Plant Circular RNA Database

Detail information of Os09g0294000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0294000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_038754
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 7001199-7002239  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0294000						
					
						Parent gene annotation
						
							Similar to Bifunctional aspartokinase/homoserine dehydrogenase 2
, chloroplast precursor (AK-HD 2) (AK-HSDH 2) [Includes: Asparto
kinase (EC 2.7.2.4); Homoserine dehydrogenase (EC 1.1.1.3)]. (Os
09t0294000-01);Similar to Aspartate kinase-homoserine dehydrogen
ase. (Os09t0294000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0294000_circ_g.1 Os09g0294000_circ_g.2 Os09g0294000_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os09t0294000-01:3
Os09t0294000-02:3

General Information
CircRNA Name	Os09g0294000_circ_g.3
ID in PlantcircBase	osa_circ_038754
Alias	NA
Organism	Oryza sativa
Position	chr9: 7001199-7002239 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0294000
Parent gene annotation	Similar to Bifunctional aspartokinase/homoserine dehydrogenase 2 , chloroplast precursor (AK-HD 2) (AK-HSDH 2) [Includes: Asparto kinase (EC 2.7.2.4); Homoserine dehydrogenase (EC 1.1.1.3)]. (Os 09t0294000-01);Similar to Aspartate kinase-homoserine dehydrogen ase. (Os09t0294000-02)
Parent gene strand	-
Alternative splicing	Os09g0294000_circ_g.1 Os09g0294000_circ_g.2 Os09g0294000_circ_g.4
Support reads	1
Tissues	shoot
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	Os09t0294000-01:3 Os09t0294000-02:3

			
						 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  
						
							AAATACATGATTTTCAGACAAATGGCGAACAAAACTATCAAGATCTGCTGGTTCTGCTTCTTTT
CGTAGAAGCTCTTTCCACTGGTTTAAGTCTACCCCTctttctggcaacatcagttcctgataga
tcatctcttggatctggctctgtatatccagcttcttttgcttcagcaacaacattactaaaag
ttcgtgta

									
								

					

						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: 508
Transcript exons: 7001199-7001334,7001498-7001643,7002014-7002239
CTTTCTGGCAACATCAGTTCCTGATAGATCATCTCTTGGATCTGGCTCTGTATATCCAGCTTCT
TTTGCTTCAGCAACAACATTACTAAAAGTTCGTGTACCTTCAAAATTGTTGAAAATATAACTCA
AAGTCCCACTGAAAATGCCCTCAATACGCAATATCTTGTCACCTGTCTCTAGAAGACCTCGTAG
GGTGCTAATGATTGGAAGGCCAGCACCAACAGTTGCTTCATAAAAGTAATGAGTATACGATGCA
CGCTGCAGAGTCCTTAATTTCAGATACCGATCAAGCGGACCAGAATTTGCTTTCTTATTTGGCG
TGATGACATGGATACCCTTCTTCAACCAATCATAATAGTGGCATGCTACGTATGTATCTGCTGT
GCAGTCCACCAAAACTTTGTTTGGAAATACATGATTTTCAGACAAATGGCGAACAAAACTATCA
AGATCTGCTGGTTCTGCTTCTTTTCGTAGAAGCTCTTTCCACTGGTTTAAGTCTACCCCT
						
					

						Genomic sequence
						
							CTTTCTGGCAACATCAGTTCCTGATAGATCATCTCTTGGATCTGGCTCTGTATATCCAGCTTCT
TTTGCTTCAGCAACAACATTACTAAAAGTTCGTGTACCTTCAAAATTGTTGAAAATATAACTCA
AAGTCCCACTGCAATGGAACAATCAACACTGTATCAGCCAACATTGTCTAATTTATGGAACACA
AAAGGATGAATTTCTATCCAAGTAAACTTCTGAGGAATTTTTGTGGTTTAGTAAAATTACAATA
TTGTCAAGTTTAATTCTGGTACATTACTGAAGCATAAACGCACCTGAAAATGCCCTCAATACGC
AATATCTTGTCACCTGTCTCTAGAAGACCTCGTAGGGTGCTAATGATTGGAAGGCCAGCACCAA
CAGTTGCTTCATAAAAGTAATGAGTATACGATGCACGCTGCAGAGTCCTTAATTTCAGATACTG
CAAACAAAGGGGGAAAATGATTTCATAGTGGATAAACAACCCAGCAGCATACAATGCTACACGA
CAGATGCACATTGATTTCTTAAGTTTCCAGTGGCTATGTATGAAATTAACAGGCTAGTAATCAG
ATTTACTTCATGGATTTTCTTAGAAATAAGTTATCTGTTGATCAGTCATGAACAAATAATTCCG
ACTCTTAGTTCGTCTTCACTGCAGGTTTCTTGAACACGGGGAATTCTTATTGAAGTAAAAACCA
ACTAGCTACCCAGACTCGGTCGGCGATTATTGAACAACTAAAAAACAGATTGTTTCAAAATAAA
AAGGCAACAATATATGCCTATACAAGTCTTGCCAGTAAGAAAATTACCCGATCAAGCGGACCAG
AATTTGCTTTCTTATTTGGCGTGATGACATGGATACCCTTCTTCAACCAATCATAATAGTGGCA
TGCTACGTATGTATCTGCTGTGCAGTCCACCAAAACTTTGTTTGGAAATACATGATTTTCAGAC
AAATGGCGAACAAAACTATCAAGATCTGCTGGTTCTGCTTCTTTTCGTAGAAGCTCTTTCCACT
GGTTTAAGTCTACCCCT
						
					

			
		

