Plant Circular RNA Database

Detail information of Os04g0437600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0437600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_023907
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 21754058-21756400  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os04g0437600						
					
						Parent gene annotation
						
							Mitogen activated protein kinase kinase kinase 3 domain containi
ng protein. (Os04t0437600-01);Similar to H0315A08.7 protein. (Os
04t0437600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0437600_circ_g.1 Os04g0437600_circ_g.3 Os04g0437600_circ_g.4 Os04g0437600_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						root, seed
					
						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
						Os04t0437600-01:7

General Information
CircRNA Name	Os04g0437600_circ_g.2
ID in PlantcircBase	osa_circ_023907
Alias	NA
Organism	Oryza sativa
Position	chr4: 21754058-21756400 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os04g0437600
Parent gene annotation	Mitogen activated protein kinase kinase kinase 3 domain containi ng protein. (Os04t0437600-01);Similar to H0315A08.7 protein. (Os 04t0437600-02)
Parent gene strand	-
Alternative splicing	Os04g0437600_circ_g.1 Os04g0437600_circ_g.3 Os04g0437600_circ_g.4 Os04g0437600_circ_g.5
Support reads	1
Tissues	root, seed
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	Os04t0437600-01:7

			
						 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  
						
							CTGAGAAATAACCTGATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATAACT
TGGACCTCCTTAATCGCACAGAACTGCCCATTTTCAcgttgtatgcgtcccatctgctggtgca
aacgcatttctcagtgcaccagatttcgcagctcttactgctggatggtcctgaacaaaagggt
gatccatc

									
								

					

						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: 790
Transcript exons: 21754058-21754291,21754366-21754473,21754566-21754625,21
755205-21755280,21755366-21755526,21756141-21756203,2175
6313-21756400
CGTTGTATGCGTCCCATCTGCTGGTGCAAACGCATTTCTCAGTGCACCAGATTTCGCAGCTCTT
ACTGCTGGATGGTCCTGAACAAAAGGGTGATCCATCAACTGAGTTGCAGTGAAGCGAGATGCAG
GATCACGTTTTAAGCACATCTGCAAGAAGCTTTTTCCTTCCTCAGAAAAGCTGTCTGGGATTTC
AGGTATCTCTTTACTGTTTGCGATCTTAAATATAGCAGCTACCCCCTCGTATTTATGCCAAGGA
GGTTTTGCCGTTGCCATTTCAATAATAGTACATCCCAAACTCCAAATGTCAACTGGTAGATGGT
AACCTCTACCGTTCATTATAACCTCAGGAGCCATCCAGTAAGGACTTCCTTTGAAAGAGCGTAT
TTCAGCAAAAGATGATATATGCTTAGCCATGCCAAAGTCAGCAAGTTTGACTTCACCATTAGGG
CCGACAAGTATGTTAGCACCTTTAATATCTCTGTGGACAGTGTTCCTCCCATGCAAGTAGGCAA
GACCAGAGAGAATTTGTCCAGTGTAATTACGGATCACAGGTTCCTTAAAAGGACCATACTCTCT
AAGTAATTTATGAATTGAGCCCCCAGAAACAAACTCCAGATAAATTGAAAGTGCATCATCAGTC
ATCTCACTTCCATAGTACTGCACAATGTTTGGGTGCGAAAGTTGCCTAAGCATATCTATTTCCT
GATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATAACTTGGACCTCCTTAAT
CGCACAGAACTGCCCATTTTCA
						
					

