Plant Circular RNA Database

Detail information of Os12g0210400_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0210400_circ_g.4
					
						ID in PlantcircBase
						osa_circ_010841
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 5770316-5771634  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						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.3 Os12g0210400_circ_g.5 						
					
						Support reads
						4
					
						Tissues
						shoot, root, 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
						Os12t0210400-01:4

General Information
CircRNA Name	Os12g0210400_circ_g.4
ID in PlantcircBase	osa_circ_010841
Alias	NA
Organism	Oryza sativa
Position	chr12: 5770316-5771634 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
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.3 Os12g0210400_circ_g.5
Support reads	4
Tissues	shoot, root, 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	Os12t0210400-01:4

			
						 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  
						
							CGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAGCTTCTCGGCGAAGACGGT
CGTGGCCAGATCACCACCCAAGTCAAGGGCACAATGgggcgttgcaaacttcaaaatcgaacac
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: 758
Transcript exons: 5770316-5770477,5770571-5770710,5770819-5771038,5771399-
5771634
GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG
AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT
CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGTTTCCTGGGACATCAAGAGCACCAGCACTA
GCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTCTCCTTCGACGAGCTGAAGAAGGTCACCAA
CAACTTCTCGGAGGCCAATGACATCGGCACCGGAGGCTACGGGAAGGTTTACAGGGGAACACTT
CCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCAACCTCGAGT
TCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCTAGTCGGATT
CTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAG
AGCCTCACAGGGAAATCTGGTGTGAGGCTGGACTGGAAGCGGCGGCTCCGGGTTGTCCTCGGTG
CGGCGAAGGGTATCGCCTACCTGCATGAGCTCGCTGACCCTCCGATCATCCACCGTGACATCAA
GTCGAGCAATGTTCTCCTCGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAG
CTTCTCGGCGAAGACGGTCGTGGCCAGATCACCACCCAAGTCAAGGGCACAATG
						
					

						Genomic sequence
						
							GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG
AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT
CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGGTAAGCACTGTTCATCATCTAATTCAGTAT
AACAACATCTCATTGTTGCATACTTTCTTCTGAATGTGGCATCACAACTGCAATCATCTGCAGT
TTCCTGGGACATCAAGAGCACCAGCACTAGCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTC
TCCTTCGACGAGCTGAAGAAGGTCACCAACAACTTCTCGGAGGCCAATGACATCGGCACCGGAG
GCTACGGGAAGGTGAAGAAGCCATTGCTGATCACTTCTGATACATTCTGTCCTCCTTTGACATG
TTCAGAACTTGAAATGTTCAGAACTTGAAATATTCAGAGCTGTTGATCACTGCAGGTTTACAGG
GGAACACTTCCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCA
ACCTCGAGTTCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCT
AGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACC
CTCAAGGAGAGCCTCACAGGTAAAACTACTACTTATTGTTATTAATTCTTAAAGATGAATGCGA
AAATGTCGACAGATTTTATAGTGGTCTAGCTCTGATACTGATAGTCTCCATGGTTTGAAATTTC
GAACCCTACCGGCAAGCACAAATCTCCACCTACATTTTCGGATTTTTTCAAATATTTGGGAATT
TGGTCAATTTGTTTAAATTCAATCGAAATATGTTAAAATTTGAAATAATTTTGGTAAAAAACAC
CGAAATTCATGATGTTTTTTTTCAAAATTCCGACAACCATCGAAATTTCGGAAATTTCAGTGGT
TATTGAAAGTGCAAACACTGATTGTCTCTCATGGTGGTGCCATCGAAAACTTTGTTCAGGGAAA
TCTGGTGTGAGGCTGGACTGGAAGCGGCGGCTCCGGGTTGTCCTCGGTGCGGCGAAGGGTATCG
CCTACCTGCATGAGCTCGCTGACCCTCCGATCATCCACCGTGACATCAAGTCGAGCAATGTTCT
CCTCGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAGCTTCTCGGCGAAGAC
GGTCGTGGCCAGATCACCACCCAAGTCAAGGGCACAATG
						
					

			
		

