Plant Circular RNA Database

Detail information of AT4G31180_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G31180_circ_g.3
					
						ID in PlantcircBase
						ath_circ_033803
					
						Alias
						4:15156669-15157707
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 15156669-15157707  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G31180						
					
						Parent gene annotation
						
							Aspartate--tRNA ligase 2, cytoplasmic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G31180_circ_g.1 AT4G31180_circ_g.2 AT4G31180_circ_g.4 AT4G31180_circ_g.5 AT4G31180_circ_g.6 AT4G31180_circ_g.7 						
					
						Support reads
						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  
						
							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
						AT4G31180.2:3
AT4G31180.1:3

General Information
CircRNA Name	AT4G31180_circ_g.3
ID in PlantcircBase	ath_circ_033803
Alias	4:15156669-15157707
Organism	Arabidpsis thaliana
Position	chr4: 15156669-15157707 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G31180
Parent gene annotation	Aspartate--tRNA ligase 2, cytoplasmic
Parent gene strand	+
Alternative splicing	AT4G31180_circ_g.1 AT4G31180_circ_g.2 AT4G31180_circ_g.4 AT4G31180_circ_g.5 AT4G31180_circ_g.6 AT4G31180_circ_g.7
Support reads	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	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	AT4G31180.2:3 AT4G31180.1:3

			
						 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  
						
							TGCTCGTGTCAATCAGGATACACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCGGCTAAT
CAAGCCATCTTCCAGCTTCAGTACGAAGTCGAATATtggactgactattcattcattctcatca
tgtcgtcggaatctgaaatcccgccgttgtcgtcatcaaccgccgcagcggaggaatctggaga
gaagacca

									
								

					

						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: 810
Transcript exons: 15156669-15157253,15157342-15157452,15157594-15157707
TGGACTGACTATTCATTCATTCTCATCATGTCGTCGGAATCTGAAATCCCGCCGTTGTCGTCAT
CAACCGCCGCAGCGGAGGAATCTGGAGAGAAGACCAGCAAGAAAGCGGCTAAGAAGGAAGCTGC
CAAGCTAGAGAAGTTAAGACGTCGTCAAGAACAAGAGGAAGCAACGCGTCGAACAGCTTCGATC
TCTCTGGAAGAGAATGACGAGTTTTCCAATAACTACGGCGACGTGACTCTTACCGAGTTGCAAT
CGTCGGCGGATCCGAAAGCCGGGAAGTGGATAGAGGCTGTTGAGGGAAAGGAGTGGACCGATGT
GAGCGATTTGGTGGAAGAGATGTTGGAATCAGAGGTTCTGATCAGAGGCCGAGTGCACACGAAT
CGTCCAACGTCTAACAAATTGGGGTTTGTGGTCTTGAGGGAGAGCGGATCAACTGTTCAGTGCG
TGGTTAGCCAATCAGAGAAGACCAAAGTAGGTGCCAACATGGTTAAATACCTCAAGCAGCTGAG
TCGCGAATCCTTTGTCGATGTTATCGGTGTCGTCACTCTCCCCAAGGAGCCGCTGACGGGAACT
ACGCAGCAGGTTGAAATTCAAGTGAGAAAAGTGTACTGCATCAACAAATCCTTGGCCAAATTAC
CACTTAGTGTGGAGGATGCTGCTCGGAGTGAAGCAGATATCGAAGCATCTCTTCAGACTCCATC
TCCAGCTGCTCGTGTCAATCAGGATACACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCG
GCTAATCAAGCCATCTTCCAGCTTCAGTACGAAGTCGAATAT
						
					

						Genomic sequence
						
							TGGACTGACTATTCATTCATTCTCATCATGTCGTCGGAATCTGAAATCCCGCCGTTGTCGTCAT
CAACCGCCGCAGCGGAGGAATCTGGAGAGAAGACCAGCAAGAAAGCGGCTAAGAAGGAAGCTGC
CAAGCTAGAGAAGTTAAGACGTCGTCAAGAACAAGAGGAAGCAACGCGTCGAACAGCTTCGATC
TCTCTGGAAGAGAATGACGAGTTTTCCAATAACTACGGCGACGTGACTCTTACCGAGTTGCAAT
CGTCGGCGGATCCGAAAGCCGGGAAGTGGATAGAGGCTGTTGAGGGAAAGGAGTGGACCGATGT
GAGCGATTTGGTGGAAGAGATGTTGGAATCAGAGGTTCTGATCAGAGGCCGAGTGCACACGAAT
CGTCCAACGTCTAACAAATTGGGGTTTGTGGTCTTGAGGGAGAGCGGATCAACTGTTCAGTGCG
TGGTTAGCCAATCAGAGAAGACCAAAGTAGGTGCCAACATGGTTAAATACCTCAAGCAGCTGAG
TCGCGAATCCTTTGTCGATGTTATCGGTGTCGTCACTCTCCCCAAGGAGCCGCTGACGGGAACT
ACGCAGCAGGTTTAGTTTCCTTGTCTTCTTCTTCTCCTCCAGATTTCTCGTTTGCTTTAACTCA
TGTTTGTGTGTGTATCGATAATTTTAATTGTAGGTTGAAATTCAAGTGAGAAAAGTGTACTGCA
TCAACAAATCCTTGGCCAAATTACCACTTAGTGTGGAGGATGCTGCTCGGAGTGAAGCAGATAT
CGAAGCATCTCTTCAGGTATAGTTTGCTGTTTCAAGATTTGGAGATTTTGTTGGACCTGGTACA
ATTGTGCTGTGAATTCTGATAACTTGTGTTCTTCTGATACTATTATGGTGGTCAATCTGTTCAT
AGGAGTTGTTGTTTTCATGACTGTTGCAGACTCCATCTCCAGCTGCTCGTGTCAATCAGGATAC
ACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCGGCTAATCAAGCCATCTTCCAGCTTCAG
TACGAAGTCGAATAT
						
