Plant Circular RNA Database

Detail information of orai.006G070400_circ_g.2

			
						 General Information
					
						CircRNA Name
						orai.006G070400_circ_g.2
					
						ID in PlantcircBase
						gra_circ_000582
					
						Alias
						Chr06:28410689|28411740
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr06: 28410689-28411740  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.006G070400						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						5
					
						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.006G070400.3:4
Gorai.006G070400.6:4
Gorai.006G070400.5:4
Gorai.006G070400.4:4
Gorai.006G070400.7:4
Gorai.006G070400.1:4
Gorai.006G070400.2:4

General Information
CircRNA Name	orai.006G070400_circ_g.2
ID in PlantcircBase	gra_circ_000582
Alias	Chr06:28410689\|28411740
Organism	Gossypium raimondii
Position	chrChr06: 28410689-28411740 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.006G070400
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	5
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.006G070400.3:4 Gorai.006G070400.6:4 Gorai.006G070400.5:4 Gorai.006G070400.4:4 Gorai.006G070400.7:4 Gorai.006G070400.1:4 Gorai.006G070400.2:4

			
						 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  
						
							ATAACCAGCAGATCTTGCGGCTTCTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAA
GCTTCAGCAAGTGCTTCACTGCCAGCCAATAAGCGGcaatttcaaggtgagctttactagggat
gctattgattgctcccgggtaaagctccaaaatccctagaaaacaaaaataataaatttatatt
agttggaa

									
								

					

						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: 461
Transcript exons: 28410689-28410751,28410879-28410970,28411354-28411456,28
411538-28411740
CAATTTCAAGGTGAGCTTTACTAGGGATGCTATTGATTGCTCCCGGGTAAAGCTCCAAAATCCC
TACTGTACCAACAGTGTCAAGTGATCCGGATTCTGTTGCATGTTTCTCGATAGCTAACATTAAC
TCGGCAGCTGCCAGTCCAGCATCATTTCTGTCTGGCATCAAGACGCCACCTGCATGACCACCAT
TGCCTTCAAAATCTACTTTTATGCTTGCAGGGGCAGCGATGTTAGTAACTACGCCAATAGATAT
ACCTTCTTCTTCGAGAATCGGCGCTTGTTCTATATGCAACTCAACAAAAGCCGAGTAACTGTCA
TTCTTCAGAAACACTCTGGATAAATCATCTTCATCTCTAGCATAACCAGCAGATCTTGCGGCTT
CTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAAGCTTCAGCAAGTGCTTCACTGCC
AGCCAATAAGCGG
						
					

						Genomic sequence
						
							CAATTTCAAGGTGAGCTTTACTAGGGATGCTATTGATTGCTCCCGGGTAAAGCTCCAAAATCCC
TAGAAAACAAAAATAATAAATTTATATTAGTTGGAAAAAAATCTATTCAGATGAAATAAAGGAA
GCTTCGTTTAGTGCAGAAGAACTCTTTTAACAAAAACATGAAAATATTTCCTTCAGATTTACCT
ACTGTACCAACAGTGTCAAGTGATCCGGATTCTGTTGCATGTTTCTCGATAGCTAACATTAACT
CGGCAGCTGCCAGTCCAGCATCATTTCTGCACTCAATAGTATACACACAGGTTATGGATCTTTT
TACTTAATAAGCATTCTAGAAAAAAGTATAATGAGGATGATCTAACAGAACCTGAATCTAATTT
AACCAAACTACTCCGACCTTTGGAAATAAATATATATATATATATATATATGAAATATGCTATT
TACAATCAGCATCAATGAAACACAAAAGTTGCAGAAGTTGGCATTAGCGTTATAAGAATGTCAC
TCTTATGTTGGACTAGGATGTTCAATTTTTTTCCCAAGTTTTTTCGTTTATTTGGAAGGTTATT
GAAGGGTCATATTCCCGTACTCACTCCATATACGTGTAGGCACTAGTATTTCAAAGAAAAAAAA
AATAGTCACTATCGGTAATATTAACCTGTCTGGCATCAAGACGCCACCTGCATGACCACCATTG
CCTTCAAAATCTACTTTTATGCTTGCAGGGGCAGCGATGTTAGTAACTACGCCAATAGATATAC
CTGAAATAAAGAATCATACGGATAAGCCGATCCCAACACATTGTAAGAAAGAGAAAACTGTAAC
ATTCAAAAGCAAGATACCTTCTTCTTCGAGAATCGGCGCTTGTTCTATATGCAACTCAACAAAA
GCCGAGTAACTGTCATTCTTCAGAAACACTCTGGATAAATCATCTTCATCTCTAGCATAACCAG
CAGATCTTGCGGCTTCTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAAGCTTCAGC
AAGTGCTTCACTGCCAGCCAATAAGCGG
						