Sequences
Splice junction sequence	AAATACATGATTTTCAGACAAATGGCGAACAAAACTATCAAGATCTGCTGGTTCTGCTTCTTTT CGTAGAAGCTCTTTCCACTGGTTTAAGTCTACCCCTctttctggcaacatcagttcctgataga tcatctcttggatctggctctgtatatccagcttcttttgcttcagcaacaacattactaaaag ttcgtgta
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: 508 Transcript exons: 7001199-7001334,7001498-7001643,7002014-7002239 CTTTCTGGCAACATCAGTTCCTGATAGATCATCTCTTGGATCTGGCTCTGTATATCCAGCTTCT TTTGCTTCAGCAACAACATTACTAAAAGTTCGTGTACCTTCAAAATTGTTGAAAATATAACTCA AAGTCCCACTGAAAATGCCCTCAATACGCAATATCTTGTCACCTGTCTCTAGAAGACCTCGTAG GGTGCTAATGATTGGAAGGCCAGCACCAACAGTTGCTTCATAAAAGTAATGAGTATACGATGCA CGCTGCAGAGTCCTTAATTTCAGATACCGATCAAGCGGACCAGAATTTGCTTTCTTATTTGGCG TGATGACATGGATACCCTTCTTCAACCAATCATAATAGTGGCATGCTACGTATGTATCTGCTGT GCAGTCCACCAAAACTTTGTTTGGAAATACATGATTTTCAGACAAATGGCGAACAAAACTATCA AGATCTGCTGGTTCTGCTTCTTTTCGTAGAAGCTCTTTCCACTGGTTTAAGTCTACCCCT
Genomic sequence	CTTTCTGGCAACATCAGTTCCTGATAGATCATCTCTTGGATCTGGCTCTGTATATCCAGCTTCT TTTGCTTCAGCAACAACATTACTAAAAGTTCGTGTACCTTCAAAATTGTTGAAAATATAACTCA AAGTCCCACTGCAATGGAACAATCAACACTGTATCAGCCAACATTGTCTAATTTATGGAACACA AAAGGATGAATTTCTATCCAAGTAAACTTCTGAGGAATTTTTGTGGTTTAGTAAAATTACAATA TTGTCAAGTTTAATTCTGGTACATTACTGAAGCATAAACGCACCTGAAAATGCCCTCAATACGC AATATCTTGTCACCTGTCTCTAGAAGACCTCGTAGGGTGCTAATGATTGGAAGGCCAGCACCAA CAGTTGCTTCATAAAAGTAATGAGTATACGATGCACGCTGCAGAGTCCTTAATTTCAGATACTG CAAACAAAGGGGGAAAATGATTTCATAGTGGATAAACAACCCAGCAGCATACAATGCTACACGA CAGATGCACATTGATTTCTTAAGTTTCCAGTGGCTATGTATGAAATTAACAGGCTAGTAATCAG ATTTACTTCATGGATTTTCTTAGAAATAAGTTATCTGTTGATCAGTCATGAACAAATAATTCCG ACTCTTAGTTCGTCTTCACTGCAGGTTTCTTGAACACGGGGAATTCTTATTGAAGTAAAAACCA ACTAGCTACCCAGACTCGGTCGGCGATTATTGAACAACTAAAAAACAGATTGTTTCAAAATAAA AAGGCAACAATATATGCCTATACAAGTCTTGCCAGTAAGAAAATTACCCGATCAAGCGGACCAG AATTTGCTTTCTTATTTGGCGTGATGACATGGATACCCTTCTTCAACCAATCATAATAGTGGCA TGCTACGTATGTATCTGCTGTGCAGTCCACCAAAACTTTGTTTGGAAATACATGATTTTCAGAC AAATGGCGAACAAAACTATCAAGATCTGCTGGTTCTGCTTCTTTTCGTAGAAGCTCTTTCCACT GGTTTAAGTCTACCCCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018889 						
					
						PMCS
						0.268702129

Conservation Information
Conserved circRNAs	osi_circ_018889
PMCS	0.268702129

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7002095-7001319(+)
7001283-7002179(-)
						
						Potential amino acid sequence
						
							MLRMYLLCSPPKLCLEIHDFQTNGEQNYQDLLVLLLFVEALSTGLSLPLFLATSVPDRSSLGSG
SVYPASFASATTLLKVRVPSKLLKI*(+)
MLLLKQKKLDIQSQIQEMIYQELMLPERGVDLNQWKELLRKEAEPADLDSFVRHLSENHVFPNK
VLVDCTADTYVACHYYDWLKKGIHVITPNKKANSGPLDRYLKLRTLQRASYTHYFYEATVGAGL
PIISTLRGLLETGDKILRIEGIFSGTLSYIFNNFEGTRTFSNVVAEAKEAGYTEPDPRDDLSGT
DVARKRGRLKPVERASTKRSRTSRS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7002095-7001319(+) 7001283-7002179(-)
Potential amino acid sequence	MLRMYLLCSPPKLCLEIHDFQTNGEQNYQDLLVLLLFVEALSTGLSLPLFLATSVPDRSSLGSG SVYPASFASATTLLKVRVPSKLLKI(+) MLLLKQKKLDIQSQIQEMIYQELMLPERGVDLNQWKELLRKEAEPADLDSFVRHLSENHVFPNK VLVDCTADTYVACHYYDWLKKGIHVITPNKKANSGPLDRYLKLRTLQRASYTHYFYEATVGAGL PIISTLRGLLETGDKILRIEGIFSGTLSYIFNNFEGTRTFSNVVAEAKEAGYTEPDPRDDLSGT DVARKRGRLKPVERASTKRSRTSRS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0294000_circ_g.3

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