Plant Circular RNA Database

Detail information of Os12g0279000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0279000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_011115
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 10463419-10464889  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os12g0279000						
					
						Parent gene annotation
						
							Helicase, C-terminal domain containing protein. (Os12t0279000-01
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0279000_circ_g.2 Os12g0279000_circ_g.3 Os12g0279000_circ_g.5 Os12g0279000_circ_g.6 						
					
						Support reads
						1
					
						Tissues
						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
						Os12t0279000-01:4

General Information
CircRNA Name	Os12g0279000_circ_g.4
ID in PlantcircBase	osa_circ_011115
Alias	NA
Organism	Oryza sativa
Position	chr12: 10463419-10464889 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os12g0279000
Parent gene annotation	Helicase, C-terminal domain containing protein. (Os12t0279000-01 )
Parent gene strand	+
Alternative splicing	Os12g0279000_circ_g.2 Os12g0279000_circ_g.3 Os12g0279000_circ_g.5 Os12g0279000_circ_g.6
Support reads	1
Tissues	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	Os12t0279000-01:4

			
						 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  
						
							CAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGA
GCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGGaagcaagtcaaggagctggaactagaga
gaaattccatgattattgaggaggaggagaacctaaagagttattatgatctcttgcagcagta
caaaaatc

									
								

					

						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: 806
Transcript exons: 10463419-10463695,10464191-10464336,10464428-10464577,10
464657-10464889
AAGCAAGTCAAGGAGCTGGAACTAGAGAGAAATTCCATGATTATTGAGGAGGAGGAGAACCTAA
AGAGTTATTATGATCTCTTGCAGCAGTACAAAAATCTAAAGAAGGATGTCCGCGATATTGTTCA
TTCTCCTAAATATGTTCTACCTTTCTTGCAACCAGGAAGGCTTGCTCGCGTTCAGTACAGTACT
GATGAGCAATCCACCTTCTCTATTGATGAAAACATCACTTGGGGAGTTACAATAAACTTTGAAA
AGGTGAAAACCCATAGTGAAGATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCAC
AAGATGTTCTGTAAGCAAGGACAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGAC
CGTGGAGAACCAGTTGTGATTTCCTTGCCACTTTCTCAGATTGATGGACTAAGCAGCATTCGGA
TGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGTTGATGA
AGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGATATGAAAGTA
CAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAAGCTCTTGAAAGTTTATTTGAGAAGC
ACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAAAAGTGTTGCATGCTAAGCAAGAATT
ATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGAT
GAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG
						
					

						Genomic sequence
						
							AAGCAAGTCAAGGAGCTGGAACTAGAGAGAAATTCCATGATTATTGAGGAGGAGGAGAACCTAA
AGAGTTATTATGATCTCTTGCAGCAGTACAAAAATCTAAAGAAGGATGTCCGCGATATTGTTCA
TTCTCCTAAATATGTTCTACCTTTCTTGCAACCAGGAAGGCTTGCTCGCGTTCAGTACAGTACT
GATGAGCAATCCACCTTCTCTATTGATGAAAACATCACTTGGGGAGTTACAATAAACTTTGAAA
AGGTGAAAACCCATAGTGAAGGTACAGAAAACTTAAATGGAAAATCTGATCGAGCCATACTGTT
ATGTAATCTTTTTCTCTTTTGTTGAAGTTGTTTCCCCCGAGTTGTTTGGCAATGCAATTCCATT
ATATAACCTACAAGTCTTGTAATTAGACATTTTAAGGTGGTTTTGGAACTGAGTTTAGGCTCCA
GCACAAGATATGCTTGCTGACTAATCGCTGCTTCAAAGTTCAAATTTGTATGACCACATTTATT
TTTTCTATGATCTTGCACTTAATCTAAATGAGCTTTGATTAATTGTGGTAGATTGATATTTGAT
AGTCTGTCCTGGATTTTTTTGTCGTCATAAAAATTAGGACCCTTTTTTTCGGCAAATTGCATTT
CATGAGTCTCATTATGTATAACTCCAGCACTGCCTGGTTGTCTGGTTGAGAACACATGACAGGG
GCATCTTATAGCTATTGTGTCTCTCTTTACTCCTGAGTTCTGATTTATTTTTTTATTAAAAAAT
TCAGATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCA
AGGACAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGT
GATTTCCTTGCCACTTTCTCAGGTTATTTCCTTTTCCTATTTGACCGGTGAACTTTTTATGTTC
TAAACATTTATAACAATGCAAAGTGGTCTGTTTTCTGTCTAATTCACAGATTGATGGACTAAGC
AGCATTCGGATGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGA
AAGTTGATGAAGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGA
TATGAAAGTAAGAAAAAAAATCATGCATATCACTCAGGTTATCTCTATATATGTAGTTCTAACA
GCTTGTTTGTTTTTCTTTTCAGGTACAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAA
GCTCTTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAA
AAGTGTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTC
TTCCACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG
						
					

			
		

