Plant Circular RNA Database

Detail information of orai.003G009500_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.003G009500_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000226
					
						Alias
						Chr03:580843|581809
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr03: 580843-581809  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.003G009500						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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.003G009500.3:5
Gorai.003G009500.6:5
Gorai.003G009500.8:5
Gorai.003G009500.4:5
Gorai.003G009500.2:5
Gorai.003G009500.5:5
Gorai.003G009500.7:5
Gorai.003G009500.1:5

General Information
CircRNA Name	orai.003G009500_circ_g.1
ID in PlantcircBase	gra_circ_000226
Alias	Chr03:580843\|581809
Organism	Gossypium raimondii
Position	chrChr03: 580843-581809 JBrowse»
Reference genome	Graimondii_221
Type	ue-circRNA
Identification method	CIRI
Parent gene	Gorai.003G009500
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
Support reads	2
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.003G009500.3:5 Gorai.003G009500.6:5 Gorai.003G009500.8:5 Gorai.003G009500.4:5 Gorai.003G009500.2:5 Gorai.003G009500.5:5 Gorai.003G009500.7:5 Gorai.003G009500.1:5

			
						 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  
						
							CGAATGCATTATAAAATTGAACCACATTTTCATGGCCTTTCAAGGCTTTCAATATCTTGACTTC
TCGCTTGACATCCTCGACAGCGATTGGAAGAATCATctccttaaatataccatcctcagtctta
tcccaaaagggacgcttcccacagagcaaaatgtaggtaattacaccgatactccatacatctg
attcaggc

									
								

					

						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: 534
Transcript exons: 580843-581012,581145-581223,581312-581423,581509-581550,
581679-581809
CTCCTTAAATATACCATCCTCAGTCTTATCCCAAAAGGGACGCTTCCCACAGAGCAAAATGTAG
GTAATTACACCGATACTCCATACATCTGATTCAGGCCCTGACCTTCTTTTTAATACTTCAGGAG
CAACATAATAGGCACTGCCAACAATATCTCGAAACCTCTTCCCAGGTTTGATAAAGTCCGACAA
ACCGAAATCTGTAGCCTTCAGAGGCGAGTCTGGACGTGTTGACTTAAATAGGAAATTCTCAGGT
TTCATGTCACGGTGCACTAAGCCATGCAGATGACACTCGGCCGCAACTTTGAGCATTTGCCGTA
CTACTACTGCAGCATCTTTTTCACTATATCGGCTATCTTTTTTGGCCAAAATCCGGTCCAACAA
TTCTCCACCCTCACATAACTCCATAACAATATACACATAGGAATCATCCTCGAATGCATTATAA
AATTGAACCACATTTTCATGGCCTTTCAAGGCTTTCAATATCTTGACTTCTCGCTTGACATCCT
CGACAGCGATTGGAAGAATCAT
						
					

						Genomic sequence
						
							CTCCTTAAATATACCATCCTCAGTCTTATCCCAAAAGGGACGCTTCCCACAGAGCAAAATGTAG
GTAATTACACCGATACTCCATACATCTGATTCAGGCCCTGACCTTCTTTTTAATACTTCAGGAG
CAACATAATAGGCACTGCCAACAATATCTCGAAACCTCTTCCCTGCATTTAGTTTTGTGTACGA
GGATTATAACATTAGCAAGTTGAACTGAAACTAAACAGAACACACAATATATTGATAATGGAAC
CTGGTAATGTTAAAAAGCATACTTTAATCAAGCAAATGCTACTCACCAGGTTTGATAAAGTCCG
ACAAACCGAAATCTGTAGCCTTCAGAGGCGAGTCTGGACGTGTTGACTTAAATAGGAAATTCTA
CAGGCAAGAAAAAACAAGAGAAACTGTAAGTAAGCAGCATGACATGAAGTTTACGAGTAAGCCA
TGTTAATGTACTTGAGCATACCTCAGGTTTCATGTCACGGTGCACTAAGCCATGCAGATGACAC
TCGGCCGCAACTTTGAGCATTTGCCGTACTACTACTGCAGCATCTTTTTCACTATATCGGCTAT
CTTTTCTGATAGAAGATGGGAAGAATAAGTTACTACAGGCTGTTTAAACTATCGAAAAATCAAG
GGAAAGAAAGTACTACATATACTTACTTGGCCAAAATCCGGTCCAACAATTCTCCACCCTCACA
TAACCTAGAATCATAGAACATCAACACATGATAGAGTCAAGATATGAAGCACAGATCAAGGTCG
AACACGAGTTCCAAGGGGGGAAAAAGAAAAGAAAAACGAGAAAAAGGAGATGAGCTTATAGAAC
TTACTCCATAACAATATACACATAGGAATCATCCTCGAATGCATTATAAAATTGAACCACATTT
TCATGGCCTTTCAAGGCTTTCAATATCTTGACTTCTCGCTTGACATCCTCGACAGCGATTGGAA
GAATCAT
						
					

			
		

