Plant Circular RNA Database

Detail information of Bra005655_circ_g.1

			
						 General Information
					
						CircRNA Name
						Bra005655_circ_g.1
					
						ID in PlantcircBase
						bra_circ_000227
					
						Alias
						A05:6786089|6787042
					
						Organism
						
							Brassica rapa						
					
						Position
						
							chrA05: 6786089-6787042  JBrowse»						
					
						Reference genome
						
							Brassica rapa v2						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Bra005655						
					
						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
						Bra0A0A5655:5

General Information
CircRNA Name	Bra005655_circ_g.1
ID in PlantcircBase	bra_circ_000227
Alias	A05:6786089\|6787042
Organism	Brassica rapa
Position	chrA05: 6786089-6787042 JBrowse»
Reference genome	Brassica rapa v2
Type	ie-circRNA
Identification method	Find_circ
Parent gene	Bra005655
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	Bra0A0A5655:5

			
						 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  
						
							GATATCAGGAAACTCTCCCAAAACCGCAGCTGAACATGAATTCAAAAGATTGAGGGCTGCTTCA
TCATTAGGCTTCTCAAACTCATGAACTTGGGAAAACctttttcttgaagagacatgatccttgt
cgaaacaattcaggaagcgttttgtaattgataccaaacttgtgaaagagaagctcatttttct
gctgcttt

									
								

					

						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: 541
Transcript exons: 6786089-6786196,6786283-6786368,6786489-6786658,6786780-
6786824,6786911-6787042
CTTTTTCTTGAAGAGACATGATCCTTGTCGAAACAATTCAGGAAGCGTTTTGTAATTGATACCA
AACTTGTGAAAGAGAAGCTCATTTTTCTGCTGCTTTTGTGTATCCTTAAGAAGCTCTTGTGCTT
CGCTTATGGTCATTCCACTTTTAACTAACATCCAAAAACAAGTTTCGTATTGATTATTGGCGTG
GCAATCTTGTTGTCTCCACGCGAGATAAGCTTGAAGAACCTCTGGCGATGCACAACTTACGACT
TTTGAGGTGAAAGAAGGAGTATATTCCAGTTTTCTTTGGGGAAAGAACTCTTTCCATTTTGTTA
CGTAGACTGCAGCAAAGAAGGAAGCTACCAACGACAAAATCTTACTGGCTCGTCTCTGGTAGAA
TCTTGATGTTTTCTTGAACACAAAGCTGTATTCATCACTGTATCCATAAGCAAAGATGATATCA
GGAAACTCTCCCAAAACCGCAGCTGAACATGAATTCAAAAGATTGAGGGCTGCTTCATCATTAG
GCTTCTCAAACTCATGAACTTGGGAAAAC
						
					

						Genomic sequence
						
							CTTTTTCTTGAAGAGACATGATCCTTGTCGAAACAATTCAGGAAGCGTTTTGTAATTGATACCA
AACTTGTGAAAGAGAAGCTCATTTTTCTGCTGCTTTTGTGTATCCTGCAGGTATCCAATGGAAA
TAGACAAACAATGAAATAACAATGCAAAGAAGGTAAAAAGAGCAATTTAAAGCACTAACAACAC
ACCTTAAGAAGCTCTTGTGCTTCGCTTATGGTCATTCCACTTTTAACTAACATCCAAAAACAAG
TTTCGTATTGATTATTGGCGTGGCCTGTAACGAATAAGAAACGGAACTTGTTAGACGTTACAGA
AGACAATTGACGCAAATAAGTATCAAAATTATCATGAACGTGGTGTCAAGTACATTATTTCTGA
GCTCAGTATGTCTTACAATCTTGTTGTCTCCACGCGAGATAAGCTTGAAGAACCTCTGGCGATG
CACAACTTACGACTTTTGAGGTGAAAGAAGGAGTATATTCCAGTTTTCTTTGGGGAAAGAACTC
TTTCCATTTTGTTACGTAGACTGCAGCAAAGAAGGAAGCTACCAACGACAAAATCTTACTGCGT
ATTAAACAAAAAACGGTAGTGTAAAGAGTAAGAGTCAATCAGAGAAATGCAAAGCACATATTAT
TCTGCAAAAGGTTTTTATTATATATCGATCAAGTTTTAGATGAATCAAGACCTGGCTCGTCTCT
GGTAGAATCTTGATGTTTTCTTGAACACAAAGCTACGGAAGACAAGGAAAATAGTAGAGAATGA
GTGAGAGTGTAAAAACCTAAGACAAATAAAGTCAAACAAAGTGAGCTTTGGAACCTGTATTCAT
CACTGTATCCATAAGCAAAGATGATATCAGGAAACTCTCCCAAAACCGCAGCTGAACATGAATT
CAAAAGATTGAGGGCTGCTTCATCATTAGGCTTCTCAAACTCATGAACTTGGGAAAAC
						
					

			
		

