Plant Circular RNA Database

Detail information of Os12g0210400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0210400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_010840
					
						Alias
						Os_ciR7565
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 5770316-5771038  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os12g0210400						
					
						Parent gene annotation
						
							Protein kinase, core domain containing protein. (Os12t0210400-01
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0210400_circ_g.8 Os12g0210400_circ_g.9 Os12g0210400_circ_g.10 Os12g0210400_circ_g.11 Os12g0210400_circ_g.12 Os12g0210400_circ_g.13 Os12g0210400_circ_g.14 Os12g0210400_circ_igg.1 Os12g0210400_circ_g.2 Os12g0210400_circ_g.4 Os12g0210400_circ_g.5 						
					
						Support reads
						2/5
					
						Tissues
						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
						Os12t0210400-01:3

General Information
CircRNA Name	Os12g0210400_circ_g.3
ID in PlantcircBase	osa_circ_010840
Alias	Os_ciR7565
Organism	Oryza sativa
Position	chr12: 5770316-5771038 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os12g0210400
Parent gene annotation	Protein kinase, core domain containing protein. (Os12t0210400-01 )
Parent gene strand	+
Alternative splicing	Os12g0210400_circ_g.8 Os12g0210400_circ_g.9 Os12g0210400_circ_g.10 Os12g0210400_circ_g.11 Os12g0210400_circ_g.12 Os12g0210400_circ_g.13 Os12g0210400_circ_g.14 Os12g0210400_circ_igg.1 Os12g0210400_circ_g.2 Os12g0210400_circ_g.4 Os12g0210400_circ_g.5
Support reads	2/5
Tissues	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	Os12t0210400-01:3

			
						 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  
						
							AAGAATGTCGTCAGCCTAGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGT
ATGTCCCCAATGGCACCCTCAAGGAGAGCCTCACAGgggcgttgcaaacttcaaaatcgaacac
aaaccacatcccgcttatcgtcggtgcttcggttggaggtgcagctgtaattgcagcattgctt
gcactcac

									
								

					

						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: 133
Transcript exons: 5770316-5770366,5770957-5771038
GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTCGGATTCTGCT
TCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAGAGCCT
CACAG
Transcript length: 522
Transcript exons: 5770316-5770477,5770571-5770710,5770819-5771038
GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG
AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT
CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGTTTCCTGGGACATCAAGAGCACCAGCACTA
GCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTCTCCTTCGACGAGCTGAAGAAGGTCACCAA
CAACTTCTCGGAGGCCAATGACATCGGCACCGGAGGCTACGGGAAGGTTTACAGGGGAACACTT
CCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCAACCTCGAGT
TCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCTAGTCGGATT
CTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAG
AGCCTCACAG
						
					

						Genomic sequence
						
							GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG
AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT
CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGGTAAGCACTGTTCATCATCTAATTCAGTAT
AACAACATCTCATTGTTGCATACTTTCTTCTGAATGTGGCATCACAACTGCAATCATCTGCAGT
TTCCTGGGACATCAAGAGCACCAGCACTAGCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTC
TCCTTCGACGAGCTGAAGAAGGTCACCAACAACTTCTCGGAGGCCAATGACATCGGCACCGGAG
GCTACGGGAAGGTGAAGAAGCCATTGCTGATCACTTCTGATACATTCTGTCCTCCTTTGACATG
TTCAGAACTTGAAATGTTCAGAACTTGAAATATTCAGAGCTGTTGATCACTGCAGGTTTACAGG
GGAACACTTCCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCA
ACCTCGAGTTCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCT
AGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACC
CTCAAGGAGAGCCTCACAG
						
					

			
		

