Plant Circular RNA Database

Detail information of Os11g0562100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os11g0562100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_009615
					
						Alias
						Os11circ07139/Os_ciR1044
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 20947082-20948800  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os11g0562100						
					
						Parent gene annotation
						
							Squalene cyclase domain containing protein. (Os11t0562100-01);Si
milar to cycloartenol synthase. (Os11t0562100-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0562100_circ_g.1 Os11g0562100_circ_g.3 Os11g0562100_circ_g.4 Os11g0562100_circ_g.5 Os11g0562100_circ_g.6 Os11g0562100_circ_g.7 Os11g0562100_circ_g.8 Os11g0562100_circ_g.9 Os11g0562100_circ_g.10 Os11g0562100_circ_g.11 						
					
						Support reads
						2/15/4/4
					
						Tissues
						leaf/root/root/shoot, root
					
						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  
						
							GT-AG							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
						Os11t0562100-01:2
Os11t0562100-02:2

General Information
CircRNA Name	Os11g0562100_circ_g.2
ID in PlantcircBase	osa_circ_009615
Alias	Os11circ07139/Os_ciR1044
Organism	Oryza sativa
Position	chr11: 20947082-20948800 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
Parent gene	Os11g0562100
Parent gene annotation	Squalene cyclase domain containing protein. (Os11t0562100-01);Si milar to cycloartenol synthase. (Os11t0562100-02)
Parent gene strand	+
Alternative splicing	Os11g0562100_circ_g.1 Os11g0562100_circ_g.3 Os11g0562100_circ_g.4 Os11g0562100_circ_g.5 Os11g0562100_circ_g.6 Os11g0562100_circ_g.7 Os11g0562100_circ_g.8 Os11g0562100_circ_g.9 Os11g0562100_circ_g.10 Os11g0562100_circ_g.11
Support reads	2/15/4/4
Tissues	leaf/root/root/shoot, root
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	GT-AG 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	Os11t0562100-01:2 Os11t0562100-02:2

			
						 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  
						
							CTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAAGGATACCTGAT
TTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAGgaggatttggtctgcccgcgcacgctgc
tgcagaatgtggtgtggacttcgctctacaagtgggtggagccggtgctaggcagcaggccgat
gaacaagc

									
								

					

						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: 187
Transcript exons: 20947082-20947180,20948713-20948800
GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGGGAAGATCCAAATTCAGATTCATTCAAGC
GGCATCTTGCAAGGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG
Transcript length: 277
Transcript exons: 20947082-20947270,20948713-20948800
GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT
GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGGA
AGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAAGGATACCTGATTTCCTGTGGCTTTCA
GAAGATGGCATGAAGGCACAG
Transcript length: 289
Transcript exons: 20947082-20947270,20948685-20948743,20948760-20948800
GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT
GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGAGG
CTCTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCTGATTTC
CTGTGGCTTTCAGAAGATGGCATGAAGGCACAG
Transcript length: 303
Transcript exons: 20947082-20947270,20948687-20948800
GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT
GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGCT
CTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAA
GGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG
						
					