						Genomic sequence
						
							CGTTGTATGCGTCCCATCTGCTGGTGCAAACGCATTTCTCAGTGCACCAGATTTCGCAGCTCTT
ACTGCTGGATGGTCCTGAACAAAAGGGTGATCCATCAACTGAGTTGCAGTGAAGCGAGATGCAG
GATCACGTTTTAAGCACATCTGCAAGAAGCTTTTTCCTTCCTCAGAAAAGCTGTCTGGGATTTC
AGGTATCTCTTTACTGTTTGCGATCTTAAATATAGCAGCTACCTGCAAGATCAGATTGGATCAG
CTTGGCATTCACAAGTTACTTGGAAAACTATAGCTACAAAGTGAAAGCATACCCCCTCGTATTT
ATGCCAAGGAGGTTTTGCCGTTGCCATTTCAATAATAGTACATCCCAAACTCCAAATGTCAACT
GGTAGATGGTAACCTCTACCGTTCATTATAACCTGCATGTTACAATCATTAGGAGAATTCAGAA
TCATATAAAGATGATGATAAATACGGTATATAAAGGTTTACTGTTAGAAAAACAATTTACCTCA
GGAGCCATCCAGTAAGGACTTCCTTTGAAAGAGCGTATTTCAGCAAAAGATGATATCTGTGTCA
AACGTAAGTAATGAAATTAAAGGCTTAAAAGAGGAGGGGTGGGGGGGGGGGGGGATACAAGCTA
CAGTAGTATTGTGTATATTCTCTTGTAGTCGTGAACTAGCAATAATAGACATCAAAAGGACCCG
AAAACTTCTGTAGATATATGTGCATGTACTAACGCAAAACACATCAACCAGACAACCATCAAAC
TTATCATCTGGGAATAGATATCAACTATCTTCAAACTTCCACAGAATCCTTTTCTACTTATGAG
TAAGGAGAAGTAAATTAAATGTAGCTTCATGAAGGAAATGGAATTGGAATGTGCTTCTATGCCT
TCCCAAAAAGGAAACAACATGGATGCTTAAGAAATTAAACCCGACAGATAAATTCAGCAGCATT
TAGAAACAACAAAGTTATCTTTTAGGAAAACATTTCTCTTTTAGAATTATTATAAGATGCATTG
GCAACATTTCAATGTTAAAGGTATTGAACCAAAAGGGATGTTGCGACCAAATTTTAAGACGATA
AGACTACATGATGCTGCACACACAGGTCAGGGGATGGAAAAGAAAAAAAAAATGCATACATGCT
TAGCCATGCCAAAGTCAGCAAGTTTGACTTCACCATTAGGGCCGACAAGTATGTTAGCACCTTT
AATATCTCTGCGAAGAGAAACAGGATGAAGTGGTTAAGGTATTTCTTTTACTACCAAAGGAATG
TAAAACAACTGTGGATAATCTGTACTACCTGTGGACAGTGTTCCTCCCATGCAAGTAGGCAAGA
CCAGAGAGAATTTGTCCAGTGTAATTACGGATCACAGGTTCCTTAAAAGGACCATACTCTCTAA
GTAATTTATGAATTGAGCCCCCAGAAACAAACTCCAGATAAATTGAAAGTGCATCATCAGTCTG
CATGGAAAAACATACAGAATTAGAAAGTATAAGCAACACAAAGTACTTTCTACTTTCTGAAGTG
CTTCGAACAAAAGATGAGAACTAAACAAGAAAACCAGAGAATTTTCTTCTGAGAGGGAAAATAA
AGAAGTAAAAAATGCAAACCAAGTGAGAGGAAATAACAGCAAAAATCTTATATTAGTAGCACAG
CAGAAGAGGTGACAGGAAATCGAACAATTTAATTATCTAAATTCAAAAGATAGACTAAAAAGTA
AAAATGAAATGCGTTACTACTCATACATAATAAACAATTAAATGCTGATGTTTTCTTCATCCTT
CCAGACACGCTTACACTTATACATGTAACAACCTCTTGCAAGTTTCATTGATCAGGATAGTGAT
TTGTAAACGCGAACCAACCAAACTAAATGCTGTTAATTATCTGGATCTGGCTCTAGTCATCACA
ATAATCATTTTGCTTTAAGACACAGGCTTTTTTTTGTAATCTTCATACGTCAGTTACATCACAA
GTCATGCATGTAACAGACAACATGGTAGTTACAAACATGTATTGAAGTTATATATAGTTGCACA
GAGATAAATGCAATTGTTTATCAAGTAAAGCTTACCATCTCACTTCCATAGTACTGCACAATGT
TTGGGTGCGAAAGTTGCCTAAGCATATCTATTTCCTGTTAATGCCCGAGTGAATTAATATGTCA
GTGAGTCCATTGAACAAGAGACACAAATGCTGTTACTACTCATCAAAAGATATTCATACTGATT
AAACTGAGAAATAACCTGATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATA
ACTTGGACCTCCTTAATCGCACAGAACTGCCCATTTTCA
						
