Plant Circular RNA Database

Detail information of orai.006G083500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.006G083500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000598
					
						Alias
						Chr06:31637238|31637719
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr06: 31637238-31637719  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.006G083500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.006G083400_circ_g.1 orai.006G083400_circ_ag.1 orai.006G083500_circ_g.2 						
					
						Support reads
						11
					
						Tissues
						ovule
					
						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
						Gorai.006G083500.2:2
Gorai.006G083500.3:3
Gorai.006G083500.1:2
Gorai.006G083500.4:2

General Information
CircRNA Name	orai.006G083500_circ_g.1
ID in PlantcircBase	gra_circ_000598
Alias	Chr06:31637238\|31637719
Organism	Gossypium raimondii
Position	chrChr06: 31637238-31637719 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.006G083500
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.006G083400_circ_g.1 orai.006G083400_circ_ag.1 orai.006G083500_circ_g.2
Support reads	11
Tissues	ovule
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	Gorai.006G083500.2:2 Gorai.006G083500.3:3 Gorai.006G083500.1:2 Gorai.006G083500.4:2

			
						 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  
						
							GCAAGACCTTTCATGCCACCTCCGTCCAACGAAAGTATGCGTATGCCTGTTTTCGGGACCTGTC
TCCCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTCtttagatccttttgcaacaactctgaaa
ctctgtgatgaacttttataaagctggtccaacttgtgtttccaagttgcggcttcatttttct
tttgcaca

						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: 314
Transcript exons: 31637238-31637359,31637459-31637609,31637679-31637719
TTTAGATCCTTTTGCAACAACTCTGAAACTCTGTGATGAACTTTTATAAAGCTGGTCCAACTTG
TGTTTCCAAGTTGCGGCTTCATTTTTCTTTTGCACAGGTTCAGAGAAAACAACTTTCCCAAGAT
TTCTGTATATTTCTTCCAATTGGTCCGAGCTCATCAACTTAATACCAAGTGCAGATGCGAAAAT
GCCACCCGTTGAAGTCCCACATATAAGGTCAAATAGCTCATGCATTCGCTTTCCTGTTCCCCTT
TCAATTTCTTGAAGGATCTGTCTCCCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTC
						
						Genomic sequence
						
							TTTAGATCCTTTTGCAACAACTCTGAAACTCTGTGATGAACTTTTATAAAGCTGGTCCAACTTG
TGTTTCCAAGTTGCGGCTTCATTTTTCTTTTGCACAGGTTCAGAGAAAACAACTTTCCCTACAA
AGTCAAAACAGGGAACACTATAAACAAAGTGAACTACAACTATATATACAGTGTTGATGAATAA
TGATTCTTTATGCAGAGCCATATAGTTACCAAGATTTCTGTATATTTCTTCCAATTGGTCCGAG
CTCATCAACTTAATACCAAGTGCAGATGCGAAAATGCCACCCGTTGAAGTCCCACATATAAGGT
CAAATAGCTCATGCATTCGCTTTCCTGTTCCCCTTTCAATTTCTTGAAGGATCTGCACAGTTGC
AAGACCTTTCATGCCACCTCCGTCCAACGAAAGTATGCGTATGCCTGTTTTCGGGACCTGTCTC
CCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTC

Sequences
Splice junction sequence	GCAAGACCTTTCATGCCACCTCCGTCCAACGAAAGTATGCGTATGCCTGTTTTCGGGACCTGTC TCCCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTCtttagatccttttgcaacaactctgaaa ctctgtgatgaacttttataaagctggtccaacttgtgtttccaagttgcggcttcatttttct tttgcaca
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: 314 Transcript exons: 31637238-31637359,31637459-31637609,31637679-31637719 TTTAGATCCTTTTGCAACAACTCTGAAACTCTGTGATGAACTTTTATAAAGCTGGTCCAACTTG TGTTTCCAAGTTGCGGCTTCATTTTTCTTTTGCACAGGTTCAGAGAAAACAACTTTCCCAAGAT TTCTGTATATTTCTTCCAATTGGTCCGAGCTCATCAACTTAATACCAAGTGCAGATGCGAAAAT GCCACCCGTTGAAGTCCCACATATAAGGTCAAATAGCTCATGCATTCGCTTTCCTGTTCCCCTT TCAATTTCTTGAAGGATCTGTCTCCCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTC
Genomic sequence	TTTAGATCCTTTTGCAACAACTCTGAAACTCTGTGATGAACTTTTATAAAGCTGGTCCAACTTG TGTTTCCAAGTTGCGGCTTCATTTTTCTTTTGCACAGGTTCAGAGAAAACAACTTTCCCTACAA AGTCAAAACAGGGAACACTATAAACAAAGTGAACTACAACTATATATACAGTGTTGATGAATAA TGATTCTTTATGCAGAGCCATATAGTTACCAAGATTTCTGTATATTTCTTCCAATTGGTCCGAG CTCATCAACTTAATACCAAGTGCAGATGCGAAAATGCCACCCGTTGAAGTCCCACATATAAGGT CAAATAGCTCATGCATTCGCTTTCCTGTTCCCCTTTCAATTTCTTGAAGGATCTGCACAGTTGC AAGACCTTTCATGCCACCTCCGTCCAACGAAAGTATGCGTATGCCTGTTTTCGGGACCTGTCTC CCTTTAATAGCACGGCGCAAGCTTTCGTTCTCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.929560858

Conservation Information
Conserved circRNAs	NA
PMCS	0.929560858

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31637324-31637691(-)
31637634-31637632(-)
31637568-31637283(+)
31637632-31637239(+)
						
						Potential amino acid sequence
						
							MKPQLGNTSWTSFIKVHHRVSELLQKDLKRERKLAPCY*(-)
MKGLATVQILQEIERGTGKRMHELFDLICGTSTGGIFASALGIKLMSSDQLEEIYRNLGKVVFS
EPVQKKNEAATWKHKLDQLYKSSSQSFRVVAKGSKERTKACAVLLKGDRSRKQAYAYFRWTEVA
*(-)
MHSLSCSPFNFLKDLHSCKTFHATSVQRKYAYACFRDLSPFNSTAQAFVLSLDPFATTLKLCDE
LL*(+)
MPPPSNESMRMPVFGTCLPLIARRKLSFSL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31637324-31637691(-) 31637634-31637632(-) 31637568-31637283(+) 31637632-31637239(+)
Potential amino acid sequence	MKPQLGNTSWTSFIKVHHRVSELLQKDLKRERKLAPCY(-) MKGLATVQILQEIERGTGKRMHELFDLICGTSTGGIFASALGIKLMSSDQLEEIYRNLGKVVFS EPVQKKNEAATWKHKLDQLYKSSSQSFRVVAKGSKERTKACAVLLKGDRSRKQAYAYFRWTEVA (-) MHSLSCSPFNFLKDLHSCKTFHATSVQRKYAYACFRDLSPFNSTAQAFVLSLDPFATTLKLCDE LL(+) MPPPSNESMRMPVFGTCLPLIARRKLSFSL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.006G083500_circ_g.1

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