					

			
		

Sequences
Splice junction sequence	ATAACCAGCAGATCTTGCGGCTTCTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAA GCTTCAGCAAGTGCTTCACTGCCAGCCAATAAGCGGcaatttcaaggtgagctttactagggat gctattgattgctcccgggtaaagctccaaaatccctagaaaacaaaaataataaatttatatt agttggaa
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: 461 Transcript exons: 28410689-28410751,28410879-28410970,28411354-28411456,28 411538-28411740 CAATTTCAAGGTGAGCTTTACTAGGGATGCTATTGATTGCTCCCGGGTAAAGCTCCAAAATCCC TACTGTACCAACAGTGTCAAGTGATCCGGATTCTGTTGCATGTTTCTCGATAGCTAACATTAAC TCGGCAGCTGCCAGTCCAGCATCATTTCTGTCTGGCATCAAGACGCCACCTGCATGACCACCAT TGCCTTCAAAATCTACTTTTATGCTTGCAGGGGCAGCGATGTTAGTAACTACGCCAATAGATAT ACCTTCTTCTTCGAGAATCGGCGCTTGTTCTATATGCAACTCAACAAAAGCCGAGTAACTGTCA TTCTTCAGAAACACTCTGGATAAATCATCTTCATCTCTAGCATAACCAGCAGATCTTGCGGCTT CTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAAGCTTCAGCAAGTGCTTCACTGCC AGCCAATAAGCGG
Genomic sequence	CAATTTCAAGGTGAGCTTTACTAGGGATGCTATTGATTGCTCCCGGGTAAAGCTCCAAAATCCC TAGAAAACAAAAATAATAAATTTATATTAGTTGGAAAAAAATCTATTCAGATGAAATAAAGGAA GCTTCGTTTAGTGCAGAAGAACTCTTTTAACAAAAACATGAAAATATTTCCTTCAGATTTACCT ACTGTACCAACAGTGTCAAGTGATCCGGATTCTGTTGCATGTTTCTCGATAGCTAACATTAACT CGGCAGCTGCCAGTCCAGCATCATTTCTGCACTCAATAGTATACACACAGGTTATGGATCTTTT TACTTAATAAGCATTCTAGAAAAAAGTATAATGAGGATGATCTAACAGAACCTGAATCTAATTT AACCAAACTACTCCGACCTTTGGAAATAAATATATATATATATATATATATGAAATATGCTATT TACAATCAGCATCAATGAAACACAAAAGTTGCAGAAGTTGGCATTAGCGTTATAAGAATGTCAC TCTTATGTTGGACTAGGATGTTCAATTTTTTTCCCAAGTTTTTTCGTTTATTTGGAAGGTTATT GAAGGGTCATATTCCCGTACTCACTCCATATACGTGTAGGCACTAGTATTTCAAAGAAAAAAAA AATAGTCACTATCGGTAATATTAACCTGTCTGGCATCAAGACGCCACCTGCATGACCACCATTG CCTTCAAAATCTACTTTTATGCTTGCAGGGGCAGCGATGTTAGTAACTACGCCAATAGATATAC CTGAAATAAAGAATCATACGGATAAGCCGATCCCAACACATTGTAAGAAAGAGAAAACTGTAAC ATTCAAAAGCAAGATACCTTCTTCTTCGAGAATCGGCGCTTGTTCTATATGCAACTCAACAAAA GCCGAGTAACTGTCATTCTTCAGAAACACTCTGGATAAATCATCTTCATCTCTAGCATAACCAG CAGATCTTGCGGCTTCTAAGAACGATATGTTTTGACCATCAACTGTCGCCTTTAAAGCTTCAGC AAGTGCTTCACTGCCAGCCAATAAGCGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							gar_circ_000196* 						
					
						PMCS
						0.800048606

Conservation Information
Conserved circRNAs	gar_circ_000196*
PMCS	0.800048606

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28411365-28411702(-)
						
						Potential amino acid sequence
						
							MPDRNDAGLAAAELMLAIEKHATESGSLDTVGTVGILELYPGAINSIPSKAHLEIAAYWLAVKH
LLKL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28411365-28411702(-)
Potential amino acid sequence	MPDRNDAGLAAAELMLAIEKHATESGSLDTVGTVGILELYPGAINSIPSKAHLEIAAYWLAVKH LLKL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.006G070400_circ_g.2

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