Sequences
Splice junction sequence	CAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGA GCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGGaagcaagtcaaggagctggaactagaga gaaattccatgattattgaggaggaggagaacctaaagagttattatgatctcttgcagcagta caaaaatc
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: 806 Transcript exons: 10463419-10463695,10464191-10464336,10464428-10464577,10 464657-10464889 AAGCAAGTCAAGGAGCTGGAACTAGAGAGAAATTCCATGATTATTGAGGAGGAGGAGAACCTAA AGAGTTATTATGATCTCTTGCAGCAGTACAAAAATCTAAAGAAGGATGTCCGCGATATTGTTCA TTCTCCTAAATATGTTCTACCTTTCTTGCAACCAGGAAGGCTTGCTCGCGTTCAGTACAGTACT GATGAGCAATCCACCTTCTCTATTGATGAAAACATCACTTGGGGAGTTACAATAAACTTTGAAA AGGTGAAAACCCATAGTGAAGATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCAC AAGATGTTCTGTAAGCAAGGACAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGAC CGTGGAGAACCAGTTGTGATTTCCTTGCCACTTTCTCAGATTGATGGACTAAGCAGCATTCGGA TGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGTTGATGA AGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGATATGAAAGTA CAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAAGCTCTTGAAAGTTTATTTGAGAAGC ACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAAAAGTGTTGCATGCTAAGCAAGAATT ATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGAT GAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG
Genomic sequence	AAGCAAGTCAAGGAGCTGGAACTAGAGAGAAATTCCATGATTATTGAGGAGGAGGAGAACCTAA AGAGTTATTATGATCTCTTGCAGCAGTACAAAAATCTAAAGAAGGATGTCCGCGATATTGTTCA TTCTCCTAAATATGTTCTACCTTTCTTGCAACCAGGAAGGCTTGCTCGCGTTCAGTACAGTACT GATGAGCAATCCACCTTCTCTATTGATGAAAACATCACTTGGGGAGTTACAATAAACTTTGAAA AGGTGAAAACCCATAGTGAAGGTACAGAAAACTTAAATGGAAAATCTGATCGAGCCATACTGTT ATGTAATCTTTTTCTCTTTTGTTGAAGTTGTTTCCCCCGAGTTGTTTGGCAATGCAATTCCATT ATATAACCTACAAGTCTTGTAATTAGACATTTTAAGGTGGTTTTGGAACTGAGTTTAGGCTCCA GCACAAGATATGCTTGCTGACTAATCGCTGCTTCAAAGTTCAAATTTGTATGACCACATTTATT TTTTCTATGATCTTGCACTTAATCTAAATGAGCTTTGATTAATTGTGGTAGATTGATATTTGAT AGTCTGTCCTGGATTTTTTTGTCGTCATAAAAATTAGGACCCTTTTTTTCGGCAAATTGCATTT CATGAGTCTCATTATGTATAACTCCAGCACTGCCTGGTTGTCTGGTTGAGAACACATGACAGGG GCATCTTATAGCTATTGTGTCTCTCTTTACTCCTGAGTTCTGATTTATTTTTTTATTAAAAAAT TCAGATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCA AGGACAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGT GATTTCCTTGCCACTTTCTCAGGTTATTTCCTTTTCCTATTTGACCGGTGAACTTTTTATGTTC TAAACATTTATAACAATGCAAAGTGGTCTGTTTTCTGTCTAATTCACAGATTGATGGACTAAGC AGCATTCGGATGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGA AAGTTGATGAAGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGA TATGAAAGTAAGAAAAAAAATCATGCATATCACTCAGGTTATCTCTATATATGTAGTTCTAACA GCTTGTTTGTTTTTCTTTTCAGGTACAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAA GCTCTTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAA AAGTGTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTC TTCCACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010381 						
					
						PMCS
						0.269900278

Conservation Information
Conserved circRNAs	osi_circ_010381
PMCS	0.269900278

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10463456-10463440(+)
10464851-10463462(+)
10463458-10464858(-)
						
						Potential amino acid sequence
						
							MIIEEEENLKSYYDLLQQYKNLKKDVRDIVHSPKYVLPFLQPGRLARVQYSTDEQSTFSIDENI
TWGVTINFEKVKTHSEDRRPEDSDYTVDVLTRCSVSKDKSGKKTMKIIPLKDRGEPVVISLPLS
QIDGLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLLDPEEDMKVQSSSFRKASRRI
EALESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRSSTALAFKDELKARKRVLRRL
GSKSRSWN*(+)
MSSRPENGFFVDWEASQGAGTREKFHDY*(+)
MEFLSSSSSLTCFPVYEEPVFGP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10463456-10463440(+) 10464851-10463462(+) 10463458-10464858(-)
Potential amino acid sequence	MIIEEEENLKSYYDLLQQYKNLKKDVRDIVHSPKYVLPFLQPGRLARVQYSTDEQSTFSIDENI TWGVTINFEKVKTHSEDRRPEDSDYTVDVLTRCSVSKDKSGKKTMKIIPLKDRGEPVVISLPLS QIDGLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLLDPEEDMKVQSSSFRKASRRI EALESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRSSTALAFKDELKARKRVLRRL GSKSRSWN(+) MSSRPENGFFVDWEASQGAGTREKFHDY(+) MEFLSSSSSLTCFPVYEEPVFGP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os12g0279000_circ_g.4

Address

Any questions?

Supported by