Sequences
Splice junction sequence	CGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAGCTTCTCGGCGAAGACGGT CGTGGCCAGATCACCACCCAAGTCAAGGGCACAATGgggcgttgcaaacttcaaaatcgaacac 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: 758 Transcript exons: 5770316-5770477,5770571-5770710,5770819-5771038,5771399- 5771634 GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGTTTCCTGGGACATCAAGAGCACCAGCACTA GCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTCTCCTTCGACGAGCTGAAGAAGGTCACCAA CAACTTCTCGGAGGCCAATGACATCGGCACCGGAGGCTACGGGAAGGTTTACAGGGGAACACTT CCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCAACCTCGAGT TCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCTAGTCGGATT CTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACCCTCAAGGAG AGCCTCACAGGGAAATCTGGTGTGAGGCTGGACTGGAAGCGGCGGCTCCGGGTTGTCCTCGGTG CGGCGAAGGGTATCGCCTACCTGCATGAGCTCGCTGACCCTCCGATCATCCACCGTGACATCAA GTCGAGCAATGTTCTCCTCGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAG CTTCTCGGCGAAGACGGTCGTGGCCAGATCACCACCCAAGTCAAGGGCACAATG
Genomic sequence	GGGCGTTGCAAACTTCAAAATCGAACACAAACCACATCCCGCTTATCGTCGGTGCTTCGGTTGG AGGTGCAGCTGTAATTGCAGCATTGCTTGCACTCACAATCTGCATTGCTAGAAGGAAGAGAAGT CCAAAGCAGACTGAAGATAGGAGCCAGTCTTATGGTAAGCACTGTTCATCATCTAATTCAGTAT AACAACATCTCATTGTTGCATACTTTCTTCTGAATGTGGCATCACAACTGCAATCATCTGCAGT TTCCTGGGACATCAAGAGCACCAGCACTAGCACTGCCCCGCAGGTGCGAGGTGCGAGGATGTTC TCCTTCGACGAGCTGAAGAAGGTCACCAACAACTTCTCGGAGGCCAATGACATCGGCACCGGAG GCTACGGGAAGGTGAAGAAGCCATTGCTGATCACTTCTGATACATTCTGTCCTCCTTTGACATG TTCAGAACTTGAAATGTTCAGAACTTGAAATATTCAGAGCTGTTGATCACTGCAGGTTTACAGG GGAACACTTCCTACTGGTCAGCTGGTTGCCGTGAAGAGATCCCAGCAAGGCTCCCTGCAGGGCA ACCTCGAGTTCAGGACTGAGATCGAGCTCCTGTCCAGGGTTCATCACAAGAATGTCGTCAGCCT AGTCGGATTCTGCTTCGACCAGGGCGAGCAGATGCTTGTCTACGAGTATGTCCCCAATGGCACC CTCAAGGAGAGCCTCACAGGTAAAACTACTACTTATTGTTATTAATTCTTAAAGATGAATGCGA AAATGTCGACAGATTTTATAGTGGTCTAGCTCTGATACTGATAGTCTCCATGGTTTGAAATTTC GAACCCTACCGGCAAGCACAAATCTCCACCTACATTTTCGGATTTTTTCAAATATTTGGGAATT TGGTCAATTTGTTTAAATTCAATCGAAATATGTTAAAATTTGAAATAATTTTGGTAAAAAACAC CGAAATTCATGATGTTTTTTTTCAAAATTCCGACAACCATCGAAATTTCGGAAATTTCAGTGGT TATTGAAAGTGCAAACACTGATTGTCTCTCATGGTGGTGCCATCGAAAACTTTGTTCAGGGAAA TCTGGTGTGAGGCTGGACTGGAAGCGGCGGCTCCGGGTTGTCCTCGGTGCGGCGAAGGGTATCG CCTACCTGCATGAGCTCGCTGACCCTCCGATCATCCACCGTGACATCAAGTCGAGCAATGTTCT CCTCGATGAGCGGCTCAACGCCAAGGTCTCCGACTTCGGCCTGTCCAAGCTTCTCGGCGAAGAC GGTCGTGGCCAGATCACCACCCAAGTCAAGGGCACAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.358155476

Conservation Information
Conserved circRNAs	NA
PMCS	0.358155476

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5771478-5770427(+)
5770631-5770390(+)
5770426-5771623(-)
						
						Potential amino acid sequence
						
							MSSLTLRSSTVTSSRAMFSSMSGSTPRSPTSACPSFSAKTVVARSPPKSRAQWGVANFKIEHKP
HPAYRRCFGWRCSCNCSIACTHNLHC*(+)
MFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSR
VHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLTGKSGVRLDWKRRLRVVLGAAKGIAYLHE
LADPPIIHRDIKSSNVLLDERLNAKVSDFGLSKLLGEDGRGQITTQVKGTMGRCKLQNRTQTTS
RLSSVLRLEVQL*(+)
MQIVSASNAAITAAPPTEAPTISGMWFVFDFEVCNAPLCP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5771478-5770427(+) 5770631-5770390(+) 5770426-5771623(-)
Potential amino acid sequence	MSSLTLRSSTVTSSRAMFSSMSGSTPRSPTSACPSFSAKTVVARSPPKSRAQWGVANFKIEHKP HPAYRRCFGWRCSCNCSIACTHNLHC(+) MFSFDELKKVTNNFSEANDIGTGGYGKVYRGTLPTGQLVAVKRSQQGSLQGNLEFRTEIELLSR VHHKNVVSLVGFCFDQGEQMLVYEYVPNGTLKESLTGKSGVRLDWKRRLRVVLGAAKGIAYLHE LADPPIIHRDIKSSNVLLDERLNAKVSDFGLSKLLGEDGRGQITTQVKGTMGRCKLQNRTQTTS RLSSVLRLEVQL(+) MQIVSASNAAITAAPPTEAPTISGMWFVFDFEVCNAPLCP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0210400_circ_g.4

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