Plant Circular RNA Database

Detail information of AT3G47340_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G47340_circ_g.5
					
						ID in PlantcircBase
						ath_circ_026377
					
						Alias
						3:17439564-17440541
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 17439564-17440541  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G47340						
					
						Parent gene annotation
						
							DIN6
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G47340_circ_g.3 AT3G47340_circ_g.4 AT3G47340_circ_g.6 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT3G47340.4:2
AT3G47340.1:4
AT3G47340.2:4
AT3G47340.3:4

General Information
CircRNA Name	AT3G47340_circ_g.5
ID in PlantcircBase	ath_circ_026377
Alias	3:17439564-17440541
Organism	Arabidpsis thaliana
Position	chr3: 17439564-17440541 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G47340
Parent gene annotation	DIN6
Parent gene strand	-
Alternative splicing	AT3G47340_circ_g.3 AT3G47340_circ_g.4 AT3G47340_circ_g.6
Support reads	1/1
Tissues	seedling;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	AT3G47340.4:2 AT3G47340.1:4 AT3G47340.2:4 AT3G47340.3:4

			
						 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  
						
							ATCACCGGAAGCAGGATCGATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGA
TATAAGCCACTCCAGTCAGGTCCTCTGTGCCTCAATctcaagaccaacgcaaaaggaatggagc
tgaggaccccattgcttagccgccttagtaccggccaagtgacgtgcagtgatggaggcaacaa
gggaagaa

									
								

					

						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: 730
Transcript exons: 17439564-17439725,17439804-17440136,17440219-17440314,17
440403-17440541
CTCAAGACCAACGCAAAAGGAATGGAGCTGAGGACCCCATTGCTTAGCCGCCTTAGTACCGGCC
AAGTGACGTGCAGTGATGGAGGCAACAAGGGAAGAATCAAGACCACCAGAGAGCAAAACTCCAA
ATGGAACATCAGTCATCAACCGCTTAATCACAGCGTTTTCAAAGGCGCGTCTTATCGCAAGAGG
CTCATAAGGCGTTGAAGGAACAGATTCATTGAACCAAGGAGGATTATACCATTGCTTAAACCCT
CCTAATTTGCTTGAATAAAAATGACCTGGAGGAAACGTTTCGAAATGCTCACAGTCATCGTTTA
GGCCTTTCATCTCTGAAGATATCCACACAGATCCGTCTAGTCCCCAACCAATGTAGAGCGAAGT
GACACCAATCGCATCACGAGCCACCATGAAAGAGTTATCTCGTGTGTCGAGCAACACAAAGGAG
AATATTCCATCCAACATATCAACAAAATCCACACCATACTCCTCGTACAAGTGAGCAATGACTT
CACAATCACTACCAGTACGGAACTTGTGATTCTTCAGACGTTTTCTCAGCTCCTCATGGTTATA
AATCTCTCCGTTCACCGTGACAACAATGGTCTTGTCCTCGTTGAAAAGAGGTTGATCACCGGAA
GCAGGATCGATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGATATAAGCCAC
TCCAGTCAGGTCCTCTGTGCCTCAAT
						
					

						Genomic sequence
						
							CTCAAGACCAACGCAAAAGGAATGGAGCTGAGGACCCCATTGCTTAGCCGCCTTAGTACCGGCC
AAGTGACGTGCAGTGATGGAGGCAACAAGGGAAGAATCAAGACCACCAGAGAGCAAAACTCCAA
ATGGAACATCAGTCATCAACCGCTTAATCACAGCCTAGAGAGAAAAACAAACATATTTCAGATT
ACCCTCTCACACACCACATACAATTAAAAAGAAGAGATGTTTTCTTACGTTTTCAAAGGCGCGT
CTTATCGCAAGAGGCTCATAAGGCGTTGAAGGAACAGATTCATTGAACCAAGGAGGATTATACC
ATTGCTTAAACCCTCCTAATTTGCTTGAATAAAAATGACCTGGAGGAAACGTTTCGAAATGCTC
ACAGTCATCGTTTAGGCCTTTCATCTCTGAAGATATCCACACAGATCCGTCTAGTCCCCAACCA
ATGTAGAGCGAAGTGACACCAATCGCATCACGAGCCACCATGAAAGAGTTATCTCGTGTGTCGA
GCAACACAAAGGAGAATATTCCATCCAACATATCAACAAAATCCACACCATACTCCTCGTACTA
TGTCCATAAAACACATCAAACTCAAATCAAAACTTGATAACCACATTAGCAGAAGAATTAAAAA
TGATACCACACTTACCAAGTGAGCAATGACTTCACAATCACTACCAGTACGGAACTTGTGATTC
TTCAGACGTTTTCTCAGCTCCTCATGGTTATAAATCTCTCCGTTCACCTTCCAAACCATCAACA
AACAAAATAAATTTCAGCTTCAAAATTATCAAAAGAGTTATTATTTTATGAGTCCATGGATATA
GCGTTACCGTGACAACAATGGTCTTGTCCTCGTTGAAAAGAGGTTGATCACCGGAAGCAGGATC
GATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGATATAAGCCACTCCAGTCA
GGTCCTCTGTGCCTCAAT
						
