Plant Circular RNA Database

Detail information of Bra001484_circ_g.1

			
						 General Information
					
						CircRNA Name
						Bra001484_circ_g.1
					
						ID in PlantcircBase
						bra_circ_000146
					
						Alias
						A03:16642841|16643256
					
						Organism
						
							Brassica rapa						
					
						Position
						
							chrA03: 16642841-16643256  JBrowse»						
					
						Reference genome
						
							Brassica rapa v2						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Bra001484						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						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
						Bra0A0A1484:2

General Information
CircRNA Name	Bra001484_circ_g.1
ID in PlantcircBase	bra_circ_000146
Alias	A03:16642841\|16643256
Organism	Brassica rapa
Position	chrA03: 16642841-16643256 JBrowse»
Reference genome	Brassica rapa v2
Type	ie-circRNA
Identification method	Find_circ
Parent gene	Bra001484
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	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	Bra0A0A1484:2

			
						 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  
						
							AAACTACCTCAATGGACATTCCTCCAGAGAGGCTTCTTTGGGTTTGACTCAGTCCAGTCACTGG
ATTTGATGATGAAGCCAATGGGGTTTCATAGATCTCctgtaagtggcttttaacatgatagatc
gtcaagccctcaacattcatgagcttcagaacagccttgggagtggcctctacatgtttttgaa
ccaacacc

						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
						
							CTGTAAGTGGCTTTTAACATGATAGATCGTCAAGCCCTCAACATTCATGAGCTTCAGAACAGCC
TTGGGAGTGGCCTCTACATGTTTTTGAACCAACACCGGTTAAGCAAACAAAAGATAGCTAACCA
ATAGCAAGCAAGATAATAACATATAAGTGCTGCCTACATATTTTCTTAAGACTAAAAGTCTAAA
AACTCACTTTCAGGGCCTTCAAGCTTGTCCACAGACTTTAAGAAACTCTCGTGGAGCTCAGGGG
TCCATCTCATTCTCGGCTTGTGGTTTGATGCTGCTGCTGATCCTGGAGAAGGGTGAGATAAAAC
TACCTCAATGGACATTCCTCCAGAGAGGCTTCTTTGGGTTTGACTCAGTCCAGTCACTGGATTT
GATGATGAAGCCAATGGGGTTTCATAGATCTC

Sequences
Splice junction sequence	AAACTACCTCAATGGACATTCCTCCAGAGAGGCTTCTTTGGGTTTGACTCAGTCCAGTCACTGG ATTTGATGATGAAGCCAATGGGGTTTCATAGATCTCctgtaagtggcttttaacatgatagatc gtcaagccctcaacattcatgagcttcagaacagccttgggagtggcctctacatgtttttgaa ccaacacc
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	CTGTAAGTGGCTTTTAACATGATAGATCGTCAAGCCCTCAACATTCATGAGCTTCAGAACAGCC TTGGGAGTGGCCTCTACATGTTTTTGAACCAACACCGGTTAAGCAAACAAAAGATAGCTAACCA ATAGCAAGCAAGATAATAACATATAAGTGCTGCCTACATATTTTCTTAAGACTAAAAGTCTAAA AACTCACTTTCAGGGCCTTCAAGCTTGTCCACAGACTTTAAGAAACTCTCGTGGAGCTCAGGGG TCCATCTCATTCTCGGCTTGTGGTTTGATGCTGCTGCTGATCCTGGAGAAGGGTGAGATAAAAC TACCTCAATGGACATTCCTCCAGAGAGGCTTCTTTGGGTTTGACTCAGTCCAGTCACTGGATTT GATGATGAAGCCAATGGGGTTTCATAGATCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.871259842

Conservation Information
Conserved circRNAs	NA
PMCS	0.871259842

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16643177-16642843(-)
16642862-16643216(-)
						
						Potential amino acid sequence
						
							MSIEVVLSHPSPGSAAASNHKPRMRWTPELHESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIY
HVKSHLQEIYETPLASSSNPVTGLSQTQRSLSGGMSIEVVLSHPSPGSAAASNHKPRMRWTPEL
HESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIYHVKSHLQEIYETPLASSSNPVTGLSQTQRS
LSGGMSIEVVLSHPSPGSAAASNHKPRMRWTPELHESFLKSVDKLEGPEKATPKAVLKLMNVEG
LTIYHVKSHLQEIYETPLASSSNPVTGLSQTQRSLSGGMSIEVVLSHPSPGSAAASNHKPRMRW
TPELHESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIYHVKSHLQ
MLKATYRRSMKPHWLHHQIQ*
						
						Sponge-miRNAs
						
							bra-miR172c-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to calcium deficiency-induced tip-burn

Functional Information
Coding potential	Y
Potential coding position	16643177-16642843(-) 16642862-16643216(-)
Potential amino acid sequence	MSIEVVLSHPSPGSAAASNHKPRMRWTPELHESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIY HVKSHLQEIYETPLASSSNPVTGLSQTQRSLSGGMSIEVVLSHPSPGSAAASNHKPRMRWTPEL HESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIYHVKSHLQEIYETPLASSSNPVTGLSQTQRS LSGGMSIEVVLSHPSPGSAAASNHKPRMRWTPELHESFLKSVDKLEGPEKATPKAVLKLMNVEG LTIYHVKSHLQEIYETPLASSSNPVTGLSQTQRSLSGGMSIEVVLSHPSPGSAAASNHKPRMRW TPELHESFLKSVDKLEGPEKATPKAVLKLMNVEGLTIYHVKSHLQ MLKATYRRSMKPHWLHHQIQ*
Sponge-miRNAs	bra-miR172c-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to calcium deficiency-induced tip-burn

			
						 Other Information
					
						References
						Wang et al., 2019

circRNA

Detail information of Bra001484_circ_g.1

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