CircRNA Name	AT5G18310_circ_g.1
ID in PlantcircBase	ath_circ_038974
Alias	At_ciR3959, Ath_circ_FC3370
Organism	Arabidpsis thaliana
Position	chr5: 6062150-6062718 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, circRNA_finder, find_circ, CIRI-full
Parent gene	AT5G18310
Parent gene annotation	AT5G18310 protein
Parent gene strand	+
Alternative splicing	AT5G18310_circ_g.2 AT5G18310_circ_g.3 AT5G18310_circ_g.4
Support reads	9/2
Tissues	leaf/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	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	AT5G18310.3:2 AT5G18310.4:3 AT5G18310.1:3 AT5G18310.2:2

			
						 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  
						
							GCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAGCCCGTTGATGAAGATCTCTAC
AAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGGgggagatatgatacttacaagaagaaaa
gtggacagattcctcggtttggagaatgggaagaagcaaatgagatgccaataacacaatactt
tgagaatc

									
								

					

						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: 366
Transcript exons: 6062150-6062261,6062346-6062404,6062524-6062718
GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG
CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGAAGCCTTAAAGCTTGC
TTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGACGGCGGGGACGAAGGAGAAA
AGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGACAAGTATTACATTGACGTCA
ACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAGCCCGTTGATGA
AGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGG
Transcript length: 450
Transcript exons: 6062150-6062404,6062524-6062718
GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG
CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGGTCTGATTCGTCACCA
ATACACAACAACTTCTTCTGCTTCTTCCACTACCACTTCATCTTCATCTTCTTCTTCTTCTTCT
GCAGAAGCCTTAAAGCTTGCTTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGA
CGGCGGGGACGAAGGAGAAAAGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGA
CAAGTATTACATTGACGTCAACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAG
CCACCTAAGCCCGTTGATGAAGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAA
GG
						
					

						Genomic sequence
						
							GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG
CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGGTCTGATTCGTCACCA
ATACACAACAACTTCTTCTGCTTCTTCCACTACCACTTCATCTTCATCTTCTTCTTCTTCTTCT
GCAGAAGCCTTAAAGCTTGCTTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGG
TTCATTCATCTAATCACTACTTATTTTTCTTAATTATATAACATTTATTTAACTCGATAAACGT
AATTAAGTATCTAAAGAAGAACGCGTTGTTTGTTTGATTAATGACTTGGCGTAGACGGCGGGGA
CGAAGGAGAAAAGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGACAAGTATTA
CATTGACGTCAACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAG
CCCGTTGATGAAGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGG
						
					

			
		

Sequences
Splice junction sequence	GCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAGCCCGTTGATGAAGATCTCTAC AAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGGgggagatatgatacttacaagaagaaaa gtggacagattcctcggtttggagaatgggaagaagcaaatgagatgccaataacacaatactt tgagaatc
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: 366 Transcript exons: 6062150-6062261,6062346-6062404,6062524-6062718 GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGAAGCCTTAAAGCTTGC TTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGACGGCGGGGACGAAGGAGAAA AGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGACAAGTATTACATTGACGTCA ACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAGCCCGTTGATGA AGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGG Transcript length: 450 Transcript exons: 6062150-6062404,6062524-6062718 GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGGTCTGATTCGTCACCA ATACACAACAACTTCTTCTGCTTCTTCCACTACCACTTCATCTTCATCTTCTTCTTCTTCTTCT GCAGAAGCCTTAAAGCTTGCTTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGA CGGCGGGGACGAAGGAGAAAAGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGA CAAGTATTACATTGACGTCAACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAG CCACCTAAGCCCGTTGATGAAGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAA GG
Genomic sequence	GGGAGATATGATACTTACAAGAAGAAAAGTGGACAGATTCCTCGGTTTGGAGAATGGGAAGAAG CAAATGAGATGCCAATAACACAATACTTTGAGAATCCAAGACAAGCTGGTCTGATTCGTCACCA ATACACAACAACTTCTTCTGCTTCTTCCACTACCACTTCATCTTCATCTTCTTCTTCTTCTTCT GCAGAAGCCTTAAAGCTTGCTTCTCACCATCCCCGTCCACGTCACCTCCACGCTCAAAGACAGG TTCATTCATCTAATCACTACTTATTTTTCTTAATTATATAACATTTATTTAACTCGATAAACGT AATTAAGTATCTAAAGAAGAACGCGTTGTTTGTTTGATTAATGACTTGGCGTAGACGGCGGGGA CGAAGGAGAAAAGAGGACCACAAAGGCGTGTGCGTGACGTCAGTGCACAGTCGGACAAGTATTA CATTGACGTCAACGGTGTTAAGCAGTTCAAAAACGACGTTGCTCTGACTTGTAAGCCACCTAAG CCCGTTGATGAAGATCTCTACAAGATTCCTCCTGAGTTTATCCATTCTTCAACAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.335290393

Conservation Information
Conserved circRNAs	NA
PMCS	0.335290393

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6062222-6062715(+)
						
						Potential amino acid sequence
						
							MPITQYFENPRQAEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGV
KQFKNDVALTCKPPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQY
FENPRQAEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKND
VALTCKPPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQYFENPRQ
AEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKNDVALTCK
PPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQYFENPRQAEALKL
ASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKNDVALTCKPPKPVD
EDLYKIPPEFIHSSTR(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6062222-6062715(+)
Potential amino acid sequence	MPITQYFENPRQAEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGV KQFKNDVALTCKPPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQY FENPRQAEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKND VALTCKPPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQYFENPRQ AEALKLASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKNDVALTCK PPKPVDEDLYKIPPEFIHSSTRGRYDTYKKKSGQIPRFGEWEEANEMPITQYFENPRQAEALKL ASHHPRPRHLHAQRQTAGTKEKRGPQRRVRDVSAQSDKYYIDVNGVKQFKNDVALTCKPPKPVD EDLYKIPPEFIHSSTR(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G18310_circ_g.1

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