					

			
		

Sequences
Splice junction sequence	ATCACCGGAAGCAGGATCGATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGA TATAAGCCACTCCAGTCAGGTCCTCTGTGCCTCAATctcaagaccaacgcaaaaggaatggagc tgaggaccccattgcttagccgccttagtaccggccaagtgacgtgcagtgatggaggcaacaa gggaagaa
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: 730 Transcript exons: 17439564-17439725,17439804-17440136,17440219-17440314,17 440403-17440541 CTCAAGACCAACGCAAAAGGAATGGAGCTGAGGACCCCATTGCTTAGCCGCCTTAGTACCGGCC AAGTGACGTGCAGTGATGGAGGCAACAAGGGAAGAATCAAGACCACCAGAGAGCAAAACTCCAA ATGGAACATCAGTCATCAACCGCTTAATCACAGCGTTTTCAAAGGCGCGTCTTATCGCAAGAGG CTCATAAGGCGTTGAAGGAACAGATTCATTGAACCAAGGAGGATTATACCATTGCTTAAACCCT CCTAATTTGCTTGAATAAAAATGACCTGGAGGAAACGTTTCGAAATGCTCACAGTCATCGTTTA GGCCTTTCATCTCTGAAGATATCCACACAGATCCGTCTAGTCCCCAACCAATGTAGAGCGAAGT GACACCAATCGCATCACGAGCCACCATGAAAGAGTTATCTCGTGTGTCGAGCAACACAAAGGAG AATATTCCATCCAACATATCAACAAAATCCACACCATACTCCTCGTACAAGTGAGCAATGACTT CACAATCACTACCAGTACGGAACTTGTGATTCTTCAGACGTTTTCTCAGCTCCTCATGGTTATA AATCTCTCCGTTCACCGTGACAACAATGGTCTTGTCCTCGTTGAAAAGAGGTTGATCACCGGAA GCAGGATCGATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGATATAAGCCAC TCCAGTCAGGTCCTCTGTGCCTCAAT
Genomic sequence	CTCAAGACCAACGCAAAAGGAATGGAGCTGAGGACCCCATTGCTTAGCCGCCTTAGTACCGGCC AAGTGACGTGCAGTGATGGAGGCAACAAGGGAAGAATCAAGACCACCAGAGAGCAAAACTCCAA ATGGAACATCAGTCATCAACCGCTTAATCACAGCCTAGAGAGAAAAACAAACATATTTCAGATT ACCCTCTCACACACCACATACAATTAAAAAGAAGAGATGTTTTCTTACGTTTTCAAAGGCGCGT CTTATCGCAAGAGGCTCATAAGGCGTTGAAGGAACAGATTCATTGAACCAAGGAGGATTATACC ATTGCTTAAACCCTCCTAATTTGCTTGAATAAAAATGACCTGGAGGAAACGTTTCGAAATGCTC ACAGTCATCGTTTAGGCCTTTCATCTCTGAAGATATCCACACAGATCCGTCTAGTCCCCAACCA ATGTAGAGCGAAGTGACACCAATCGCATCACGAGCCACCATGAAAGAGTTATCTCGTGTGTCGA GCAACACAAAGGAGAATATTCCATCCAACATATCAACAAAATCCACACCATACTCCTCGTACTA TGTCCATAAAACACATCAAACTCAAATCAAAACTTGATAACCACATTAGCAGAAGAATTAAAAA TGATACCACACTTACCAAGTGAGCAATGACTTCACAATCACTACCAGTACGGAACTTGTGATTC TTCAGACGTTTTCTCAGCTCCTCATGGTTATAAATCTCTCCGTTCACCTTCCAAACCATCAACA AACAAAATAAATTTCAGCTTCAAAATTATCAAAAGAGTTATTATTTTATGAGTCCATGGATATA GCGTTACCGTGACAACAATGGTCTTGTCCTCGTTGAAAAGAGGTTGATCACCGGAAGCAGGATC GATGACGGCAAGACGTTGATGGGCCAAGTAATTATCTCCGTTCTGATATAAGCCACTCCAGTCA GGTCCTCTGTGCCTCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.258554091

Conservation Information
Conserved circRNAs	NA
PMCS	0.258554091

			
						 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 AT3G47340_circ_g.5

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