Sequences
Splice junction sequence	CGAATGCATTATAAAATTGAACCACATTTTCATGGCCTTTCAAGGCTTTCAATATCTTGACTTC TCGCTTGACATCCTCGACAGCGATTGGAAGAATCATctccttaaatataccatcctcagtctta tcccaaaagggacgcttcccacagagcaaaatgtaggtaattacaccgatactccatacatctg attcaggc
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: 534 Transcript exons: 580843-581012,581145-581223,581312-581423,581509-581550, 581679-581809 CTCCTTAAATATACCATCCTCAGTCTTATCCCAAAAGGGACGCTTCCCACAGAGCAAAATGTAG GTAATTACACCGATACTCCATACATCTGATTCAGGCCCTGACCTTCTTTTTAATACTTCAGGAG CAACATAATAGGCACTGCCAACAATATCTCGAAACCTCTTCCCAGGTTTGATAAAGTCCGACAA ACCGAAATCTGTAGCCTTCAGAGGCGAGTCTGGACGTGTTGACTTAAATAGGAAATTCTCAGGT TTCATGTCACGGTGCACTAAGCCATGCAGATGACACTCGGCCGCAACTTTGAGCATTTGCCGTA CTACTACTGCAGCATCTTTTTCACTATATCGGCTATCTTTTTTGGCCAAAATCCGGTCCAACAA TTCTCCACCCTCACATAACTCCATAACAATATACACATAGGAATCATCCTCGAATGCATTATAA AATTGAACCACATTTTCATGGCCTTTCAAGGCTTTCAATATCTTGACTTCTCGCTTGACATCCT CGACAGCGATTGGAAGAATCAT
Genomic sequence	CTCCTTAAATATACCATCCTCAGTCTTATCCCAAAAGGGACGCTTCCCACAGAGCAAAATGTAG GTAATTACACCGATACTCCATACATCTGATTCAGGCCCTGACCTTCTTTTTAATACTTCAGGAG CAACATAATAGGCACTGCCAACAATATCTCGAAACCTCTTCCCTGCATTTAGTTTTGTGTACGA GGATTATAACATTAGCAAGTTGAACTGAAACTAAACAGAACACACAATATATTGATAATGGAAC CTGGTAATGTTAAAAAGCATACTTTAATCAAGCAAATGCTACTCACCAGGTTTGATAAAGTCCG ACAAACCGAAATCTGTAGCCTTCAGAGGCGAGTCTGGACGTGTTGACTTAAATAGGAAATTCTA CAGGCAAGAAAAAACAAGAGAAACTGTAAGTAAGCAGCATGACATGAAGTTTACGAGTAAGCCA TGTTAATGTACTTGAGCATACCTCAGGTTTCATGTCACGGTGCACTAAGCCATGCAGATGACAC TCGGCCGCAACTTTGAGCATTTGCCGTACTACTACTGCAGCATCTTTTTCACTATATCGGCTAT CTTTTCTGATAGAAGATGGGAAGAATAAGTTACTACAGGCTGTTTAAACTATCGAAAAATCAAG GGAAAGAAAGTACTACATATACTTACTTGGCCAAAATCCGGTCCAACAATTCTCCACCCTCACA TAACCTAGAATCATAGAACATCAACACATGATAGAGTCAAGATATGAAGCACAGATCAAGGTCG AACACGAGTTCCAAGGGGGGAAAAAGAAAAGAAAAACGAGAAAAAGGAGATGAGCTTATAGAAC TTACTCCATAACAATATACACATAGGAATCATCCTCGAATGCATTATAAAATTGAACCACATTT TCATGGCCTTTCAAGGCTTTCAATATCTTGACTTCTCGCTTGACATCCTCGACAGCGATTGGAA GAATCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.55240848

Conservation Information
Conserved circRNAs	NA
PMCS	0.55240848

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							581743-581507(-)
581741-580932(+)
						
						Potential amino acid sequence
						
							MKMWFNFIMHSRMIPMCILLWSYVRVENCWTGFWPSKKDSRYSEKDAAVVVRQMLKVAAECHLH
GLVHRDMKPENFLFKSTRPDSPLKATDFGLSDFIKPGKRFRDIVGSAYYVAPEVLKRRSGPESD
VWSIGVITYILLCGKRPFWDKTEDGIFKEMILPIAVEDVKREVKILKALKGHENVVQFYNAFED
DSYVYIVMELCEGGELLDRILAK*(-)
MAFQGFQYLDFSLDILDSDWKNHLLKYTILSLIPKGTLPTEQNVGNYTDTPYI*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	581743-581507(-) 581741-580932(+)
Potential amino acid sequence	MKMWFNFIMHSRMIPMCILLWSYVRVENCWTGFWPSKKDSRYSEKDAAVVVRQMLKVAAECHLH GLVHRDMKPENFLFKSTRPDSPLKATDFGLSDFIKPGKRFRDIVGSAYYVAPEVLKRRSGPESD VWSIGVITYILLCGKRPFWDKTEDGIFKEMILPIAVEDVKREVKILKALKGHENVVQFYNAFED DSYVYIVMELCEGGELLDRILAK(-) MAFQGFQYLDFSLDILDSDWKNHLLKYTILSLIPKGTLPTEQNVGNYTDTPYI(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.003G009500_circ_g.1

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