Sequences
Splice junction sequence	AAGAATGTCGTCAGCCTAGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGT ATGTCCCCAATGGCACCCTCAAGGAGAGCCTCACAGgggcgttgcaaacttcaaaatcgaacac aaaccacatcccgcttatcgtcggtgcttcggttggaggtgcagctgtaattgcagcattgctt gcactcac
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: 133 Transcript exons: 5770316-5770366,5770957-5771038 GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTCGGATTCTGCT TCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAGAGCCT CACAG Transcript length: 522 Transcript exons: 5770316-5770477,5770571-5770710,5770819-5771038 GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGTTTCCTGGGACATCAAGAGCACCAGCACTA GCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTCTCCTTCGACGAGCTGAAGAAGGTCACCAA CAACTTCTCGGAGGCCAATGACATCGGCACCGGAGGCTACGGGAAGGTTTACAGGGGAACACTT CCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCAACCTCGAGT TCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCTAGTCGGATT CTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAG AGCCTCACAG
Genomic sequence	GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGGTAAGCACTGTTCATCATCTAATTCAGTAT AACAACATCTCATTGTTGCATACTTTCTTCTGAATGTGGCATCACAACTGCAATCATCTGCAGT TTCCTGGGACATCAAGAGCACCAGCACTAGCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTC TCCTTCGACGAGCTGAAGAAGGTCACCAACAACTTCTCGGAGGCCAATGACATCGGCACCGGAG GCTACGGGAAGGTGAAGAAGCCATTGCTGATCACTTCTGATACATTCTGTCCTCCTTTGACATG TTCAGAACTTGAAATGTTCAGAACTTGAAATATTCAGAGCTGTTGATCACTGCAGGTTTACAGG GGAACACTTCCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCA ACCTCGAGTTCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCT AGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACC CTCAAGGAGAGCCTCACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010234 osi_circ_010235 						
					
						PMCS
						0.383165725

Conservation Information
Conserved circRNAs	osi_circ_010234 osi_circ_010235
PMCS	0.383165725

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5771004-5770390(+)
5770631-5771035(+)
5770426-5770997(-)
						
						Potential amino acid sequence
						
							MSPMAPSRRASQGRCKLQNRTQTTSRLSSVLRLEVQL*(+)
MFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSR
VHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLTGALQTSKSNTNHIPLIVGASVGGAAVIA
ALLALTICIARRKRSPKQTEDRSQSYVSWDIKSTSTSTAPQVRGARMFSFDELKKVTNNFSEAN
DIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSRVHHKNVVSLVGFCFDQGE
QMLVYEYVPNGTLKESLTGALQTSKSNTNHIPLIVGASVGGAAVIAALLALTICIARRKRSPKQ
TEDRSQSYVSWDIKSTSTSTAPQVRGARMFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTG
QLVAVKRSQQGSLQGNLEFRTEIELLSRVHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLT
GALQTSKSNTNHIPLIVGASVGGAAVIAALLALTICIARRKRSPKQTEDRSQSYVSWDIKSTST
STAPQVRGARMFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLE
FRTEIELLSRVHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLT(+)
MQIVSASNAAITAAPPTEAPTISGMWFVFDFEVCNAPVRLSLRVPLGTYS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5771004-5770390(+) 5770631-5771035(+) 5770426-5770997(-)
Potential amino acid sequence	MSPMAPSRRASQGRCKLQNRTQTTSRLSSVLRLEVQL(+) MFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSR VHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLTGALQTSKSNTNHIPLIVGASVGGAAVIA ALLALTICIARRKRSPKQTEDRSQSYVSWDIKSTSTSTAPQVRGARMFSFDELKKVTNNFSEAN DIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSRVHHKNVVSLVGFCFDQGE QMLVYEYVPNGTLKESLTGALQTSKSNTNHIPLIVGASVGGAAVIAALLALTICIARRKRSPKQ TEDRSQSYVSWDIKSTSTSTAPQVRGARMFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTG QLVAVKRSQQGSLQGNLEFRTEIELLSRVHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLT GALQTSKSNTNHIPLIVGASVGGAAVIAALLALTICIARRKRSPKQTEDRSQSYVSWDIKSTST STAPQVRGARMFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLE FRTEIELLSRVHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLT(+) MQIVSASNAAITAAPPTEAPTISGMWFVFDFEVCNAPVRLSLRVPLGTYS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os12g0210400_circ_g.3

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