					

			
		

Sequences
Splice junction sequence	CTGAGAAATAACCTGATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATAACT TGGACCTCCTTAATCGCACAGAACTGCCCATTTTCAcgttgtatgcgtcccatctgctggtgca aacgcatttctcagtgcaccagatttcgcagctcttactgctggatggtcctgaacaaaagggt gatccatc
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: 790 Transcript exons: 21754058-21754291,21754366-21754473,21754566-21754625,21 755205-21755280,21755366-21755526,21756141-21756203,2175 6313-21756400 CGTTGTATGCGTCCCATCTGCTGGTGCAAACGCATTTCTCAGTGCACCAGATTTCGCAGCTCTT ACTGCTGGATGGTCCTGAACAAAAGGGTGATCCATCAACTGAGTTGCAGTGAAGCGAGATGCAG GATCACGTTTTAAGCACATCTGCAAGAAGCTTTTTCCTTCCTCAGAAAAGCTGTCTGGGATTTC AGGTATCTCTTTACTGTTTGCGATCTTAAATATAGCAGCTACCCCCTCGTATTTATGCCAAGGA GGTTTTGCCGTTGCCATTTCAATAATAGTACATCCCAAACTCCAAATGTCAACTGGTAGATGGT AACCTCTACCGTTCATTATAACCTCAGGAGCCATCCAGTAAGGACTTCCTTTGAAAGAGCGTAT TTCAGCAAAAGATGATATATGCTTAGCCATGCCAAAGTCAGCAAGTTTGACTTCACCATTAGGG CCGACAAGTATGTTAGCACCTTTAATATCTCTGTGGACAGTGTTCCTCCCATGCAAGTAGGCAA GACCAGAGAGAATTTGTCCAGTGTAATTACGGATCACAGGTTCCTTAAAAGGACCATACTCTCT AAGTAATTTATGAATTGAGCCCCCAGAAACAAACTCCAGATAAATTGAAAGTGCATCATCAGTC ATCTCACTTCCATAGTACTGCACAATGTTTGGGTGCGAAAGTTGCCTAAGCATATCTATTTCCT GATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATAACTTGGACCTCCTTAAT CGCACAGAACTGCCCATTTTCA
Genomic sequence	CGTTGTATGCGTCCCATCTGCTGGTGCAAACGCATTTCTCAGTGCACCAGATTTCGCAGCTCTT ACTGCTGGATGGTCCTGAACAAAAGGGTGATCCATCAACTGAGTTGCAGTGAAGCGAGATGCAG GATCACGTTTTAAGCACATCTGCAAGAAGCTTTTTCCTTCCTCAGAAAAGCTGTCTGGGATTTC AGGTATCTCTTTACTGTTTGCGATCTTAAATATAGCAGCTACCTGCAAGATCAGATTGGATCAG CTTGGCATTCACAAGTTACTTGGAAAACTATAGCTACAAAGTGAAAGCATACCCCCTCGTATTT ATGCCAAGGAGGTTTTGCCGTTGCCATTTCAATAATAGTACATCCCAAACTCCAAATGTCAACT GGTAGATGGTAACCTCTACCGTTCATTATAACCTGCATGTTACAATCATTAGGAGAATTCAGAA TCATATAAAGATGATGATAAATACGGTATATAAAGGTTTACTGTTAGAAAAACAATTTACCTCA GGAGCCATCCAGTAAGGACTTCCTTTGAAAGAGCGTATTTCAGCAAAAGATGATATCTGTGTCA AACGTAAGTAATGAAATTAAAGGCTTAAAAGAGGAGGGGTGGGGGGGGGGGGGGATACAAGCTA CAGTAGTATTGTGTATATTCTCTTGTAGTCGTGAACTAGCAATAATAGACATCAAAAGGACCCG