Plant Circular RNA Database

Detail information of Os04g0466600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0466600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024122
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 23317108-23318171  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0466600						
					
						Parent gene annotation
						
							Agmatine deiminase domain containing protein. (Os04t0466600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0466600_circ_g.2 Os04g0466600_circ_g.4 						
					
						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
						Os04t0466600-01:5

General Information
CircRNA Name	Os04g0466600_circ_g.3
ID in PlantcircBase	osa_circ_024122
Alias	NA
Organism	Oryza sativa
Position	chr4: 23317108-23318171 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0466600
Parent gene annotation	Agmatine deiminase domain containing protein. (Os04t0466600-01)
Parent gene strand	+
Alternative splicing	Os04g0466600_circ_g.2 Os04g0466600_circ_g.4
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	Os04t0466600-01:5

			
						 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  
						
							CTTCTACATAGCCAATGGCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGAAGCG
TGTGCTGTTCTTCAGAAGGCATTTCCTGATCATGAGgagccactgatggttgctatgttgattg
gagccttgacagctatgttgccaagaaagtaagaagagaataaccttcttaaagaaaatttgac
atctttca

									
								

					

						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: 659
Transcript exons: 23317108-23317163,23317278-23317356,23317445-23317579,23
317688-23317923,23318019-23318171
GAGCCACTGATGGTTGCTATGTTGATTGGAGCCTTGACAGCTATGTTGCCAAGAAAATAGTTGA
GATTGAGAGGATCCCTAGATTTCCACACACGATGGTTCTTGAAGGTGGAAGCATTCATGTAGAT
GGAGAAGGTACATGCATCACAACAGAAGAATGCTTGTTGAATCCTAACAGAAACCCCAACATGA
CCAAACTAGAGATAGAGAATGAGCTGAAGGATTTTCTTGGAGTCGCAAAGGTCATCTGGATACC
TCATGGGCTTTATGGTGATGATGATACAAATGGTCATGTTGACAATCTATGCTGCTTCATTAAA
CCTGGGGTGGTCCTCTTGTCATGGACCGATGATGAGAACGACCCACAGTACCAAAGGTCCGTTG
ATGCACTCTCAACTCTCTCCAAGTCCGTTGATGCGAAAGGACGGCAGATAGAAGTTGTGAAAAT
CCACGTCCCAGGGCCTCTGTACATGACAAAGGAAGAGTCAGAGGGTGTTGTAAAAACAGAGCAT
GCTATACCGAGGGAACCAGGCACGAGATTGGCTGCCTCGTACGTAAACTTCTACATAGCCAATG
GCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGAAGCGTGTGCTGTTCTTCAGAA
GGCATTTCCTGATCATGAG
						
					

						Genomic sequence
						
							GAGCCACTGATGGTTGCTATGTTGATTGGAGCCTTGACAGCTATGTTGCCAAGAAAGTAAGAAG
AGAATAACCTTCTTAAAGAAAATTTGACATCTTTCAAGGTCAAAAAGATCTTTTGCTAGTCTCC
ATCTGGTCTGAGAACTAGTTCTGTTTTGGACATTGATTTCAGATAGTTGAGATTGAGAGGATCC
CTAGATTTCCACACACGATGGTTCTTGAAGGTGGAAGCATTCATGTAGATGGAGAAGGTTGTTC
ATGTGTTGAATCTTTGCTGACAAGCATATAGTTTCAGTATATTTGTTGGTATCTTGCTAATGAA
TTGCCATATTCCAACAGGTACATGCATCACAACAGAAGAATGCTTGTTGAATCCTAACAGAAAC
CCCAACATGACCAAACTAGAGATAGAGAATGAGCTGAAGGATTTTCTTGGAGTCGCAAAGGTCA
TCTGGATACCTCATGGGCTTTATGGTAACCACCAAAAACATTCTGTCACATAAAGGTGTAAAAC
CATAATAGTTCTGTTCCCTGCTTCTTCAACCATTCTACTGATAAATAGGCCTGCAATGGTTTCT
CTAGGTGATGATGATACAAATGGTCATGTTGACAATCTATGCTGCTTCATTAAACCTGGGGTGG
TCCTCTTGTCATGGACCGATGATGAGAACGACCCACAGTACCAAAGGTCCGTTGATGCACTCTC
AACTCTCTCCAAGTCCGTTGATGCGAAAGGACGGCAGATAGAAGTTGTGAAAATCCACGTCCCA
GGGCCTCTGTACATGACAAAGGAAGAGTCAGAGGGTGTTGTAAAAACAGTCAGTATTTCTGTCA
TATTCATTACTAACTTCAATCCATTGAAAATGAGCGTGTTCATCCCTTTCTAAGAATGAATAGT
CCTTTTTTTTTCTAGGAGCATGCTATACCGAGGGAACCAGGCACGAGATTGGCTGCCTCGTACG
TAAACTTCTACATAGCCAATGGCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGA
AGCGTGTGCTGTTCTTCAGAAGGCATTTCCTGATCATGAG
						
					

			
		

