Plant Circular RNA Database

Detail information of AT3G15950_circ_g.56

			
						 General Information
					
						CircRNA Name
						AT3G15950_circ_g.56
					
						ID in PlantcircBase
						ath_circ_022068
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 5401080-5401293  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, CIRI-full
					
						Parent gene
						
							AT3G15950						
					
						Parent gene annotation
						
							TSA1-like protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G15950_circ_g.1 AT3G15950_circ_g.2 AT3G15950_circ_g.3 AT3G15950_circ_g.4 3_circ_igg.5 AT3G15950_circ_g.6 AT3G15950_circ_g.7 AT3G15950_circ_g.8 AT3G15950_circ_g.9 AT3G15950_circ_g.10 AT3G15950_circ_g.11 AT3G15950_circ_g.12 AT3G15950_circ_g.13 AT3G15950_circ_g.14 AT3G15950_circ_g.15 AT3G15950_circ_g.16 AT3G15950_circ_g.17 AT3G15950_circ_g.18 AT3G15950_circ_g.19 AT3G15950_circ_g.20 AT3G15950_circ_g.21 AT3G15950_circ_g.22 AT3G15950_circ_g.23 AT3G15950_circ_g.24 AT3G15950_circ_g.25 AT3G15950_circ_g.26 AT3G15950_circ_g.27 AT3G15950_circ_g.28 AT3G15950_circ_g.29 AT3G15950_circ_g.30 AT3G15950_circ_g.31 AT3G15950_circ_g.32 AT3G15950_circ_g.33 AT3G15950_circ_g.34 AT3G15950_circ_g.35 AT3G15950_circ_g.36 AT3G15950_circ_g.37 AT3G15950_circ_g.38 AT3G15950_circ_g.39 AT3G15950_circ_g.40 AT3G15950_circ_g.41 AT3G15950_circ_g.42 AT3G15950_circ_g.43 AT3G15950_circ_g.44 AT3G15950_circ_g.45 AT3G15950_circ_g.46 AT3G15950_circ_g.47 AT3G15950_circ_g.48 AT3G15950_circ_g.49 AT3G15950_circ_g.50 AT3G15950_circ_g.51 AT3G15950_circ_g.52 AT3G15950_circ_g.53 AT3G15950_circ_g.54 AT3G15950_circ_g.55 AT3G15950_circ_g.57 AT3G15950_circ_g.58 AT3G15950_circ_g.59 AT3G15950_circ_g.60 AT3G15950_circ_g.61 AT3G15950_circ_g.62 AT3G15950_circ_g.63 AT3G15950_circ_g.64 AT3G15950_circ_g.65 AT3G15950_circ_g.66 						
					
						Support reads
						14
					
						Tissues
						root, aerial, seed
					
						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
						AT3G15950.1:2
AT3G15950.5:1

General Information
CircRNA Name	AT3G15950_circ_g.56
ID in PlantcircBase	ath_circ_022068
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 5401080-5401293 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circRNA_finder, CIRI-full
Parent gene	AT3G15950
Parent gene annotation	TSA1-like protein
Parent gene strand	-
Alternative splicing	AT3G15950_circ_g.1 AT3G15950_circ_g.2 AT3G15950_circ_g.3 AT3G15950_circ_g.4 3_circ_igg.5 AT3G15950_circ_g.6 AT3G15950_circ_g.7 AT3G15950_circ_g.8 AT3G15950_circ_g.9 AT3G15950_circ_g.10 AT3G15950_circ_g.11 AT3G15950_circ_g.12 AT3G15950_circ_g.13 AT3G15950_circ_g.14 AT3G15950_circ_g.15 AT3G15950_circ_g.16 AT3G15950_circ_g.17 AT3G15950_circ_g.18 AT3G15950_circ_g.19 AT3G15950_circ_g.20 AT3G15950_circ_g.21 AT3G15950_circ_g.22 AT3G15950_circ_g.23 AT3G15950_circ_g.24 AT3G15950_circ_g.25 AT3G15950_circ_g.26 AT3G15950_circ_g.27 AT3G15950_circ_g.28 AT3G15950_circ_g.29 AT3G15950_circ_g.30 AT3G15950_circ_g.31 AT3G15950_circ_g.32 AT3G15950_circ_g.33 AT3G15950_circ_g.34 AT3G15950_circ_g.35 AT3G15950_circ_g.36 AT3G15950_circ_g.37 AT3G15950_circ_g.38 AT3G15950_circ_g.39 AT3G15950_circ_g.40 AT3G15950_circ_g.41 AT3G15950_circ_g.42 AT3G15950_circ_g.43 AT3G15950_circ_g.44 AT3G15950_circ_g.45 AT3G15950_circ_g.46 AT3G15950_circ_g.47 AT3G15950_circ_g.48 AT3G15950_circ_g.49 AT3G15950_circ_g.50 AT3G15950_circ_g.51 AT3G15950_circ_g.52 AT3G15950_circ_g.53 AT3G15950_circ_g.54 AT3G15950_circ_g.55 AT3G15950_circ_g.57 AT3G15950_circ_g.58 AT3G15950_circ_g.59 AT3G15950_circ_g.60 AT3G15950_circ_g.61 AT3G15950_circ_g.62 AT3G15950_circ_g.63 AT3G15950_circ_g.64 AT3G15950_circ_g.65 AT3G15950_circ_g.66
Support reads	14
Tissues	root, aerial, seed
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	AT3G15950.1:2 AT3G15950.5:1

