Plant Circular RNA Database

Detail information of Os11g0298400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0298400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_009135
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 11019723-11021627  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os11g0298400						
					
						Parent gene annotation
						
							Protein of unknown function DUF663 domain containing protein. (O
s11t0298400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0298400_circ_g.2 						
					
						Support reads
						8
					
						Tissues
						seed
					
						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
						Os11t0298400-01:4

General Information
CircRNA Name	Os11g0298400_circ_g.3
ID in PlantcircBase	osa_circ_009135
Alias	NA
Organism	Oryza sativa
Position	chr11: 11019723-11021627 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os11g0298400
Parent gene annotation	Protein of unknown function DUF663 domain containing protein. (O s11t0298400-01)
Parent gene strand	+
Alternative splicing	Os11g0298400_circ_g.2
Support reads	8
Tissues	seed
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	Os11t0298400-01:4

			
						 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  
						
							TAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGAAAAGTGTGGATCC
GGACCGGATTATTCTTAAGAAAATTGTTTTGACTGGaatttcccgatgaggtggagacaccctt
agatgtcccagcaaaaaggcgatttgcaaaatacagagggctaaagtcatttaggacatcatcc
tgggatcc

									
								

					

						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: 679
Transcript exons: 11019723-11019826,11019924-11020183,11021216-11021302,11
021400-11021627
AATTTCCCGATGAGGTGGAGACACCCTTAGATGTCCCAGCAAAAAGGCGATTTGCAAAATACAG
AGGGCTAAAGTCATTTAGGACATCATCCTGGGATCCAAAGGAATCACTGCCACAGGATTATGCA
AGAATATTTGCATTCGATAACTTTACAAGAACACAAAAGCATGTTCTTGCTAAAATGGCAGAGC
GAGATGAAGGAACCTTGAAGGATTGTGCTCAAAGAGGATCATTTGTGAGGCTCCATCTGAAAAA
TGTTCCTACTGAGATTGCCTCAAAACTTGTTCATCCATCAAGGAGATTGCCTGTGGTTGTTTCT
GGTCTTCTTCAACATGAGTCAAAAATATCGGTTCTCCATTTCAGCATAAAGAAACATGACTCCT
ATGAAGCTCCTATCAAATCAAAGGACTCCTTAATTTTCAATGTTGGGTTCCGGCAGTTTACTGC
TAGGCCATTGTTTTCAACTGACAACATCAATTGCAATAAGCATAAGATGGAGAGGTTTCTACAT
CATGGGCGGTTTTCTGTTGCCTCTGTATATGCTCCAATTTGCTTTCCTCCACTCCCTCTTATTG
TTCTAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGAAAAGTGTGGA
TCCGGACCGGATTATTCTTAAGAAAATTGTTTTGACTGG
						
					

