Plant Circular RNA Database

Detail information of Os04g0692750_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0692750_circ_g.2
					
						ID in PlantcircBase
						osa_circ_026116
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 35456403-35457751  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0692750						
					
						Parent gene annotation
						
							SNF2 family chromatin-remodeling helicase, Syncytial endosperm d
evelopment (Os04t0692750-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0692700_circ_ag.1 Os04g0692700_circ_ag.2 Os04g0692750_circ_g.1 						
					
						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  
						
							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
						Os04t0692750-01:5

General Information
CircRNA Name	Os04g0692750_circ_g.2
ID in PlantcircBase	osa_circ_026116
Alias	NA
Organism	Oryza sativa
Position	chr4: 35456403-35457751 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0692750
Parent gene annotation	SNF2 family chromatin-remodeling helicase, Syncytial endosperm d evelopment (Os04t0692750-01)
Parent gene strand	-
Alternative splicing	Os04g0692700_circ_ag.1 Os04g0692700_circ_ag.2 Os04g0692750_circ_g.1
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	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	Os04t0692750-01:5

			
						 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  
						
							ATGTTTCTTCCTCGTCATCAAAATCATTGGTGAAGTTGCCTTTTATCATCTTGAAATTGTTTCG
AACAATGTCATATGTTGTTAAAAGGATTCCACCCTCcgtgattgcggccaagggtgacccttgc
attgatgaatgaactagttcactgttaagaaaagcttcatataattgcctctgcatccaaaaaa
taaaaaag

									
								

					

						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: 597
Transcript exons: 35456403-35456480,35456573-35456710,35457203-35457293,35
457385-35457440,35457518-35457751
CGTGATTGCGGCCAAGGGTGACCCTTGCATTGATGAATGAACTAGTTCACTGTTAAGAAAAGCT
TCATATAATTGCCTCTGGCAAGATGTTAATTTCAGCCAGATAATTAGCTCATTCTTCTTAGCAA
GCTTTTTATCTTCTCCCGTGCCGCTATCAAGAAACACTTCATTCTTCATGCGTCGCAAAAAGTA
TGGCTTTATCCGTTCTCTTAATTCCTTTGCTACATTTGAGCCTATGTGCTTTTGTCGATTGGTA
GCATTCTTGTCATTTCCTTGAATGATAGCGTGCTCATACCTTGCTTTGAACTGCTCCTTATCAC
CCAAGACTTCTGGGCAACAGAAATAAAACAGAGCCCACATTTCCTTCAAGTTATTTTGTATGGG
TGTTCCACTGATGACAATACGATGTGCACAGGGTATTTCAAATAGACTTTGAGCCCTCTGAGTC
TTTGGATTCTTGATAATATGCCCCTCATCAAGAATAACATAGTTCCATAATGTTTCTTCCTCGT
CATCAAAATCATTGGTGAAGTTGCCTTTTATCATCTTGAAATTGTTTCGAACAATGTCATATGT
TGTTAAAAGGATTCCACCCTC
						
					

