Plant Circular RNA Database

Detail information of Os04g0640800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0640800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025564
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 32600890-32602315  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0640800						
					
						Parent gene annotation
						
							Programmed cell death protein 2, C-terminal domain containing pr
otein. (Os04t0640800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0640800-01:5

General Information
CircRNA Name	Os04g0640800_circ_g.1
ID in PlantcircBase	osa_circ_025564
Alias	NA
Organism	Oryza sativa
Position	chr4: 32600890-32602315 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0640800
Parent gene annotation	Programmed cell death protein 2, C-terminal domain containing pr otein. (Os04t0640800-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	1
Tissues	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	Os04t0640800-01:5

			
						 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  
						
							TCCATTGTCATATTTCCTCCATGAAGCTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGG
ACCTGGCTGACTCTTATCATATACACCTGCTCAAAGgactggccaaccgaggatatgggcatta
aacctcacttgctccaatgcggtttatgtggaaccaagttgtgccttgttgctcaggcgagtat
ttactgtt

									
								

					

						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: 906
Transcript exons: 32600890-32600968,32601189-32601285,32601382-32601677,32
601757-32601985,32602111-32602315
GACTGGCCAACCGAGGATATGGGCATTAAACCTCACTTGCTCCAATGCGGTTTATGTGGAACCA
AGTTGTGCCTTGTTGCTCAGGTTCATGCTCCTGTGGCAAAGTTCAACATTGAGAACAGGACTAT
CTATGTGCTTGTTTGTCCGAAGCCAAAATGTGGGACGAACCCGCAAAGTTGGAAGGTCCTAAGA
GTCCAAAAGTGCCACACCAGTGCACAAACAGATGGCAAGGTTGACGAAACAGATCAAATAAACG
GAAATGTTTGCTCAAGTGAGCCTTCTTCTTCAAGTTTACTGAACAAGAGCCATGAGGTCAGTGA
TGATGATTTCGATCTAGATGCCTTAGCCAATGCACTTGAGGAAGCAGCGACTTTAGCATCTAAC
TCAAAGAAGCAAAACAAACCAAAGCGTAGTAATGCCCCTATAAAATGCCCTGTAGGAAAGCAGA
AAGTGGATGATCCAAGCTTACCAGTTCTTCCTTGCTTCTACATCTATTATGGTAAGGAGCAATT
TAGAGACAAAGGCAGTGTAGGTTCAAATAGCAGCAAGTCAGTTTTAGCGAAAGAAATTGCAGAT
GTAGCAAATGACGAAGAAGAGAAATGGGAAGGAGAAAACTATGAATATGACAGAGCTATTGGTG
CTGACAGAACGTTCTTAAAATTCAAGAAACGGTTGGATGCATATCCGCAGCAATGCTTTAGGTA
TTCTTATGGTGGTAAGCCACTGTTGGCTGCAACAAACCTTCAAGATTCTGGCACATGCCAGCTT
TGTGGTTCACCACGCCAATATGAGCTACAATTGATGTCTCCATTGTCATATTTCCTCCATGAAG
CTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGGACCTGGCTGACTCTTATCATATACAC
CTGCTCAAAG
						
					

						Genomic sequence
						
							GACTGGCCAACCGAGGATATGGGCATTAAACCTCACTTGCTCCAATGCGGTTTATGTGGAACCA
AGTTGTGCCTTGTTGCTCAGGCGAGTATTTACTGTTTCGCAAGAATTCAGTACTTGCAATAGGA
GCATGTGTGGATGAACGTTTGTATGAGAAAATAGAGCAGTAATAAGATGCCTGGACATTTGTTA
CAATGCATTAAAGTGTATCAGAGCTTATTTTCCTACTGATTTATGACGATAGAGTGCTTCTACC
TCGCTACTAGTACTGTTGCTTCGTTTTTATGAGATGTGATGGTCTCAGGTTCATGCTCCTGTGG
CAAAGTTCAACATTGAGAACAGGACTATCTATGTGCTTGTTTGTCCGAAGCCAAAATGTGGGAC
GAACCCGCAAAGGTGAGCATGTCTCCCTTTGTTTCTTTATGTAATATGATTATAGTTTACAAGT
TAGCTTGGGAATTTTTATGCTTTTCTTTTTCTTTTTCTTTACAGTTGGAAGGTCCTAAGAGTCC
AAAAGTGCCACACCAGTGCACAAACAGATGGCAAGGTTGACGAAACAGATCAAATAAACGGAAA
TGTTTGCTCAAGTGAGCCTTCTTCTTCAAGTTTACTGAACAAGAGCCATGAGGTCAGTGATGAT
GATTTCGATCTAGATGCCTTAGCCAATGCACTTGAGGAAGCAGCGACTTTAGCATCTAACTCAA
AGAAGCAAAACAAACCAAAGCGTAGTAATGCCCCTATAAAATGCCCTGTAGGAAAGCAGAAAGT
GGATGATCCAAGCTTACCAGGTAAAGTTAAAGTCTTAAGTACTAAGTGCTATACTCACAAAGTC
TTATATTTTGATCTCATAAAATTTTCTTCTTGCAGTTCTTCCTTGCTTCTACATCTATTATGGT
AAGGAGCAATTTAGAGACAAAGGCAGTGTAGGTTCAAATAGCAGCAAGTCAGTTTTAGCGAAAG
AAATTGCAGATGTAGCAAATGACGAAGAAGAGAAATGGGAAGGAGAAAACTATGAATATGACAG
AGCTATTGGTGCTGACAGAACGTTCTTAAAATTCAAGAAACGGTTGGATGCATATCCGCAGCAA
TGCTTTAGGTGGTTAAATTCATATGTCCTTGCAAACTCATCTTTCAATTATGTGATGTACTGGT
TATCTATTATGCATTAATTGTCTATTACCTTCTTGACTTTCGGAACCTGAATTTTGTGATGTTA
TGCAGGTATTCTTATGGTGGTAAGCCACTGTTGGCTGCAACAAACCTTCAAGATTCTGGCACAT
GCCAGCTTTGTGGTTCACCACGCCAATATGAGCTACAATTGATGTCTCCATTGTCATATTTCCT
CCATGAAGCTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGGACCTGGCTGACTCTTATC
ATATACACCTGCTCAAAG
						
