Plant Circular RNA Database

Detail information of orai.003G175400_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.003G175400_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000288
					
						Alias
						Chr03:44717046|44717922
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr03: 44717046-44717922  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.003G175400						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							orai.003G175400_circ_g.1 						
					
						Support reads
						17/116
					
						Tissues
						leaf/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.003G175400.1:3

General Information
CircRNA Name	orai.003G175400_circ_g.2
ID in PlantcircBase	gra_circ_000288
Alias	Chr03:44717046\|44717922
Organism	Gossypium raimondii
Position	chrChr03: 44717046-44717922 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.003G175400
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	orai.003G175400_circ_g.1
Support reads	17/116
Tissues	leaf/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.003G175400.1:3

			
						 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  
						
							TTCCGCTTGACCCAATCCTTGACAACCTTCTCATCCAGTAGCAAAGCAGTGATAGCATCACTGG
AAACAGCAGTTTCATCCATGCATATATCTGTAACATaattgcttgctttgcaaccaccaaatca
gaactaccacatagaaagaggatgtccacagcagcctggagactttcaaatgggtaacaccctc
tcaatccc

									
								

					

						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: 713
Transcript exons: 44717046-44717447,44717524-44717699,44717788-44717922
AATTGCTTGCTTTGCAACCACCAAATCAGAACTACCACATAGAAAGAGGATGTCCACAGCAGCC
TGGAGACTTTCAAATGGGTAACACCCTCTCAATCCCTCTATTTTAGACCGAGAAAAGGAGGAGC
TGTCCTTCAGTAAAAATGCAAAATATGACTCTTCTCCAAGCTCCTGATCACATGCTTGTTCGAT
GTCAAGGTTTGCTAATGCATCTTCAATGAATAGAGAGCCATCCTGTCTAGTGGAGTCGGCTGAG
CGATCGACTACATCAGGCCATGCACGTGCAGTTGCAGCCGATTTTCTTTCACGGACAAGATTAT
GCCAGGATGTGAAATTAGCATGACGAGACCTCACATGTTCCAAGAATTGGTGCCTTATACACCA
CATTATGATCTCAAGATGCTGCTTCGTCTTCAATATACTCTCTTGAAGGTGATGCAAGTCATGG
AGCTGTGCCAAAGGACGACCCTTGAAAGATGATTCCAAAACTTCAAGAATACTGGATAAGCTAG
CCAGATATGCTGAATATTTGTGAAGCAAACCTAAACTCTTTTCCATTTCTCCTACCTTGAGATA
ATATATCTGTTGAAGTTCTGTTGTAATATTTTTAAACTTCCGCTTGACCCAATCCTTGACAACC
TTCTCATCCAGTAGCAAAGCAGTGATAGCATCACTGGAAACAGCAGTTTCATCCATGCATATAT
CTGTAACAT
						
					

						Genomic sequence
						
							AATTGCTTGCTTTGCAACCACCAAATCAGAACTACCACATAGAAAGAGGATGTCCACAGCAGCC
TGGAGACTTTCAAATGGGTAACACCCTCTCAATCCCTCTATTTTAGACCGAGAAAAGGAGGAGC
TGTCCTTCAGTAAAAATGCAAAATATGACTCTTCTCCAAGCTCCTGATCACATGCTTGTTCGAT
GTCAAGGTTTGCTAATGCATCTTCAATGAATAGAGAGCCATCCTGTCTAGTGGAGTCGGCTGAG
CGATCGACTACATCAGGCCATGCACGTGCAGTTGCAGCCGATTTTCTTTCACGGACAAGATTAT
GCCAGGATGTGAAATTAGCATGACGAGACCTCACATGTTCCAAGAATTGGTGCCTTATACACCA
CATTATGATCTCAAGATGCTGAAAATTTTATAACAGTTGTTGCTCTTAAAAAGATGCTAATATA
TGGTTAAATATCTTCTTAATTGAATCAAACCTGCTTCGTCTTCAATATACTCTCTTGAAGGTGA
TGCAAGTCATGGAGCTGTGCCAAAGGACGACCCTTGAAAGATGATTCCAAAACTTCAAGAATAC
TGGATAAGCTAGCCAGATATGCTGAATATTTGTGAAGCAAACCTAAACTCTTTTCCATTTCTCC
TACCTTGAGATAATCTGATAAAACGGTTAGGGAACACCCAATGCACATGGTATAAACAAAAGTC
ATAGTTCTCAAAGAATTCCACAAACTATTTAAGGATACATATCTGTTGAAGTTCTGTTGTAATA
TTTTTAAACTTCCGCTTGACCCAATCCTTGACAACCTTCTCATCCAGTAGCAAAGCAGTGATAG
CATCACTGGAAACAGCAGTTTCATCCATGCATATATCTGTAACAT
						
					

			
		