						Genomic sequence
						
							GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG
TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT
GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGTA
AATTTGAAATATAGGCGACCGACCTTGCTTTCAGGGCAAAAAAAAAAAAAAACAAAAAAAACAA
CATTAGAAAATTCTGACTAATGATTGAACTAACAAAATTATGTGTTTTTAAGTATTATGCATGT
AATATCACTATATTCTTCGTATTTGAAAAATACTTTCATATATATGATGTTAATTTTGTAGTTT
TTTATAATATATTATGAAAGAAATCAATGATATTTAAAGTAGAGTAAAATACAACAGCGGTCCT
TAAACTTATTGTCAAGTTACACTTAGGTCCACGAACTTATAAAACGCACATCGAGGTCTCTAAA
CTTGGTTTATTGTATCATCTCGGTCCAAAGTCTCGTTTGACCGTGGTCTTGCCTACGTGGCACG
CCACGTGGATGATGACATGAAATTTTTTATTTTTTTCTCCCTCCTTCCTTCTTTTTCTCTCTCT
TCTTCTTTTTTCTCCCTTCTTTTTTTTTCTCTCTGGCGGCCGCTGTACCGTGAGCTCCACAGCC
ACGCCTCCATCTCCTTCTCCATCAGCCTCCGCTCCACTCGCCGAGCCGCCGTGCCGGAGGCGAG
CGCACAACGGGAGGGAGGACAGCGGCGCTGACGGGAGGGAGGGGGACGGCGGCGACTTGGGGAG
GATAGTGGCGCTGACGGGAGGGAGGGGGACGACGGCGCATAGATGTCCTCCTCGATCTCCTCCG
GGGTGAGCGCCACCAAGAACGGCGCGCGCTTCCGGCGTCGGTACGAGGACGGCACGGGCACCGC
CGCCGCCCATGATATGGAGGCGGCTGGGCACCGCCGCGTCCGTTGCCGCAGGTTCCACGGCCTC
GCTGTACCGTTTGCTTGCGGCTCTGGCAGGGCAAGAAGTGGAGGCAGAGGTAGCGCATTGAGCT
CGGGCTCGGAGTCCATCTCCACAGGTAGGCTCTCGGGCTTCGTCGTCGTCGTTGGCGGCGGCGG
CGGGGGTGGGGGGCTAGGCTGGGGCACGTGGAGACGGTCGGCGGGTCCAAAAAACAAGGGAGAA
AAAAAGGGAGAAAAAATTCCATGTCATCGTCCATGTGGCGTGCCACGTAGACAAGCTCACGGTC
AAACGCGGTTTTGGACCGGGATGATACCATAAACCAAGTTTAGGGACCTCGACGTGCACTTTGG
AAGTTCGTGGACTTAAGTGAAACCTCCCGACAAGTTTAAGGACCGCTGGTGTATTTTACTCTTT
GAAGTATAATGCTAGAGAGCATGTAAAAAAGCTAATACATCTTATATATTAGAATGGAGGGAGT
ATATATGTATGTGGCTGGAATATTTCCCCTTTATGATCTATGCATTATGTGGCAAATGTCATTA
TAATTGATTGTTAGTTTTGATTCCCAGCCAAGGGTATGTCATACTTCTTCTGTCCTTAACAATA
CACAGGCTCTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCA
TCTTGCAAGGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG
						
					

			
		

