Plant Circular RNA Database

Detail information of Os11g0294600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0294600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_009111
					
						Alias
						Os_ciR4263
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 10787816-10788948  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os11g0294600						
					
						Parent gene annotation
						
							Zinc finger, RING/FYVE/PHD-type domain containing protein. (Os11
t0294600-01);Zinc finger, RING/FYVE/PHD-type domain containing p
rotein. (Os11t0294600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0294600_circ_g.2 Os11g0294600_circ_g.4 						
					
						Support reads
						6
					
						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  
						
							CT-AC							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
						Os11t0294600-02:3
Os11t0294600-01:3

General Information
CircRNA Name	Os11g0294600_circ_g.3
ID in PlantcircBase	osa_circ_009111
Alias	Os_ciR4263
Organism	Oryza sativa
Position	chr11: 10787816-10788948 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os11g0294600
Parent gene annotation	Zinc finger, RING/FYVE/PHD-type domain containing protein. (Os11 t0294600-01);Zinc finger, RING/FYVE/PHD-type domain containing p rotein. (Os11t0294600-02)
Parent gene strand	-
Alternative splicing	Os11g0294600_circ_g.2 Os11g0294600_circ_g.4
Support reads	6
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	CT-AC 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	Os11t0294600-02:3 Os11t0294600-01:3

			
						 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  
						
							ATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATCATAGGCTGA
AGACAATGGTTCATGCTCCTCTTGATTTTGCTGACGctggtcacaaactgggcaggtatcactt
cgctccatccattcaagtatgcaacaaagatggaaatgatgctcacatttagttaaagagcgag
gattttct

									
								

					

						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: 118
Transcript exons: 10787816-10787876,10788892-10788948
CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAGA
TGATCCATCATAGGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG
Transcript length: 426
Transcript exons: 10787816-10787925,10788540-10788680,10788774-10788948
CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAAA
TGATGCTCACATTTAGTTAAAGAGCGAGGATTTTCTGCATCATATTCTTCAAGACAGATTGGGC
AAACATCCTCCTCATCAGGCTTATCTTCAGCGACACATTTTTCACATGATTTGAACTCATCCAC
CTCTAAAGATTCCTCCTGTTGGTCATCGGTTTTGCTCTTCAGGTCTGACTTCTCCAAATCAGGG
TTTTCTGGGACTGGCAAACTAACATCATAAGGCAATGGTGCAGGTGGTGCTCGGTAAGTATCAG
GAGTGGATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATCATA
GGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG
						
					

						Genomic sequence
						
							CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAAA
TGATGCTCACATTTAGTTAAAGAGCGAGGATTTTCTGCATCATATTCTGGTGAAAGGACAAACA
GAAGTCATGACTGGAGTTTTGTGGTCCGTAAGAAAATAAGCAAATAAGATTTAGAGTATCAATA
AATGTTAATGGAGTGCAAGTACAATGCACATTGTTACCCAATATTGCACCTAGGAATCAACAAA
AGGGTATGTACCAATTGAGAAAAAAGAATATACACAATTGGAACCCTTCATCTCTTTGAGAAGC
AACTATCTAAGATTGGTTGCATATTAAGCACAACACTTCTTAAGGCTTATTTCATATGCAGCAT
GGCCATATACATCCATTAAGGATGTGCATACATATTACATCTATTGAAGGTAAATAAAAGGAGC
ACAAGCAATCCTTTAATTGGTAAATTATAGGTAAGATATCCTAAACCATTATTTCCGAAATTAA
GAATAGTTTCTTTCAGCTAAAAACAAACGGATCAAACATACAGTGTACTTTTACCAGTTTTACT
GTGACAGTAGTAAAATAGCACTACAGCAGGCAGAACACGTGTATCCAATTCTACATTCAACCAG
GTAAAGTTTGTACTCAAACAAATATCCAGTTATTATTATGGCAATCTAAGGAATCGGGTTTTCA
ATGGTCAAAAGAAATACAACCTTCAAGACAGATTGGGCAAACATCCTCCTCATCAGGCTTATCT
TCAGCGACACATTTTTCACATGATTTGAACTCATCCACCTCTAAAGATTCCTCCTGTTGGTCAT
CGGTTTTGCTCTTCAGGTCTGACTTCTCCAAATCTGAAAATGAATTTGAAACTATAAGCTTCCA
CCACTACCATTTGAGGTTAATTCCATTCCTCATGTTCACAGGCTCAAAGGTAGTTAGTTTACCA
GGGTTTTCTGGGACTGGCAAACTAACATCATAAGGCAATGGTGCAGGTGGTGCTCGGTAAGTAT
CAGGAGTGGATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATC
ATAGGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG
						
					

			
		