Sequences
Splice junction sequence	CTTCTACATAGCCAATGGCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGAAGCG TGTGCTGTTCTTCAGAAGGCATTTCCTGATCATGAGgagccactgatggttgctatgttgattg gagccttgacagctatgttgccaagaaagtaagaagagaataaccttcttaaagaaaatttgac atctttca
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: 659 Transcript exons: 23317108-23317163,23317278-23317356,23317445-23317579,23 317688-23317923,23318019-23318171 GAGCCACTGATGGTTGCTATGTTGATTGGAGCCTTGACAGCTATGTTGCCAAGAAAATAGTTGA GATTGAGAGGATCCCTAGATTTCCACACACGATGGTTCTTGAAGGTGGAAGCATTCATGTAGAT GGAGAAGGTACATGCATCACAACAGAAGAATGCTTGTTGAATCCTAACAGAAACCCCAACATGA CCAAACTAGAGATAGAGAATGAGCTGAAGGATTTTCTTGGAGTCGCAAAGGTCATCTGGATACC TCATGGGCTTTATGGTGATGATGATACAAATGGTCATGTTGACAATCTATGCTGCTTCATTAAA CCTGGGGTGGTCCTCTTGTCATGGACCGATGATGAGAACGACCCACAGTACCAAAGGTCCGTTG ATGCACTCTCAACTCTCTCCAAGTCCGTTGATGCGAAAGGACGGCAGATAGAAGTTGTGAAAAT CCACGTCCCAGGGCCTCTGTACATGACAAAGGAAGAGTCAGAGGGTGTTGTAAAAACAGAGCAT GCTATACCGAGGGAACCAGGCACGAGATTGGCTGCCTCGTACGTAAACTTCTACATAGCCAATG GCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGAAGCGTGTGCTGTTCTTCAGAA GGCATTTCCTGATCATGAG
Genomic sequence	GAGCCACTGATGGTTGCTATGTTGATTGGAGCCTTGACAGCTATGTTGCCAAGAAAGTAAGAAG AGAATAACCTTCTTAAAGAAAATTTGACATCTTTCAAGGTCAAAAAGATCTTTTGCTAGTCTCC ATCTGGTCTGAGAACTAGTTCTGTTTTGGACATTGATTTCAGATAGTTGAGATTGAGAGGATCC CTAGATTTCCACACACGATGGTTCTTGAAGGTGGAAGCATTCATGTAGATGGAGAAGGTTGTTC ATGTGTTGAATCTTTGCTGACAAGCATATAGTTTCAGTATATTTGTTGGTATCTTGCTAATGAA TTGCCATATTCCAACAGGTACATGCATCACAACAGAAGAATGCTTGTTGAATCCTAACAGAAAC CCCAACATGACCAAACTAGAGATAGAGAATGAGCTGAAGGATTTTCTTGGAGTCGCAAAGGTCA TCTGGATACCTCATGGGCTTTATGGTAACCACCAAAAACATTCTGTCACATAAAGGTGTAAAAC CATAATAGTTCTGTTCCCTGCTTCTTCAACCATTCTACTGATAAATAGGCCTGCAATGGTTTCT CTAGGTGATGATGATACAAATGGTCATGTTGACAATCTATGCTGCTTCATTAAACCTGGGGTGG TCCTCTTGTCATGGACCGATGATGAGAACGACCCACAGTACCAAAGGTCCGTTGATGCACTCTC AACTCTCTCCAAGTCCGTTGATGCGAAAGGACGGCAGATAGAAGTTGTGAAAATCCACGTCCCA GGGCCTCTGTACATGACAAAGGAAGAGTCAGAGGGTGTTGTAAAAACAGTCAGTATTTCTGTCA TATTCATTACTAACTTCAATCCATTGAAAATGAGCGTGTTCATCCCTTTCTAAGAATGAATAGT CCTTTTTTTTTCTAGGAGCATGCTATACCGAGGGAACCAGGCACGAGATTGGCTGCCTCGTACG TAAACTTCTACATAGCCAATGGCGGAATTGTAGCACCAGCTTTTGGCGACAAGTGGGACGAAGA AGCGTGTGCTGTTCTTCAGAAGGCATTTCCTGATCATGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.272744486

Conservation Information
Conserved circRNAs	NA
PMCS	0.272744486

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23317318-23317278(+)
23317345-23318167(-)
						
						Potential amino acid sequence
						
							MVLEGGSIHVDGEGTCITTEECLLNPNRNPNMTKLEIENELKDFLGVAKVIWIPHGLYGDDDTN
GHVDNLCCFIKPGVVLLSWTDDENDPQYQRSVDALSTLSKSVDAKGRQIEVVKIHVPGPLYMTK
EESEGVVKTEHAIPREPGTRLAASYVNFYIANGGIVAPAFGDKWDEEACAVLQKAFPDHEEPLM
VAMLIGALTAMLPRK*(+)
MNASTFKNHRVWKSRDPLNLNYFLGNIAVKAPINIATISGSS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23317318-23317278(+) 23317345-23318167(-)
Potential amino acid sequence	MVLEGGSIHVDGEGTCITTEECLLNPNRNPNMTKLEIENELKDFLGVAKVIWIPHGLYGDDDTN GHVDNLCCFIKPGVVLLSWTDDENDPQYQRSVDALSTLSKSVDAKGRQIEVVKIHVPGPLYMTK EESEGVVKTEHAIPREPGTRLAASYVNFYIANGGIVAPAFGDKWDEEACAVLQKAFPDHEEPLM VAMLIGALTAMLPRK(+) MNASTFKNHRVWKSRDPLNLNYFLGNIAVKAPINIATISGSS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0466600_circ_g.3

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