Plant Circular RNA Database

Detail information of Bra028087_circ_g.42

			
						 General Information
					
						CircRNA Name
						Bra028087_circ_g.42
					
						ID in PlantcircBase
						bra_circ_000499
					
						Alias
						A09:18513265|18513414
					
						Organism
						
							Brassica rapa						
					
						Position
						
							chrA09: 18513265-18513414  JBrowse»						
					
						Reference genome
						
							Brassica rapa v2						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Bra028087						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Bra028087_circ_g.1 Bra028087_circ_g.2 Bra028087_circ_g.3 Bra028087_circ_g.4 Bra028087_circ_g.5 Bra028087_circ_g.6 Bra028087_circ_g.7 Bra028087_circ_g.8 Bra028087_circ_g.9 Bra028087_circ_g.10 Bra028087_circ_g.11 Bra028087_circ_g.12 Bra028087_circ_g.13 Bra028087_circ_g.14 Bra028087_circ_g.15 Bra028087_circ_g.16 Bra028087_circ_g.17 Bra028087_circ_g.18 Bra028087_circ_g.19 Bra028087_circ_g.20 Bra028087_circ_g.21 Bra028087_circ_g.22 Bra028087_circ_g.23 Bra028087_circ_g.24 Bra028087_circ_g.25 Bra028087_circ_g.26 Bra028087_circ_g.27 Bra028087_circ_g.28 Bra028087_circ_g.29 Bra028087_circ_g.30 Bra028087_circ_g.31 Bra028087_circ_g.32 Bra028087_circ_g.33 Bra028087_circ_g.34 Bra028087_circ_g.35 Bra028087_circ_g.36 Bra028087_circ_g.37 Bra028087_circ_g.38 Bra028087_circ_g.39 Bra028087_circ_g.40 Bra028087_circ_g.41 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							No-No							"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
						Bra0A280A87:1

General Information
CircRNA Name	Bra028087_circ_g.42
ID in PlantcircBase	bra_circ_000499
Alias	A09:18513265\|18513414
Organism	Brassica rapa
Position	chrA09: 18513265-18513414 JBrowse»
Reference genome	Brassica rapa v2
Type	ie-circRNA
Identification method	Find_circ
Parent gene	Bra028087
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Bra028087_circ_g.1 Bra028087_circ_g.2 Bra028087_circ_g.3 Bra028087_circ_g.4 Bra028087_circ_g.5 Bra028087_circ_g.6 Bra028087_circ_g.7 Bra028087_circ_g.8 Bra028087_circ_g.9 Bra028087_circ_g.10 Bra028087_circ_g.11 Bra028087_circ_g.12 Bra028087_circ_g.13 Bra028087_circ_g.14 Bra028087_circ_g.15 Bra028087_circ_g.16 Bra028087_circ_g.17 Bra028087_circ_g.18 Bra028087_circ_g.19 Bra028087_circ_g.20 Bra028087_circ_g.21 Bra028087_circ_g.22 Bra028087_circ_g.23 Bra028087_circ_g.24 Bra028087_circ_g.25 Bra028087_circ_g.26 Bra028087_circ_g.27 Bra028087_circ_g.28 Bra028087_circ_g.29 Bra028087_circ_g.30 Bra028087_circ_g.31 Bra028087_circ_g.32 Bra028087_circ_g.33 Bra028087_circ_g.34 Bra028087_circ_g.35 Bra028087_circ_g.36 Bra028087_circ_g.37 Bra028087_circ_g.38 Bra028087_circ_g.39 Bra028087_circ_g.40 Bra028087_circ_g.41
Support reads	NA
Tissues	leaf
Exon boundary	No-No "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	Bra0A280A87:1

			
						 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  
						
							GGTTTCATATTCAGGAGTATAATAATTTAATTTATACTCTTTAACACCAGCTTTGAATCCAACA
CTTGCTTTAGTcgcagcccctgcttcttcaggtggaactccgggttgaggagttactcggaatg
ctgccaagatatcagtatcctt

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CGCAGCCCCTGCTTCTTCAGGTGGAACTCCGGGTTGAGGAGTTACTCGGAATGCTGCCAAGATA
TCAGTATCCTTGGTTTCATATTCAGGAGTATAATAATTTAATTTATACTCTTTAACACCAGCTT
TGAATCCAACACTTGCTTTAGT

Sequences
Splice junction sequence	GGTTTCATATTCAGGAGTATAATAATTTAATTTATACTCTTTAACACCAGCTTTGAATCCAACA CTTGCTTTAGTcgcagcccctgcttcttcaggtggaactccgggttgaggagttactcggaatg ctgccaagatatcagtatcctt
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CGCAGCCCCTGCTTCTTCAGGTGGAACTCCGGGTTGAGGAGTTACTCGGAATGCTGCCAAGATA TCAGTATCCTTGGTTTCATATTCAGGAGTATAATAATTTAATTTATACTCTTTAACACCAGCTT TGAATCCAACACTTGCTTTAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							ath_circ_032789 ath_circ_032774 ath_circ_032802 ath_circ_032764 
ath_circ_032807 ath_circ_032763 ath_circ_032782 ath_circ_032773 
gra_circ_000092 ath_circ_032798 ath_circ_032754 ath_circ_032739 
gra_circ_000093 ath_circ_032762 						
					
						PMCS
						0.724998778

Conservation Information
Conserved circRNAs	ath_circ_032789 ath_circ_032774 ath_circ_032802 ath_circ_032764 ath_circ_032807 ath_circ_032763 ath_circ_032782 ath_circ_032773 gra_circ_000092 ath_circ_032798 ath_circ_032754 ath_circ_032739 gra_circ_000093 ath_circ_032762
PMCS	0.724998778

			
						 Functional Information
					
						Coding potential
						N
					
						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	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Wang et al., 2019

circRNA

Detail information of Bra028087_circ_g.42

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