						Genomic sequence
						
							AATTTCCCGATGAGGTGGAGACACCCTTAGATGTCCCAGCAAAAAGGCGATTTGCAAAATACAG
AGGGCTAAAGTCATTTAGGACATCATCCTGGGATCCAAAGGTAAGTGTGATTGAATTATCTTTA
GCTGCTGCAGTTTGACCTTATGAATTTCACGTGTCATTTATTATGGTTCTTTTTCTTCATTTTG
TTTCTGTAGGAATCACTGCCACAGGATTATGCAAGAATATTTGCATTCGATAACTTTACAAGAA
CACAAAAGCATGTTCTTGCTAAAATGGCAGAGCGAGATGAAGGAACCTTGAAGGATTGTGCTCA
AAGAGGATCATTTGTGAGGCTCCATCTGAAAAATGTTCCTACTGAGATTGCCTCAAAACTTGTT
CATCCATCAAGGAGATTGCCTGTGGTTGTTTCTGGTCTTCTTCAACATGAGTCAAAAATATCGG
TTCTCCATTTCAGGTATTCACCTACCCATTGCACTCAACAAATTCGTGTGATCTAGTTTTAGGC
TGTGGTGTCATTTCCACTACTAAATTGTGATGTACTCCTCCGTCCCAAAATATAGTAACCTAGT
ACTAGATTAGACATGGACCCGCCAAGATTCATAGTATTAGGATATATCTAATCCAGTCCTAGGT
TGCTATATTTTGGGACGGATGGAGTAGTTGATGATATTTGGCCAACTTTTAGCATGTGTTGTTT
CTTTACTGTATATCAGTAATAAGATTTCTTATGCTCTGTGATTCATGCCAAATTGGCAATCATT
GAGAGCTGCATTTCCTTTCTCATCCCTGGTAGATCATATATGGACTATAGGTGGAGGGTGAAGA
ACCTGAGACTGCATGAGATTAATCTTCAATACTTAATTCCAAAAGACTAGCCGAAAATCTCTTA
TGGGCTTGCACTTAACAATCCAATCTGATAGATAATAATCATTCTAATCAAATCCTATGTCTAA
GGAAACCTCCTTCCCCAAATCTGGCCATGGTCTTGTGTGCCTTAGGCACCACCTTGGCTGTCTA
TGCCCCTTCCTTGGCCTCAGTGGACCTCGGCCTTTGGCCCAATTCCCATTACAATAGGCTGACA
TTATTTTGGTGCAGTTCAATGCAGATACATTTGACGGTGTTGCCACCCAGAATGGTACAAAATT
AGTTTTCTTTTCTAAAAAAAGAATTTTTCATGCCGTGGTATTCCAAACCATGACATCAGCAAAG
TCTGTAAAATGCATCTGTAATCAGTAATTTTAAAATCTATTTTTATATATTTGTAGAACCGACA
CAACTGTTATGCATGAAAGCAGTTTTCAAGAGTTGTGCATCTTATTTTTATTTGTCCATTATTC
CAATCTATATCTATATTTAAAAGTGTATTGATGCTCAAAGTTCTGAAAGATGACTTGACTATGT
CCAGAGTATTTCTTTTTTTTGACTAAAAGGAGTAATAATATAATGCTATCATGTGATCATTCAT
TACATTTCCTTTTTGCTGCAGCATAAAGAAACATGACTCCTATGAAGCTCCTATCAAATCAAAG
GACTCCTTAATTTTCAATGTTGGGTTCCGGCAGTTTACTGCTAGGTAGGTAGTGGAAGCTCAGT
CATGCTAATGCAGAAAAAACAGATGCTCGTCTTTTCATTGAGAAATGTCTCATTGGTTATTTAT
GAATCTATCACAGGCCATTGTTTTCAACTGACAACATCAATTGCAATAAGCATAAGATGGAGAG
GTTTCTACATCATGGGCGGTTTTCTGTTGCCTCTGTATATGCTCCAATTTGCTTTCCTCCACTC
CCTCTTATTGTTCTAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGA
AAAGTGTGGATCCGGACCGGATTATTCTTAAGAAAATTGTTTTGACTGG
						
					

			
		

