Plant Circular RNA Database

Detail information of AT4G37490_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G37490_circ_g.3
					
						ID in PlantcircBase
						ath_circ_035216
					
						Alias
						4:17622644-17623900
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 17622644-17623900  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G37490						
					
						Parent gene annotation
						
							Cyclin-B1-1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G37490_circ_g.1 AT4G37490_circ_g.2 AT4G37490_circ_g.4 AT4G37490_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						flower
					
						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
						AT4G37490.1:5

General Information
CircRNA Name	AT4G37490_circ_g.3
ID in PlantcircBase	ath_circ_035216
Alias	4:17622644-17623900
Organism	Arabidpsis thaliana
Position	chr4: 17622644-17623900 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G37490
Parent gene annotation	Cyclin-B1-1
Parent gene strand	-
Alternative splicing	AT4G37490_circ_g.1 AT4G37490_circ_g.2 AT4G37490_circ_g.4 AT4G37490_circ_g.5
Support reads	2
Tissues	flower
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	AT4G37490.1:5

			
						 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  
						
							TTCTTTGGGTAATTTCCTCGAACAACATTACCTATATCACCAAGAACTTGACGGTTTCTTCCTT
TCGCTACGTTTTTGCCATCTACCACAACAACATCATcttttcgtctgcaatggaagctttgatg
aaacgagctaggaagacataatgagtcggaactgtcaagtaccactcaagtgtagacagtattg
tcttctcc

									
								

					

						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: 899
Transcript exons: 17622644-17622802,17622886-17623134,17623223-17623348,17
623439-17623624,17623722-17623900
CTTTTCGTCTGCAATGGAAGCTTTGATGAAACGAGCTAGGAAGACATAATGAGTCGGAACTGTC
AAGTACCACTCAAGTGTAGACAGTATTGTCTTCTCCATCACCAGAATCTGTTTGTGACTGTATG
CATGGTCTGCAATATCAACTAGATCCTCCACCTGTGGTGGCCAAATTTCTTCATACTTGGCCGA
CATGAGAAGAGCACTGAGACCAACAAGCTGCAGTTCTTTTCGAGGCACTGGCTTAACCGACAAG
AACCGATCCAGAATGTTAACAGTGAGGTAAAATGTTTCCGGGTTTAGCTCGAATCGGACATGCA
CATCAATCAACCACTCCACCAGGATCAGTCTCATCTTTTCATTAATATCAGGCTGAGATGCCAT
GTAATCTCGTGGCCTCCATTCACTCTCAACAGACTTGTAAAAACTGTAAATATCTTCCACATAT
TCCACAGCTGCGAGGTCATTCTCAACATCAGCAGAATCGATATCAACAATCTTTTCTTTCTGTT
TCTTCTCTAAACCACAAGCAGCCTTGCTTCTAGCAGTAAGAACAGATGTGTAAGTGGTCGCTTT
CTTCTTAGTAGCCTTCTTCTCTCGAGCAGCAACTAAACCAAGTTCTTCATCACTGTCTGAACTT
ATCTCAATCACGTCTACTACCTTTGGTTTCCCAGCCACTTTCTTCGGCTTTGGTACTGCGTTTC
TCTTGACTACAGGTTTTTTGAGATTATCCTCCACAAGAAGCGTGGGATTTTGAGATCGTGTACG
AGGACGATGATTGATCTTTTCCGGTTCGTTGTTCTTTGGGTAATTTCCTCGAACAACATTACCT
ATATCACCAAGAACTTGACGGTTTCTTCCTTTCGCTACGTTTTTGCCATCTACCACAACAACAT
CAT
						
					