Sequences
Splice junction sequence	TTCCGCTTGACCCAATCCTTGACAACCTTCTCATCCAGTAGCAAAGCAGTGATAGCATCACTGG AAACAGCAGTTTCATCCATGCATATATCTGTAACATaattgcttgctttgcaaccaccaaatca gaactaccacatagaaagaggatgtccacagcagcctggagactttcaaatgggtaacaccctc tcaatccc
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: 713 Transcript exons: 44717046-44717447,44717524-44717699,44717788-44717922 AATTGCTTGCTTTGCAACCACCAAATCAGAACTACCACATAGAAAGAGGATGTCCACAGCAGCC TGGAGACTTTCAAATGGGTAACACCCTCTCAATCCCTCTATTTTAGACCGAGAAAAGGAGGAGC TGTCCTTCAGTAAAAATGCAAAATATGACTCTTCTCCAAGCTCCTGATCACATGCTTGTTCGAT GTCAAGGTTTGCTAATGCATCTTCAATGAATAGAGAGCCATCCTGTCTAGTGGAGTCGGCTGAG CGATCGACTACATCAGGCCATGCACGTGCAGTTGCAGCCGATTTTCTTTCACGGACAAGATTAT GCCAGGATGTGAAATTAGCATGACGAGACCTCACATGTTCCAAGAATTGGTGCCTTATACACCA CATTATGATCTCAAGATGCTGCTTCGTCTTCAATATACTCTCTTGAAGGTGATGCAAGTCATGG AGCTGTGCCAAAGGACGACCCTTGAAAGATGATTCCAAAACTTCAAGAATACTGGATAAGCTAG CCAGATATGCTGAATATTTGTGAAGCAAACCTAAACTCTTTTCCATTTCTCCTACCTTGAGATA ATATATCTGTTGAAGTTCTGTTGTAATATTTTTAAACTTCCGCTTGACCCAATCCTTGACAACC TTCTCATCCAGTAGCAAAGCAGTGATAGCATCACTGGAAACAGCAGTTTCATCCATGCATATAT CTGTAACAT
Genomic sequence	AATTGCTTGCTTTGCAACCACCAAATCAGAACTACCACATAGAAAGAGGATGTCCACAGCAGCC TGGAGACTTTCAAATGGGTAACACCCTCTCAATCCCTCTATTTTAGACCGAGAAAAGGAGGAGC TGTCCTTCAGTAAAAATGCAAAATATGACTCTTCTCCAAGCTCCTGATCACATGCTTGTTCGAT GTCAAGGTTTGCTAATGCATCTTCAATGAATAGAGAGCCATCCTGTCTAGTGGAGTCGGCTGAG CGATCGACTACATCAGGCCATGCACGTGCAGTTGCAGCCGATTTTCTTTCACGGACAAGATTAT GCCAGGATGTGAAATTAGCATGACGAGACCTCACATGTTCCAAGAATTGGTGCCTTATACACCA CATTATGATCTCAAGATGCTGAAAATTTTATAACAGTTGTTGCTCTTAAAAAGATGCTAATATA TGGTTAAATATCTTCTTAATTGAATCAAACCTGCTTCGTCTTCAATATACTCTCTTGAAGGTGA TGCAAGTCATGGAGCTGTGCCAAAGGACGACCCTTGAAAGATGATTCCAAAACTTCAAGAATAC TGGATAAGCTAGCCAGATATGCTGAATATTTGTGAAGCAAACCTAAACTCTTTTCCATTTCTCC TACCTTGAGATAATCTGATAAAACGGTTAGGGAACACCCAATGCACATGGTATAAACAAAAGTC ATAGTTCTCAAAGAATTCCACAAACTATTTAAGGATACATATCTGTTGAAGTTCTGTTGTAATA TTTTTAAACTTCCGCTTGACCCAATCCTTGACAACCTTCTCATCCAGTAGCAAAGCAGTGATAG CATCACTGGAAACAGCAGTTTCATCCATGCATATATCTGTAACAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							ghi_circ_000264* ghi_circ_000860* gar_circ_000826* gar_circ_000746 
ghi_circ_000199 ghi_circ_000420 						
					
						PMCS
						1.116116059

Conservation Information
Conserved circRNAs	ghi_circ_000264* ghi_circ_000860* gar_circ_000826* gar_circ_000746 ghi_circ_000199 ghi_circ_000420
PMCS	1.116116059

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							44717906-44717687(-)
						
						Potential amino acid sequence
						
							MDETAVSSDAITALLLDEKVVKDWVKRKFKNITTELQQIYYLKVGEMEKSLGLLHKYSAYLASL
SSILEVLESSFKGRPLAQLHDLHHLQESILKTKQHLEIIMWCIRHQFLEHVRSRHANFTSWHNL
VRERKSAATARAWPDVVDRSADSTRQDGSLFIEDALANLDIEQACDQELGEESYFAFLLKDSSS
FSRSKIEGLRGCYPFESLQAAVDILFLCGSSDLVVAKQAIMLQIYAWMKLLFPVMLSLLCYWMR
RLSRIGSSGSLKILQQNFNRYIISR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	44717906-44717687(-)
Potential amino acid sequence	MDETAVSSDAITALLLDEKVVKDWVKRKFKNITTELQQIYYLKVGEMEKSLGLLHKYSAYLASL SSILEVLESSFKGRPLAQLHDLHHLQESILKTKQHLEIIMWCIRHQFLEHVRSRHANFTSWHNL VRERKSAATARAWPDVVDRSADSTRQDGSLFIEDALANLDIEQACDQELGEESYFAFLLKDSSS FSRSKIEGLRGCYPFESLQAAVDILFLCGSSDLVVAKQAIMLQIYAWMKLLFPVMLSLLCYWMR RLSRIGSSGSLKILQQNFNRYIISR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.003G175400_circ_g.2

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