					

			
		

Sequences
Splice junction sequence	TCCATTGTCATATTTCCTCCATGAAGCTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGG ACCTGGCTGACTCTTATCATATACACCTGCTCAAAGgactggccaaccgaggatatgggcatta aacctcacttgctccaatgcggtttatgtggaaccaagttgtgccttgttgctcaggcgagtat ttactgtt
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: 906 Transcript exons: 32600890-32600968,32601189-32601285,32601382-32601677,32 601757-32601985,32602111-32602315 GACTGGCCAACCGAGGATATGGGCATTAAACCTCACTTGCTCCAATGCGGTTTATGTGGAACCA AGTTGTGCCTTGTTGCTCAGGTTCATGCTCCTGTGGCAAAGTTCAACATTGAGAACAGGACTAT CTATGTGCTTGTTTGTCCGAAGCCAAAATGTGGGACGAACCCGCAAAGTTGGAAGGTCCTAAGA GTCCAAAAGTGCCACACCAGTGCACAAACAGATGGCAAGGTTGACGAAACAGATCAAATAAACG GAAATGTTTGCTCAAGTGAGCCTTCTTCTTCAAGTTTACTGAACAAGAGCCATGAGGTCAGTGA TGATGATTTCGATCTAGATGCCTTAGCCAATGCACTTGAGGAAGCAGCGACTTTAGCATCTAAC TCAAAGAAGCAAAACAAACCAAAGCGTAGTAATGCCCCTATAAAATGCCCTGTAGGAAAGCAGA AAGTGGATGATCCAAGCTTACCAGTTCTTCCTTGCTTCTACATCTATTATGGTAAGGAGCAATT TAGAGACAAAGGCAGTGTAGGTTCAAATAGCAGCAAGTCAGTTTTAGCGAAAGAAATTGCAGAT GTAGCAAATGACGAAGAAGAGAAATGGGAAGGAGAAAACTATGAATATGACAGAGCTATTGGTG CTGACAGAACGTTCTTAAAATTCAAGAAACGGTTGGATGCATATCCGCAGCAATGCTTTAGGTA TTCTTATGGTGGTAAGCCACTGTTGGCTGCAACAAACCTTCAAGATTCTGGCACATGCCAGCTT TGTGGTTCACCACGCCAATATGAGCTACAATTGATGTCTCCATTGTCATATTTCCTCCATGAAG CTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGGACCTGGCTGACTCTTATCATATACAC CTGCTCAAAG
Genomic sequence	GACTGGCCAACCGAGGATATGGGCATTAAACCTCACTTGCTCCAATGCGGTTTATGTGGAACCA AGTTGTGCCTTGTTGCTCAGGCGAGTATTTACTGTTTCGCAAGAATTCAGTACTTGCAATAGGA GCATGTGTGGATGAACGTTTGTATGAGAAAATAGAGCAGTAATAAGATGCCTGGACATTTGTTA CAATGCATTAAAGTGTATCAGAGCTTATTTTCCTACTGATTTATGACGATAGAGTGCTTCTACC TCGCTACTAGTACTGTTGCTTCGTTTTTATGAGATGTGATGGTCTCAGGTTCATGCTCCTGTGG CAAAGTTCAACATTGAGAACAGGACTATCTATGTGCTTGTTTGTCCGAAGCCAAAATGTGGGAC GAACCCGCAAAGGTGAGCATGTCTCCCTTTGTTTCTTTATGTAATATGATTATAGTTTACAAGT TAGCTTGGGAATTTTTATGCTTTTCTTTTTCTTTTTCTTTACAGTTGGAAGGTCCTAAGAGTCC AAAAGTGCCACACCAGTGCACAAACAGATGGCAAGGTTGACGAAACAGATCAAATAAACGGAAA TGTTTGCTCAAGTGAGCCTTCTTCTTCAAGTTTACTGAACAAGAGCCATGAGGTCAGTGATGAT GATTTCGATCTAGATGCCTTAGCCAATGCACTTGAGGAAGCAGCGACTTTAGCATCTAACTCAA AGAAGCAAAACAAACCAAAGCGTAGTAATGCCCCTATAAAATGCCCTGTAGGAAAGCAGAAAGT GGATGATCCAAGCTTACCAGGTAAAGTTAAAGTCTTAAGTACTAAGTGCTATACTCACAAAGTC TTATATTTTGATCTCATAAAATTTTCTTCTTGCAGTTCTTCCTTGCTTCTACATCTATTATGGT AAGGAGCAATTTAGAGACAAAGGCAGTGTAGGTTCAAATAGCAGCAAGTCAGTTTTAGCGAAAG AAATTGCAGATGTAGCAAATGACGAAGAAGAGAAATGGGAAGGAGAAAACTATGAATATGACAG AGCTATTGGTGCTGACAGAACGTTCTTAAAATTCAAGAAACGGTTGGATGCATATCCGCAGCAA TGCTTTAGGTGGTTAAATTCATATGTCCTTGCAAACTCATCTTTCAATTATGTGATGTACTGGT TATCTATTATGCATTAATTGTCTATTACCTTCTTGACTTTCGGAACCTGAATTTTGTGATGTTA TGCAGGTATTCTTATGGTGGTAAGCCACTGTTGGCTGCAACAAACCTTCAAGATTCTGGCACAT GCCAGCTTTGTGGTTCACCACGCCAATATGAGCTACAATTGATGTCTCCATTGTCATATTTCCT CCATGAAGCTGGTGATGGTTCCTCAGATTATGCACCTGATGGCTGGACCTGGCTGACTCTTATC ATATACACCTGCTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.253197955