Sequences
Splice junction sequence	ATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATCATAGGCTGA AGACAATGGTTCATGCTCCTCTTGATTTTGCTGACGctggtcacaaactgggcaggtatcactt cgctccatccattcaagtatgcaacaaagatggaaatgatgctcacatttagttaaagagcgag gattttct
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: 118 Transcript exons: 10787816-10787876,10788892-10788948 CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAGA TGATCCATCATAGGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG Transcript length: 426 Transcript exons: 10787816-10787925,10788540-10788680,10788774-10788948 CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAAA TGATGCTCACATTTAGTTAAAGAGCGAGGATTTTCTGCATCATATTCTTCAAGACAGATTGGGC AAACATCCTCCTCATCAGGCTTATCTTCAGCGACACATTTTTCACATGATTTGAACTCATCCAC CTCTAAAGATTCCTCCTGTTGGTCATCGGTTTTGCTCTTCAGGTCTGACTTCTCCAAATCAGGG TTTTCTGGGACTGGCAAACTAACATCATAAGGCAATGGTGCAGGTGGTGCTCGGTAAGTATCAG GAGTGGATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATCATA GGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG
Genomic sequence	CTGGTCACAAACTGGGCAGGTATCACTTCGCTCCATCCATTCAAGTATGCAACAAAGATGGAAA TGATGCTCACATTTAGTTAAAGAGCGAGGATTTTCTGCATCATATTCTGGTGAAAGGACAAACA GAAGTCATGACTGGAGTTTTGTGGTCCGTAAGAAAATAAGCAAATAAGATTTAGAGTATCAATA AATGTTAATGGAGTGCAAGTACAATGCACATTGTTACCCAATATTGCACCTAGGAATCAACAAA AGGGTATGTACCAATTGAGAAAAAAGAATATACACAATTGGAACCCTTCATCTCTTTGAGAAGC AACTATCTAAGATTGGTTGCATATTAAGCACAACACTTCTTAAGGCTTATTTCATATGCAGCAT GGCCATATACATCCATTAAGGATGTGCATACATATTACATCTATTGAAGGTAAATAAAAGGAGC ACAAGCAATCCTTTAATTGGTAAATTATAGGTAAGATATCCTAAACCATTATTTCCGAAATTAA GAATAGTTTCTTTCAGCTAAAAACAAACGGATCAAACATACAGTGTACTTTTACCAGTTTTACT GTGACAGTAGTAAAATAGCACTACAGCAGGCAGAACACGTGTATCCAATTCTACATTCAACCAG GTAAAGTTTGTACTCAAACAAATATCCAGTTATTATTATGGCAATCTAAGGAATCGGGTTTTCA ATGGTCAAAAGAAATACAACCTTCAAGACAGATTGGGCAAACATCCTCCTCATCAGGCTTATCT TCAGCGACACATTTTTCACATGATTTGAACTCATCCACCTCTAAAGATTCCTCCTGTTGGTCAT CGGTTTTGCTCTTCAGGTCTGACTTCTCCAAATCTGAAAATGAATTTGAAACTATAAGCTTCCA CCACTACCATTTGAGGTTAATTCCATTCCTCATGTTCACAGGCTCAAAGGTAGTTAGTTTACCA GGGTTTTCTGGGACTGGCAAACTAACATCATAAGGCAATGGTGCAGGTGGTGCTCGGTAAGTAT CAGGAGTGGATGTATCCAGATTTGTGTCAACAGCAACTATAGCAGAAGCTGGAGATGATCCATC ATAGGCTGAAGACAATGGTTCATGCTCCTCTTGATTTTGCTGACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009546 						
					
						PMCS
						0.360302073

Conservation Information
Conserved circRNAs	osi_circ_009546
PMCS	0.360302073

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10788926-10787896(+)
10788895-10787892(+)
10787853-10787818(-)
						
						Potential amino acid sequence
						
							MLLLILLTLVTNWAGITSLHPFKYATKMEMMLTFS*(+)
MIHHRLKTMVHAPLDFADAGHKLGRYHFAPSIQVCNKDGNDAHI*(+)
MERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAIVAVDTNLDTSTPDTYRAPPAPLPYDVSL
PVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKCVAEDKPDEEDVCPICLEEYDAENPRSLT
KCEHHFHLCCILEWMERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAIVAVDTNLDTSTPDT
YRAPPAPLPYDVSLPVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKCVAEDKPDEEDVCPI
CLEEYDAENPRSLTKCEHHFHLCCILEWMERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAI
VAVDTNLDTSTPDTYRAPPAPLPYDVSLPVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKC
VAEDKPDEEDVCPICLEEYDAENPRSLTKCEHHFHLCCILEWMERSDTCPVCDQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10788926-10787896(+) 10788895-10787892(+) 10787853-10787818(-)
Potential amino acid sequence	MLLLILLTLVTNWAGITSLHPFKYATKMEMMLTFS(+) MIHHRLKTMVHAPLDFADAGHKLGRYHFAPSIQVCNKDGNDAHI(+) MERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAIVAVDTNLDTSTPDTYRAPPAPLPYDVSL PVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKCVAEDKPDEEDVCPICLEEYDAENPRSLT KCEHHFHLCCILEWMERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAIVAVDTNLDTSTPDT YRAPPAPLPYDVSLPVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKCVAEDKPDEEDVCPI CLEEYDAENPRSLTKCEHHFHLCCILEWMERSDTCPVCDQRQQNQEEHEPLSSAYDGSSPASAI VAVDTNLDTSTPDTYRAPPAPLPYDVSLPVPENPDLEKSDLKSKTDDQQEESLEVDEFKSCEKC VAEDKPDEEDVCPICLEEYDAENPRSLTKCEHHFHLCCILEWMERSDTCPVCDQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os11g0294600_circ_g.3

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