			
						 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  
						
							TTTTCAGGTTCAAGAACTTAAGTAAACAAGAATAAAGATTTTGTAGAGAGACCTTCAAAATCAC
GTTCAATCTCGTCCAACATGCTTTGTCTCTTTGCAGcgtgttcttcatcgttgattccagttaa
atcatcagcctttagttgctcaagaccttttgtagcagctgcaagtggaaatggaacagaagac
acaaccca

						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: 114
Transcript exons: 5401080-5401293
CGTGTTCTTCATCGTTGATTCCAGTTAAATCATCAGCCTTTAGTTGCTCAAGACCTTTTGTAGC
AGCTTCAAAATCACGTTCAATCTCGTCCAACATGCTTTGTCTCTTTGCAG
						
						Genomic sequence
						
							CGTGTTCTTCATCGTTGATTCCAGTTAAATCATCAGCCTTTAGTTGCTCAAGACCTTTTGTAGC
AGCTGCAAGTGGAAATGGAACAGAAGACACAACCCAATTGTTACTTCAACTTTTCAGGTTCAAG
AACTTAAGTAAACAAGAATAAAGATTTTGTAGAGAGACCTTCAAAATCACGTTCAATCTCGTCC
AACATGCTTTGTCTCTTTGCAG

Sequences
Splice junction sequence	TTTTCAGGTTCAAGAACTTAAGTAAACAAGAATAAAGATTTTGTAGAGAGACCTTCAAAATCAC GTTCAATCTCGTCCAACATGCTTTGTCTCTTTGCAGcgtgttcttcatcgttgattccagttaa atcatcagcctttagttgctcaagaccttttgtagcagctgcaagtggaaatggaacagaagac acaaccca
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: 114 Transcript exons: 5401080-5401293 CGTGTTCTTCATCGTTGATTCCAGTTAAATCATCAGCCTTTAGTTGCTCAAGACCTTTTGTAGC AGCTTCAAAATCACGTTCAATCTCGTCCAACATGCTTTGTCTCTTTGCAG
Genomic sequence	CGTGTTCTTCATCGTTGATTCCAGTTAAATCATCAGCCTTTAGTTGCTCAAGACCTTTTGTAGC AGCTGCAAGTGGAAATGGAACAGAAGACACAACCCAATTGTTACTTCAACTTTTCAGGTTCAAG AACTTAAGTAAACAAGAATAAAGATTTTGTAGAGAGACCTTCAAAATCACGTTCAATCTCGTCC AACATGCTTTGTCTCTTTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.276354141

Conservation Information
Conserved circRNAs	NA
PMCS	0.276354141

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5401277-5401082(-)
5401275-5401290(+)
						
						Potential amino acid sequence
						
							MLDEIERDFEAATKGLEQLKADDLTGINDEEHAAKRQSMLDEIERDFEAATKGLEQLKADDLTG
INDEEHAAKRQSMLDEIERDFEAATKGLEQLKADDLTGINDEEHAAKRQSMLDEIERDFEAATK
GLEQLKADDLTGINDEEH(-)
MLCLFAACSSSLIPVKSSAFSCSRPFVAASKSRSISSNMLCLFAACSSSLIPVKSSAFSCSRPF
VAASKSRSISSNMLCLFAACSSSLIPVKSSAFSCSRPFVAASKSRSISSNMLCLFA(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5401277-5401082(-) 5401275-5401290(+)
Potential amino acid sequence	MLDEIERDFEAATKGLEQLKADDLTGINDEEHAAKRQSMLDEIERDFEAATKGLEQLKADDLTG INDEEHAAKRQSMLDEIERDFEAATKGLEQLKADDLTGINDEEHAAKRQSMLDEIERDFEAATK GLEQLKADDLTGINDEEH(-) MLCLFAACSSSLIPVKSSAFSCSRPFVAASKSRSISSNMLCLFAACSSSLIPVKSSAFSCSRPF VAASKSRSISSNMLCLFAACSSSLIPVKSSAFSCSRPFVAASKSRSISSNMLCLFA(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G15950_circ_g.56

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