						Genomic sequence
						
							CTTTTCGTCTGCAATGGAAGCTTTGATGAAACGAGCTAGGAAGACATAATGAGTCGGAACTGTC
AAGTACCACTCAAGTGTAGACAGTATTGTCTTCTCCATCACCAGAATCTGTTTGTGACTGTATG
CATGGTCTGCAATATCAACTAGATCCTCCACCTGCAAAAGAATTATCTTTTCATTTAGCCGAAG
ACAAAAAAGAATCAAAACCAGAAGATTCAAAAGTTCTCTGTTTTTATCACCTGTGGTGGCCAAA
TTTCTTCATACTTGGCCGACATGAGAAGAGCACTGAGACCAACAAGCTGCAGTTCTTTTCGAGG
CACTGGCTTAACCGACAAGAACCGATCCAGAATGTTAACAGTGAGGTAAAATGTTTCCGGGTTT
AGCTCGAATCGGACATGCACATCAATCAACCACTCCACCAGGATCAGTCTCATCTTTTCATTAA
TATCAGGCTGAGATGCCATGTAATCTCGTGGCCTCCATTCACTCTGCCAATCCAAATGATAATT
TAAGTAAACAAGTTAATACTACAACAAAGCTGCAAGGAAAGATTCATGAATAGTATAGTATACA
AACCTCAACAGACTTGTAAAAACTGTAAATATCTTCCACATATTCCACAGCTGCGAGGTCATTC
TCAACATCAGCAGAATCGATATCAACAATCTTTTCTTTCTGTTTCTTCTCTAAACCACAAGCAG
CCTGAAAAGCAAAAGAAGTTTATTCAGAACAGACCAAAACATTTTCTTACTTCACACTAAAGAA
TCATCATTTCACAAGGTAAAAAATTACCTTGCTTCTAGCAGTAAGAACAGATGTGTAAGTGGTC
GCTTTCTTCTTAGTAGCCTTCTTCTCTCGAGCAGCAACTAAACCAAGTTCTTCATCACTGTCTG
AACTTATCTCAATCACGTCTACTACCTTTGGTTTCCCAGCCACTTTCTTCGGCTTTGGTACTGC
GTTTCTCTTGACTACAGGTTTCTGCAGATCAAAGACATATACACATATGACATGAGTTTAACAA
ATCTAACGAAGAAACCTAATTTGTTCACCAAAATACAGGGGAAAAGGAACAAACTTTGAGATTA
TCCTCCACAAGAAGCGTGGGATTTTGAGATCGTGTACGAGGACGATGATTGATCTTTTCCGGTT
CGTTGTTCTTTGGGTAATTTCCTCGAACAACATTACCTATATCACCAAGAACTTGACGGTTTCT
TCCTTTCGCTACGTTTTTGCCATCTACCACAACAACATCAT
						
					

			
		