						Genomic sequence
						
							CGTGATTGCGGCCAAGGGTGACCCTTGCATTGATGAATGAACTAGTTCACTGTTAAGAAAAGCT
TCATATAATTGCCTCTGCATCCAAAAAATAAAAAAGGACTAATATTAAGATGGCAGTTAACCAA
TAACAAAACCAGAGTTTTGCATCAGTGGAAAATGATCTGTACCTGGCAAGATGTTAATTTCAGC
CAGATAATTAGCTCATTCTTCTTAGCAAGCTTTTTATCTTCTCCCGTGCCGCTATCAAGAAACA
CTTCATTCTTCATGCGTCGCAAAAAGTATGGCTTTATCCGTTCTCTTAATTCCTGTAATAAATG
ATCATGTACAAAACCAAAAACCACATATTATATAAAAAGTAGAACAGCAGACCTGAAGAAATAA
TCTGGAAGAATGGGTGGCAGTTAAAGAAATGCAACAAAGGAGGAGGCTCAATGTAAATAGCTTT
CCCTCTCATGGAACCAACTAAAAGCCCATTTTTATTAGTTGGTATGGAAACATAATTCCATTGC
TTTACAAGTCAAATTGGAGTACACGACTGTACTACTTTGATGATACATGATTGCAGTACCTATA
ATAAGAAGTATGTCTGTGTCCAAATTGCTGTCTTCTCAATGAAATAATAATAACAAAAAATAAT
AATTCCGCAAAAATTGGAATAGAGTAAACACCATAATCATTAATAGTCAAAATGCTAATGTGGT
GGAAAATCTGGCTCTCCTAATAATTAAATATCCAGTTCAGACACAAAAGTAACATGAAACAGGA
TCATCTATCACAACATGAAAAAGGATTAGTACCTTTGCTACATTTGAGCCTATGTGCTTTTGTC
GATTGGTAGCATTCTTGTCATTTCCTTGAATGATAGCGTGCTCATACCTTGCTTTGAACCTGCC
AAAAACAAGAGAAATAAACAACACTAGATTGTGTAATATGAAGCAACAATGGCAATGCAGAAAA
ACAACGGGCATAAGTGTATTACTGCTCCTTATCACCCAAGACTTCTGGGCAACAGAAATAAAAC
AGAGCCCACATTTCCTGCAAGAATAATCAGGATTACTTGCATTGGTTCGTGCGCCAATTATAAG
GCATTAAAAATTAAGAGAGTAGGATACCTTCAAGTTATTTTGTATGGGTGTTCCACTGATGACA
ATACGATGTGCACAGGGTATTTCAAATAGACTTTGAGCCCTCTGAGTCTTTGGATTCTTGATAA
TATGCCCCTCATCAAGAATAACATAGTTCCATAATGTTTCTTCCTCGTCATCAAAATCATTGGT
GAAGTTGCCTTTTATCATCTTGAAATTGTTTCGAACAATGTCATATGTTGTTAAAAGGATTCCA
CCCTC
						
					

			
		

Sequences
Splice junction sequence	ATGTTTCTTCCTCGTCATCAAAATCATTGGTGAAGTTGCCTTTTATCATCTTGAAATTGTTTCG AACAATGTCATATGTTGTTAAAAGGATTCCACCCTCcgtgattgcggccaagggtgacccttgc attgatgaatgaactagttcactgttaagaaaagcttcatataattgcctctgcatccaaaaaa taaaaaag
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: 597 Transcript exons: 35456403-35456480,35456573-35456710,35457203-35457293,35 457385-35457440,35457518-35457751 CGTGATTGCGGCCAAGGGTGACCCTTGCATTGATGAATGAACTAGTTCACTGTTAAGAAAAGCT TCATATAATTGCCTCTGGCAAGATGTTAATTTCAGCCAGATAATTAGCTCATTCTTCTTAGCAA GCTTTTTATCTTCTCCCGTGCCGCTATCAAGAAACACTTCATTCTTCATGCGTCGCAAAAAGTA TGGCTTTATCCGTTCTCTTAATTCCTTTGCTACATTTGAGCCTATGTGCTTTTGTCGATTGGTA GCATTCTTGTCATTTCCTTGAATGATAGCGTGCTCATACCTTGCTTTGAACTGCTCCTTATCAC CCAAGACTTCTGGGCAACAGAAATAAAACAGAGCCCACATTTCCTTCAAGTTATTTTGTATGGG TGTTCCACTGATGACAATACGATGTGCACAGGGTATTTCAAATAGACTTTGAGCCCTCTGAGTC TTTGGATTCTTGATAATATGCCCCTCATCAAGAATAACATAGTTCCATAATGTTTCTTCCTCGT CATCAAAATCATTGGTGAAGTTGCCTTTTATCATCTTGAAATTGTTTCGAACAATGTCATATGT TGTTAAAAGGATTCCACCCTC
Genomic sequence	CGTGATTGCGGCCAAGGGTGACCCTTGCATTGATGAATGAACTAGTTCACTGTTAAGAAAAGCT TCATATAATTGCCTCTGCATCCAAAAAATAAAAAAGGACTAATATTAAGATGGCAGTTAACCAA TAACAAAACCAGAGTTTTGCATCAGTGGAAAATGATCTGTACCTGGCAAGATGTTAATTTCAGC CAGATAATTAGCTCATTCTTCTTAGCAAGCTTTTTATCTTCTCCCGTGCCGCTATCAAGAAACA CTTCATTCTTCATGCGTCGCAAAAAGTATGGCTTTATCCGTTCTCTTAATTCCTGTAATAAATG ATCATGTACAAAACCAAAAACCACATATTATATAAAAAGTAGAACAGCAGACCTGAAGAAATAA TCTGGAAGAATGGGTGGCAGTTAAAGAAATGCAACAAAGGAGGAGGCTCAATGTAAATAGCTTT CCCTCTCATGGAACCAACTAAAAGCCCATTTTTATTAGTTGGTATGGAAACATAATTCCATTGC TTTACAAGTCAAATTGGAGTACACGACTGTACTACTTTGATGATACATGATTGCAGTACCTATA ATAAGAAGTATGTCTGTGTCCAAATTGCTGTCTTCTCAATGAAATAATAATAACAAAAAATAAT AATTCCGCAAAAATTGGAATAGAGTAAACACCATAATCATTAATAGTCAAAATGCTAATGTGGT GGAAAATCTGGCTCTCCTAATAATTAAATATCCAGTTCAGACACAAAAGTAACATGAAACAGGA TCATCTATCACAACATGAAAAAGGATTAGTACCTTTGCTACATTTGAGCCTATGTGCTTTTGTC GATTGGTAGCATTCTTGTCATTTCCTTGAATGATAGCGTGCTCATACCTTGCTTTGAACCTGCC AAAAACAAGAGAAATAAACAACACTAGATTGTGTAATATGAAGCAACAATGGCAATGCAGAAAA ACAACGGGCATAAGTGTATTACTGCTCCTTATCACCCAAGACTTCTGGGCAACAGAAATAAAAC AGAGCCCACATTTCCTGCAAGAATAATCAGGATTACTTGCATTGGTTCGTGCGCCAATTATAAG GCATTAAAAATTAAGAGAGTAGGATACCTTCAAGTTATTTTGTATGGGTGTTCCACTGATGACA ATACGATGTGCACAGGGTATTTCAAATAGACTTTGAGCCCTCTGAGTCTTTGGATTCTTGATAA TATGCCCCTCATCAAGAATAACATAGTTCCATAATGTTTCTTCCTCGTCATCAAAATCATTGGT GAAGTTGCCTTTTATCATCTTGAAATTGTTTCGAACAATGTCATATGTTGTTAAAAGGATTCCA CCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005877* osi_circ_015063 						
					