Sequences
Splice junction sequence	GATATCAGGAAACTCTCCCAAAACCGCAGCTGAACATGAATTCAAAAGATTGAGGGCTGCTTCA TCATTAGGCTTCTCAAACTCATGAACTTGGGAAAACctttttcttgaagagacatgatccttgt cgaaacaattcaggaagcgttttgtaattgataccaaacttgtgaaagagaagctcatttttct gctgcttt
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: 541 Transcript exons: 6786089-6786196,6786283-6786368,6786489-6786658,6786780- 6786824,6786911-6787042 CTTTTTCTTGAAGAGACATGATCCTTGTCGAAACAATTCAGGAAGCGTTTTGTAATTGATACCA AACTTGTGAAAGAGAAGCTCATTTTTCTGCTGCTTTTGTGTATCCTTAAGAAGCTCTTGTGCTT CGCTTATGGTCATTCCACTTTTAACTAACATCCAAAAACAAGTTTCGTATTGATTATTGGCGTG GCAATCTTGTTGTCTCCACGCGAGATAAGCTTGAAGAACCTCTGGCGATGCACAACTTACGACT TTTGAGGTGAAAGAAGGAGTATATTCCAGTTTTCTTTGGGGAAAGAACTCTTTCCATTTTGTTA CGTAGACTGCAGCAAAGAAGGAAGCTACCAACGACAAAATCTTACTGGCTCGTCTCTGGTAGAA TCTTGATGTTTTCTTGAACACAAAGCTGTATTCATCACTGTATCCATAAGCAAAGATGATATCA GGAAACTCTCCCAAAACCGCAGCTGAACATGAATTCAAAAGATTGAGGGCTGCTTCATCATTAG GCTTCTCAAACTCATGAACTTGGGAAAAC
Genomic sequence	CTTTTTCTTGAAGAGACATGATCCTTGTCGAAACAATTCAGGAAGCGTTTTGTAATTGATACCA AACTTGTGAAAGAGAAGCTCATTTTTCTGCTGCTTTTGTGTATCCTGCAGGTATCCAATGGAAA TAGACAAACAATGAAATAACAATGCAAAGAAGGTAAAAAGAGCAATTTAAAGCACTAACAACAC ACCTTAAGAAGCTCTTGTGCTTCGCTTATGGTCATTCCACTTTTAACTAACATCCAAAAACAAG TTTCGTATTGATTATTGGCGTGGCCTGTAACGAATAAGAAACGGAACTTGTTAGACGTTACAGA AGACAATTGACGCAAATAAGTATCAAAATTATCATGAACGTGGTGTCAAGTACATTATTTCTGA GCTCAGTATGTCTTACAATCTTGTTGTCTCCACGCGAGATAAGCTTGAAGAACCTCTGGCGATG CACAACTTACGACTTTTGAGGTGAAAGAAGGAGTATATTCCAGTTTTCTTTGGGGAAAGAACTC TTTCCATTTTGTTACGTAGACTGCAGCAAAGAAGGAAGCTACCAACGACAAAATCTTACTGCGT ATTAAACAAAAAACGGTAGTGTAAAGAGTAAGAGTCAATCAGAGAAATGCAAAGCACATATTAT TCTGCAAAAGGTTTTTATTATATATCGATCAAGTTTTAGATGAATCAAGACCTGGCTCGTCTCT GGTAGAATCTTGATGTTTTCTTGAACACAAAGCTACGGAAGACAAGGAAAATAGTAGAGAATGA GTGAGAGTGTAAAAACCTAAGACAAATAAAGTCAAACAAAGTGAGCTTTGGAACCTGTATTCAT CACTGTATCCATAAGCAAAGATGATATCAGGAAACTCTCCCAAAACCGCAGCTGAACATGAATT CAAAAGATTGAGGGCTGCTTCATCATTAGGCTTCTCAAACTCATGAACTTGGGAAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.732802795

Conservation Information
Conserved circRNAs	NA
PMCS	0.732802795

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6786109-6786986(-)
6786335-6787027(-)
6786176-6787027(-)
						
						Potential amino acid sequence
						
							MSLQEKGFPKFMSLRSLMMKQPSIF*
MLVKSGMTISEAQELLKDTQKQQKNELLFHKFGINYKTLPELFRQGSCLFKKKVFPSS*
MSFSFTSLVSITKRFLNCFDKDHVSSRKRFSQVHEFEKPNDEAALNLLNSCSAAVLGEFPDIIF
AYGYSDEYSFVFKKTSRFYQRRASKILSLVASFFAAVYVTKWKEFFPQRKLEYTPSFTSKVVSC
ASPEVLQAYLAWRQQDCHANNQYETCFWMLVKSGMTISEAQELLKDTQKQQKNELLFHKFGINY
KTLPELFRQGSCLFKKKVFPSS*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6786109-6786986(-) 6786335-6787027(-) 6786176-6787027(-)
Potential amino acid sequence	MSLQEKGFPKFMSLRSLMMKQPSIF* MLVKSGMTISEAQELLKDTQKQQKNELLFHKFGINYKTLPELFRQGSCLFKKKVFPSS* MSFSFTSLVSITKRFLNCFDKDHVSSRKRFSQVHEFEKPNDEAALNLLNSCSAAVLGEFPDIIF AYGYSDEYSFVFKKTSRFYQRRASKILSLVASFFAAVYVTKWKEFFPQRKLEYTPSFTSKVVSC ASPEVLQAYLAWRQQDCHANNQYETCFWMLVKSGMTISEAQELLKDTQKQQKNELLFHKFGINY KTLPELFRQGSCLFKKKVFPSS*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Wang et al., 2019

circRNA

Detail information of Bra005655_circ_g.1

Address

Any questions?

Supported by