					

			
		

Sequences
Splice junction sequence	TGCTCGTGTCAATCAGGATACACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCGGCTAAT CAAGCCATCTTCCAGCTTCAGTACGAAGTCGAATATtggactgactattcattcattctcatca tgtcgtcggaatctgaaatcccgccgttgtcgtcatcaaccgccgcagcggaggaatctggaga gaagacca
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: 810 Transcript exons: 15156669-15157253,15157342-15157452,15157594-15157707 TGGACTGACTATTCATTCATTCTCATCATGTCGTCGGAATCTGAAATCCCGCCGTTGTCGTCAT CAACCGCCGCAGCGGAGGAATCTGGAGAGAAGACCAGCAAGAAAGCGGCTAAGAAGGAAGCTGC CAAGCTAGAGAAGTTAAGACGTCGTCAAGAACAAGAGGAAGCAACGCGTCGAACAGCTTCGATC TCTCTGGAAGAGAATGACGAGTTTTCCAATAACTACGGCGACGTGACTCTTACCGAGTTGCAAT CGTCGGCGGATCCGAAAGCCGGGAAGTGGATAGAGGCTGTTGAGGGAAAGGAGTGGACCGATGT GAGCGATTTGGTGGAAGAGATGTTGGAATCAGAGGTTCTGATCAGAGGCCGAGTGCACACGAAT CGTCCAACGTCTAACAAATTGGGGTTTGTGGTCTTGAGGGAGAGCGGATCAACTGTTCAGTGCG TGGTTAGCCAATCAGAGAAGACCAAAGTAGGTGCCAACATGGTTAAATACCTCAAGCAGCTGAG TCGCGAATCCTTTGTCGATGTTATCGGTGTCGTCACTCTCCCCAAGGAGCCGCTGACGGGAACT ACGCAGCAGGTTGAAATTCAAGTGAGAAAAGTGTACTGCATCAACAAATCCTTGGCCAAATTAC CACTTAGTGTGGAGGATGCTGCTCGGAGTGAAGCAGATATCGAAGCATCTCTTCAGACTCCATC TCCAGCTGCTCGTGTCAATCAGGATACACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCG GCTAATCAAGCCATCTTCCAGCTTCAGTACGAAGTCGAATAT
Genomic sequence	TGGACTGACTATTCATTCATTCTCATCATGTCGTCGGAATCTGAAATCCCGCCGTTGTCGTCAT CAACCGCCGCAGCGGAGGAATCTGGAGAGAAGACCAGCAAGAAAGCGGCTAAGAAGGAAGCTGC CAAGCTAGAGAAGTTAAGACGTCGTCAAGAACAAGAGGAAGCAACGCGTCGAACAGCTTCGATC TCTCTGGAAGAGAATGACGAGTTTTCCAATAACTACGGCGACGTGACTCTTACCGAGTTGCAAT CGTCGGCGGATCCGAAAGCCGGGAAGTGGATAGAGGCTGTTGAGGGAAAGGAGTGGACCGATGT GAGCGATTTGGTGGAAGAGATGTTGGAATCAGAGGTTCTGATCAGAGGCCGAGTGCACACGAAT CGTCCAACGTCTAACAAATTGGGGTTTGTGGTCTTGAGGGAGAGCGGATCAACTGTTCAGTGCG TGGTTAGCCAATCAGAGAAGACCAAAGTAGGTGCCAACATGGTTAAATACCTCAAGCAGCTGAG TCGCGAATCCTTTGTCGATGTTATCGGTGTCGTCACTCTCCCCAAGGAGCCGCTGACGGGAACT ACGCAGCAGGTTTAGTTTCCTTGTCTTCTTCTTCTCCTCCAGATTTCTCGTTTGCTTTAACTCA TGTTTGTGTGTGTATCGATAATTTTAATTGTAGGTTGAAATTCAAGTGAGAAAAGTGTACTGCA TCAACAAATCCTTGGCCAAATTACCACTTAGTGTGGAGGATGCTGCTCGGAGTGAAGCAGATAT CGAAGCATCTCTTCAGGTATAGTTTGCTGTTTCAAGATTTGGAGATTTTGTTGGACCTGGTACA ATTGTGCTGTGAATTCTGATAACTTGTGTTCTTCTGATACTATTATGGTGGTCAATCTGTTCAT AGGAGTTGTTGTTTTCATGACTGTTGCAGACTCCATCTCCAGCTGCTCGTGTCAATCAGGATAC ACGTTTGAACTATAGGGTGCTCGACCTCAGAACACCGGCTAATCAAGCCATCTTCCAGCTTCAG TACGAAGTCGAATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.264120298

Conservation Information
Conserved circRNAs	NA
PMCS	0.264120298

			
						 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 AT4G31180_circ_g.3

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