Sequences
Splice junction sequence	CTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAAGGATACCTGAT TTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAGgaggatttggtctgcccgcgcacgctgc tgcagaatgtggtgtggacttcgctctacaagtgggtggagccggtgctaggcagcaggccgat gaacaagc
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: 187 Transcript exons: 20947082-20947180,20948713-20948800 GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGGGAAGATCCAAATTCAGATTCATTCAAGC GGCATCTTGCAAGGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG Transcript length: 277 Transcript exons: 20947082-20947270,20948713-20948800 GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGGA AGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAAGGATACCTGATTTCCTGTGGCTTTCA GAAGATGGCATGAAGGCACAG Transcript length: 289 Transcript exons: 20947082-20947270,20948685-20948743,20948760-20948800 GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGAGG CTCTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCTGATTTC CTGTGGCTTTCAGAAGATGGCATGAAGGCACAG Transcript length: 303 Transcript exons: 20947082-20947270,20948687-20948800 GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGCT CTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCATCTTGCAA GGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG
Genomic sequence	GAGGATTTGGTCTGCCCGCGCACGCTGCTGCAGAATGTGGTGTGGACTTCGCTCTACAAGTGGG TGGAGCCGGTGCTAGGCAGCAGGCCGATGAACAAGCTGAGGGAGAGAGCTTTGGATAGACTCAT GGAGCATATCCATTACGAAGATGAAAACTCACAGTACCTCTGCCTATGTCCTGTCAACAAGGTA AATTTGAAATATAGGCGACCGACCTTGCTTTCAGGGCAAAAAAAAAAAAAAACAAAAAAAACAA CATTAGAAAATTCTGACTAATGATTGAACTAACAAAATTATGTGTTTTTAAGTATTATGCATGT AATATCACTATATTCTTCGTATTTGAAAAATACTTTCATATATATGATGTTAATTTTGTAGTTT TTTATAATATATTATGAAAGAAATCAATGATATTTAAAGTAGAGTAAAATACAACAGCGGTCCT TAAACTTATTGTCAAGTTACACTTAGGTCCACGAACTTATAAAACGCACATCGAGGTCTCTAAA CTTGGTTTATTGTATCATCTCGGTCCAAAGTCTCGTTTGACCGTGGTCTTGCCTACGTGGCACG CCACGTGGATGATGACATGAAATTTTTTATTTTTTTCTCCCTCCTTCCTTCTTTTTCTCTCTCT TCTTCTTTTTTCTCCCTTCTTTTTTTTTCTCTCTGGCGGCCGCTGTACCGTGAGCTCCACAGCC ACGCCTCCATCTCCTTCTCCATCAGCCTCCGCTCCACTCGCCGAGCCGCCGTGCCGGAGGCGAG CGCACAACGGGAGGGAGGACAGCGGCGCTGACGGGAGGGAGGGGGACGGCGGCGACTTGGGGAG GATAGTGGCGCTGACGGGAGGGAGGGGGACGACGGCGCATAGATGTCCTCCTCGATCTCCTCCG GGGTGAGCGCCACCAAGAACGGCGCGCGCTTCCGGCGTCGGTACGAGGACGGCACGGGCACCGC CGCCGCCCATGATATGGAGGCGGCTGGGCACCGCCGCGTCCGTTGCCGCAGGTTCCACGGCCTC GCTGTACCGTTTGCTTGCGGCTCTGGCAGGGCAAGAAGTGGAGGCAGAGGTAGCGCATTGAGCT CGGGCTCGGAGTCCATCTCCACAGGTAGGCTCTCGGGCTTCGTCGTCGTCGTTGGCGGCGGCGG CGGGGGTGGGGGGCTAGGCTGGGGCACGTGGAGACGGTCGGCGGGTCCAAAAAACAAGGGAGAA AAAAAGGGAGAAAAAATTCCATGTCATCGTCCATGTGGCGTGCCACGTAGACAAGCTCACGGTC AAACGCGGTTTTGGACCGGGATGATACCATAAACCAAGTTTAGGGACCTCGACGTGCACTTTGG AAGTTCGTGGACTTAAGTGAAACCTCCCGACAAGTTTAAGGACCGCTGGTGTATTTTACTCTTT GAAGTATAATGCTAGAGAGCATGTAAAAAAGCTAATACATCTTATATATTAGAATGGAGGGAGT ATATATGTATGTGGCTGGAATATTTCCCCTTTATGATCTATGCATTATGTGGCAAATGTCATTA TAATTGATTGTTAGTTTTGATTCCCAGCCAAGGGTATGTCATACTTCTTCTGTCCTTAACAATA CACAGGCTCTTAACATGGTCTGCTGCTGGGTGGAAGATCCAAATTCAGATTCATTCAAGCGGCA TCTTGCAAGGATACCTGATTTCCTGTGGCTTTCAGAAGATGGCATGAAGGCACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003188* osi_circ_009111 zma_circ_008594 						
					
						PMCS
						0.462383844

Conservation Information
Conserved circRNAs	osi_circ_003188* osi_circ_009111 zma_circ_008594
PMCS	0.462383844

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20947173-20948797(+)
						
						Potential amino acid sequence
						
							MNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLS
EDGMKAQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLC
LCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQEDLVCPRTLLQNVVWTSLYK
WVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHL
ARIPDFLWLSEDGMKAQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIH
YEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20947173-20948797(+)
Potential amino acid sequence	MNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLS EDGMKAQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLC LCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQEDLVCPRTLLQNVVWTSLYK WVEPVLGSRPMNKLRERALDRLMEHIHYEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHL ARIPDFLWLSEDGMKAQEDLVCPRTLLQNVVWTSLYKWVEPVLGSRPMNKLRERALDRLMEHIH YEDENSQYLCLCPVNKALNMVCCWVEDPNSDSFKRHLARIPDFLWLSEDGMKAQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os11g0562100_circ_g.2

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