Sequences
Splice junction sequence	TAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGAAAAGTGTGGATCC GGACCGGATTATTCTTAAGAAAATTGTTTTGACTGGaatttcccgatgaggtggagacaccctt agatgtcccagcaaaaaggcgatttgcaaaatacagagggctaaagtcatttaggacatcatcc tgggatcc
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: 679 Transcript exons: 11019723-11019826,11019924-11020183,11021216-11021302,11 021400-11021627 AATTTCCCGATGAGGTGGAGACACCCTTAGATGTCCCAGCAAAAAGGCGATTTGCAAAATACAG AGGGCTAAAGTCATTTAGGACATCATCCTGGGATCCAAAGGAATCACTGCCACAGGATTATGCA AGAATATTTGCATTCGATAACTTTACAAGAACACAAAAGCATGTTCTTGCTAAAATGGCAGAGC GAGATGAAGGAACCTTGAAGGATTGTGCTCAAAGAGGATCATTTGTGAGGCTCCATCTGAAAAA TGTTCCTACTGAGATTGCCTCAAAACTTGTTCATCCATCAAGGAGATTGCCTGTGGTTGTTTCT GGTCTTCTTCAACATGAGTCAAAAATATCGGTTCTCCATTTCAGCATAAAGAAACATGACTCCT ATGAAGCTCCTATCAAATCAAAGGACTCCTTAATTTTCAATGTTGGGTTCCGGCAGTTTACTGC TAGGCCATTGTTTTCAACTGACAACATCAATTGCAATAAGCATAAGATGGAGAGGTTTCTACAT CATGGGCGGTTTTCTGTTGCCTCTGTATATGCTCCAATTTGCTTTCCTCCACTCCCTCTTATTG TTCTAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGAAAAGTGTGGA TCCGGACCGGATTATTCTTAAGAAAATTGTTTTGACTGG
Genomic sequence	AATTTCCCGATGAGGTGGAGACACCCTTAGATGTCCCAGCAAAAAGGCGATTTGCAAAATACAG AGGGCTAAAGTCATTTAGGACATCATCCTGGGATCCAAAGGTAAGTGTGATTGAATTATCTTTA GCTGCTGCAGTTTGACCTTATGAATTTCACGTGTCATTTATTATGGTTCTTTTTCTTCATTTTG TTTCTGTAGGAATCACTGCCACAGGATTATGCAAGAATATTTGCATTCGATAACTTTACAAGAA CACAAAAGCATGTTCTTGCTAAAATGGCAGAGCGAGATGAAGGAACCTTGAAGGATTGTGCTCA AAGAGGATCATTTGTGAGGCTCCATCTGAAAAATGTTCCTACTGAGATTGCCTCAAAACTTGTT CATCCATCAAGGAGATTGCCTGTGGTTGTTTCTGGTCTTCTTCAACATGAGTCAAAAATATCGG TTCTCCATTTCAGGTATTCACCTACCCATTGCACTCAACAAATTCGTGTGATCTAGTTTTAGGC TGTGGTGTCATTTCCACTACTAAATTGTGATGTACTCCTCCGTCCCAAAATATAGTAACCTAGT ACTAGATTAGACATGGACCCGCCAAGATTCATAGTATTAGGATATATCTAATCCAGTCCTAGGT TGCTATATTTTGGGACGGATGGAGTAGTTGATGATATTTGGCCAACTTTTAGCATGTGTTGTTT CTTTACTGTATATCAGTAATAAGATTTCTTATGCTCTGTGATTCATGCCAAATTGGCAATCATT GAGAGCTGCATTTCCTTTCTCATCCCTGGTAGATCATATATGGACTATAGGTGGAGGGTGAAGA ACCTGAGACTGCATGAGATTAATCTTCAATACTTAATTCCAAAAGACTAGCCGAAAATCTCTTA TGGGCTTGCACTTAACAATCCAATCTGATAGATAATAATCATTCTAATCAAATCCTATGTCTAA GGAAACCTCCTTCCCCAAATCTGGCCATGGTCTTGTGTGCCTTAGGCACCACCTTGGCTGTCTA TGCCCCTTCCTTGGCCTCAGTGGACCTCGGCCTTTGGCCCAATTCCCATTACAATAGGCTGACA TTATTTTGGTGCAGTTCAATGCAGATACATTTGACGGTGTTGCCACCCAGAATGGTACAAAATT AGTTTTCTTTTCTAAAAAAAGAATTTTTCATGCCGTGGTATTCCAAACCATGACATCAGCAAAG TCTGTAAAATGCATCTGTAATCAGTAATTTTAAAATCTATTTTTATATATTTGTAGAACCGACA CAACTGTTATGCATGAAAGCAGTTTTCAAGAGTTGTGCATCTTATTTTTATTTGTCCATTATTC CAATCTATATCTATATTTAAAAGTGTATTGATGCTCAAAGTTCTGAAAGATGACTTGACTATGT CCAGAGTATTTCTTTTTTTTGACTAAAAGGAGTAATAATATAATGCTATCATGTGATCATTCAT TACATTTCCTTTTTGCTGCAGCATAAAGAAACATGACTCCTATGAAGCTCCTATCAAATCAAAG GACTCCTTAATTTTCAATGTTGGGTTCCGGCAGTTTACTGCTAGGTAGGTAGTGGAAGCTCAGT CATGCTAATGCAGAAAAAACAGATGCTCGTCTTTTCATTGAGAAATGTCTCATTGGTTATTTAT GAATCTATCACAGGCCATTGTTTTCAACTGACAACATCAATTGCAATAAGCATAAGATGGAGAG GTTTCTACATCATGGGCGGTTTTCTGTTGCCTCTGTATATGCTCCAATTTGCTTTCCTCCACTC CCTCTTATTGTTCTAAAGAGCAGAGATGGGGAGCAGCCTGCCATTGCTGCTGTTGGTTCACTGA AAAGTGTGGATCCGGACCGGATTATTCTTAAGAAAATTGTTTTGACTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.24333189

Conservation Information
Conserved circRNAs	NA
PMCS	0.24333189

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11020003-11019732(+)
11019802-11021462(-)
						
						Potential amino acid sequence
						
							MAERDEGTLKDCAQRGSFVRLHLKNVPTEIASKLVHPSRRLPVVVSGLLQHESKISVLHFSIKK
HDSYEAPIKSKDSLIFNVGFRQFTARPLFSTDNINCNKHKMERFLHHGRFSVASVYAPICFPPL
PLIVLKSRDGEQPAIAAVGSLKSVDPDRIILKKIVLTGISR*(+)
MTLALCILQIAFLLGHLRVSPPHREIPVKTIFLRIIRSGSTLFSEPTAAMAGCSPSLLFRTIRG
SGGKQIGAYTEATENRP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11020003-11019732(+) 11019802-11021462(-)
Potential amino acid sequence	MAERDEGTLKDCAQRGSFVRLHLKNVPTEIASKLVHPSRRLPVVVSGLLQHESKISVLHFSIKK HDSYEAPIKSKDSLIFNVGFRQFTARPLFSTDNINCNKHKMERFLHHGRFSVASVYAPICFPPL PLIVLKSRDGEQPAIAAVGSLKSVDPDRIILKKIVLTGISR(+) MTLALCILQIAFLLGHLRVSPPHREIPVKTIFLRIIRSGSTLFSEPTAAMAGCSPSLLFRTIRG SGGKQIGAYTEATENRP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os11g0298400_circ_g.3

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