						PMCS
						0.253345046

Conservation Information
Conserved circRNAs	osi_circ_005877* osi_circ_015063
PMCS	0.253345046

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35457721-35456439(+)
35457702-35456405(-)
						
						Potential amino acid sequence
						
							MSYVVKRIPPSVIAAKGDPCIDE*(+)
MIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIVISGTPIQNNLKEMW
ALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRERIKPYFLRRMKNEV
FLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPLAAITEGGILLTTYD
IVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIVISGTPIQ
NNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRERIKPYFL
RRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPLAAITEGG
ILLTTYDIVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIV
ISGTPIQNNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRE
RIKPYFLRRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPL
AAITEGGILLTTYDIVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEI
PCAHRIVISGTPIQNNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSN
VAKELRERIKPYFLRRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHS
SMQGSPLAAIT(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35457721-35456439(+) 35457702-35456405(-)
Potential amino acid sequence	MSYVVKRIPPSVIAAKGDPCIDE*(+) MIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIVISGTPIQNNLKEMW ALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRERIKPYFLRRMKNEV FLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPLAAITEGGILLTTYD IVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIVISGTPIQ NNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRERIKPYFL RRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPLAAITEGG ILLTTYDIVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEIPCAHRIV ISGTPIQNNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSNVAKELRE RIKPYFLRRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHSSMQGSPL AAITEGGILLTTYDIVRNNFKMIKGNFTNDFDDEEETLWNYVILDEGHIIKNPKTQRAQSLFEI PCAHRIVISGTPIQNNLKEMWALFYFCCPEVLGDKEQFKARYEHAIIQGNDKNATNRQKHIGSN VAKELRERIKPYFLRRMKNEVFLDSGTGEDKKLAKKNELIIWLKLTSCQRQLYEAFLNSELVHS SMQGSPLAAIT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0692750_circ_g.2

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