Conservation Information
Conserved circRNAs	NA
PMCS	0.253197955

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32600909-32602312(+)
32600917-32602263(-)
						
						Potential amino acid sequence
						
							MGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSWKVLRVQKCHT
SAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAATLASNSKKQNK
PKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAKEIADVANDEE
EKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSGTCQLCGSPRQ
YELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIYTCSKDWPTEDMGIKPHLLQCGLCGTKLC
LVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSWKVLRVQKCHTSAQTDGKVDETDQINGNV
CSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAATLASNSKKQNKPKRSNAPIKCPVGKQKVD
DPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAKEIADVANDEEEKWEGENYEYDRAIGADR
TFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSGTCQLCGSPRQYELQLMSPLSYFLHEAGD
GSSDYAPDGWTWLTLIIYTCSKDWPTEDMGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRT
IYVLVCPKPKCGTNPQSWKVLRVQKCHTSAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVS
DDDFDLDALANALEEAATLASNSKKQNKPKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQ
FRDKGSVGSNSSKSVLAKEIADVANDEEEKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFR
YSYGGKPLLAATNLQDSGTCQLCGSPRQYELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIY
TCSKDWPTEDMGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSW
KVLRVQKCHTSAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAAT
LASNSKKQNKPKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAK
EIADVANDEEEKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSG
TCQLCGSPRQYELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIYTCSK(+)
MPISSVGQSFEQVYMIRVSQVQPSGA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	32600909-32602312(+) 32600917-32602263(-)
Potential amino acid sequence	MGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSWKVLRVQKCHT SAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAATLASNSKKQNK PKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAKEIADVANDEE EKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSGTCQLCGSPRQ YELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIYTCSKDWPTEDMGIKPHLLQCGLCGTKLC LVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSWKVLRVQKCHTSAQTDGKVDETDQINGNV CSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAATLASNSKKQNKPKRSNAPIKCPVGKQKVD DPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAKEIADVANDEEEKWEGENYEYDRAIGADR TFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSGTCQLCGSPRQYELQLMSPLSYFLHEAGD GSSDYAPDGWTWLTLIIYTCSKDWPTEDMGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRT IYVLVCPKPKCGTNPQSWKVLRVQKCHTSAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVS DDDFDLDALANALEEAATLASNSKKQNKPKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQ FRDKGSVGSNSSKSVLAKEIADVANDEEEKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFR YSYGGKPLLAATNLQDSGTCQLCGSPRQYELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIY TCSKDWPTEDMGIKPHLLQCGLCGTKLCLVAQVHAPVAKFNIENRTIYVLVCPKPKCGTNPQSW KVLRVQKCHTSAQTDGKVDETDQINGNVCSSEPSSSSLLNKSHEVSDDDFDLDALANALEEAAT LASNSKKQNKPKRSNAPIKCPVGKQKVDDPSLPVLPCFYIYYGKEQFRDKGSVGSNSSKSVLAK EIADVANDEEEKWEGENYEYDRAIGADRTFLKFKKRLDAYPQQCFRYSYGGKPLLAATNLQDSG TCQLCGSPRQYELQLMSPLSYFLHEAGDGSSDYAPDGWTWLTLIIYTCSK(+) MPISSVGQSFEQVYMIRVSQVQPSGA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0640800_circ_g.1

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