Sequences
Splice junction sequence	TTCTTTGGGTAATTTCCTCGAACAACATTACCTATATCACCAAGAACTTGACGGTTTCTTCCTT TCGCTACGTTTTTGCCATCTACCACAACAACATCATcttttcgtctgcaatggaagctttgatg aaacgagctaggaagacataatgagtcggaactgtcaagtaccactcaagtgtagacagtattg tcttctcc
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: 899 Transcript exons: 17622644-17622802,17622886-17623134,17623223-17623348,17 623439-17623624,17623722-17623900 CTTTTCGTCTGCAATGGAAGCTTTGATGAAACGAGCTAGGAAGACATAATGAGTCGGAACTGTC AAGTACCACTCAAGTGTAGACAGTATTGTCTTCTCCATCACCAGAATCTGTTTGTGACTGTATG CATGGTCTGCAATATCAACTAGATCCTCCACCTGTGGTGGCCAAATTTCTTCATACTTGGCCGA CATGAGAAGAGCACTGAGACCAACAAGCTGCAGTTCTTTTCGAGGCACTGGCTTAACCGACAAG AACCGATCCAGAATGTTAACAGTGAGGTAAAATGTTTCCGGGTTTAGCTCGAATCGGACATGCA CATCAATCAACCACTCCACCAGGATCAGTCTCATCTTTTCATTAATATCAGGCTGAGATGCCAT GTAATCTCGTGGCCTCCATTCACTCTCAACAGACTTGTAAAAACTGTAAATATCTTCCACATAT TCCACAGCTGCGAGGTCATTCTCAACATCAGCAGAATCGATATCAACAATCTTTTCTTTCTGTT TCTTCTCTAAACCACAAGCAGCCTTGCTTCTAGCAGTAAGAACAGATGTGTAAGTGGTCGCTTT CTTCTTAGTAGCCTTCTTCTCTCGAGCAGCAACTAAACCAAGTTCTTCATCACTGTCTGAACTT ATCTCAATCACGTCTACTACCTTTGGTTTCCCAGCCACTTTCTTCGGCTTTGGTACTGCGTTTC TCTTGACTACAGGTTTTTTGAGATTATCCTCCACAAGAAGCGTGGGATTTTGAGATCGTGTACG AGGACGATGATTGATCTTTTCCGGTTCGTTGTTCTTTGGGTAATTTCCTCGAACAACATTACCT ATATCACCAAGAACTTGACGGTTTCTTCCTTTCGCTACGTTTTTGCCATCTACCACAACAACAT CAT
Genomic sequence	CTTTTCGTCTGCAATGGAAGCTTTGATGAAACGAGCTAGGAAGACATAATGAGTCGGAACTGTC AAGTACCACTCAAGTGTAGACAGTATTGTCTTCTCCATCACCAGAATCTGTTTGTGACTGTATG CATGGTCTGCAATATCAACTAGATCCTCCACCTGCAAAAGAATTATCTTTTCATTTAGCCGAAG ACAAAAAAGAATCAAAACCAGAAGATTCAAAAGTTCTCTGTTTTTATCACCTGTGGTGGCCAAA TTTCTTCATACTTGGCCGACATGAGAAGAGCACTGAGACCAACAAGCTGCAGTTCTTTTCGAGG CACTGGCTTAACCGACAAGAACCGATCCAGAATGTTAACAGTGAGGTAAAATGTTTCCGGGTTT AGCTCGAATCGGACATGCACATCAATCAACCACTCCACCAGGATCAGTCTCATCTTTTCATTAA TATCAGGCTGAGATGCCATGTAATCTCGTGGCCTCCATTCACTCTGCCAATCCAAATGATAATT TAAGTAAACAAGTTAATACTACAACAAAGCTGCAAGGAAAGATTCATGAATAGTATAGTATACA AACCTCAACAGACTTGTAAAAACTGTAAATATCTTCCACATATTCCACAGCTGCGAGGTCATTC TCAACATCAGCAGAATCGATATCAACAATCTTTTCTTTCTGTTTCTTCTCTAAACCACAAGCAG CCTGAAAAGCAAAAGAAGTTTATTCAGAACAGACCAAAACATTTTCTTACTTCACACTAAAGAA TCATCATTTCACAAGGTAAAAAATTACCTTGCTTCTAGCAGTAAGAACAGATGTGTAAGTGGTC GCTTTCTTCTTAGTAGCCTTCTTCTCTCGAGCAGCAACTAAACCAAGTTCTTCATCACTGTCTG AACTTATCTCAATCACGTCTACTACCTTTGGTTTCCCAGCCACTTTCTTCGGCTTTGGTACTGC GTTTCTCTTGACTACAGGTTTCTGCAGATCAAAGACATATACACATATGACATGAGTTTAACAA ATCTAACGAAGAAACCTAATTTGTTCACCAAAATACAGGGGAAAAGGAACAAACTTTGAGATTA TCCTCCACAAGAAGCGTGGGATTTTGAGATCGTGTACGAGGACGATGATTGATCTTTTCCGGTT CGTTGTTCTTTGGGTAATTTCCTCGAACAACATTACCTATATCACCAAGAACTTGACGGTTTCT TCCTTTCGCTACGTTTTTGCCATCTACCACAACAACATCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.29131858

Conservation Information
Conserved circRNAs	NA
PMCS	0.29131858

			
						 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 AT4G37490_circ_g.3

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