AAAACTTCTGTAGATATATGTGCATGTACTAACGCAAAACACATCAACCAGACAACCATCAAAC TTATCATCTGGGAATAGATATCAACTATCTTCAAACTTCCACAGAATCCTTTTCTACTTATGAG TAAGGAGAAGTAAATTAAATGTAGCTTCATGAAGGAAATGGAATTGGAATGTGCTTCTATGCCT TCCCAAAAAGGAAACAACATGGATGCTTAAGAAATTAAACCCGACAGATAAATTCAGCAGCATT TAGAAACAACAAAGTTATCTTTTAGGAAAACATTTCTCTTTTAGAATTATTATAAGATGCATTG GCAACATTTCAATGTTAAAGGTATTGAACCAAAAGGGATGTTGCGACCAAATTTTAAGACGATA AGACTACATGATGCTGCACACACAGGTCAGGGGATGGAAAAGAAAAAAAAAATGCATACATGCT TAGCCATGCCAAAGTCAGCAAGTTTGACTTCACCATTAGGGCCGACAAGTATGTTAGCACCTTT AATATCTCTGCGAAGAGAAACAGGATGAAGTGGTTAAGGTATTTCTTTTACTACCAAAGGAATG TAAAACAACTGTGGATAATCTGTACTACCTGTGGACAGTGTTCCTCCCATGCAAGTAGGCAAGA CCAGAGAGAATTTGTCCAGTGTAATTACGGATCACAGGTTCCTTAAAAGGACCATACTCTCTAA GTAATTTATGAATTGAGCCCCCAGAAACAAACTCCAGATAAATTGAAAGTGCATCATCAGTCTG CATGGAAAAACATACAGAATTAGAAAGTATAAGCAACACAAAGTACTTTCTACTTTCTGAAGTG CTTCGAACAAAAGATGAGAACTAAACAAGAAAACCAGAGAATTTTCTTCTGAGAGGGAAAATAA AGAAGTAAAAAATGCAAACCAAGTGAGAGGAAATAACAGCAAAAATCTTATATTAGTAGCACAG CAGAAGAGGTGACAGGAAATCGAACAATTTAATTATCTAAATTCAAAAGATAGACTAAAAAGTA AAAATGAAATGCGTTACTACTCATACATAATAAACAATTAAATGCTGATGTTTTCTTCATCCTT CCAGACACGCTTACACTTATACATGTAACAACCTCTTGCAAGTTTCATTGATCAGGATAGTGAT TTGTAAACGCGAACCAACCAAACTAAATGCTGTTAATTATCTGGATCTGGCTCTAGTCATCACA ATAATCATTTTGCTTTAAGACACAGGCTTTTTTTTGTAATCTTCATACGTCAGTTACATCACAA GTCATGCATGTAACAGACAACATGGTAGTTACAAACATGTATTGAAGTTATATATAGTTGCACA GAGATAAATGCAATTGTTTATCAAGTAAAGCTTACCATCTCACTTCCATAGTACTGCACAATGT TTGGGTGCGAAAGTTGCCTAAGCATATCTATTTCCTGTTAATGCCCGAGTGAATTAATATGTCA GTGAGTCCATTGAACAAGAGACACAAATGCTGTTACTACTCATCAAAAGATATTCATACTGATT AAACTGAGAAATAACCTGATTCAATTGCTTGAGTCGTTCTTTTGAATGTGGATCATCCGAAATA ACTTGGACCTCCTTAATCGCACAGAACTGCCCATTTTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.140124011

Conservation Information
Conserved circRNAs	NA
PMCS	0.140124011

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21756344-21754170(+)
21754094-21756400(-)
						
						Potential amino acid sequence
						
							MWIIRNNLDLLNRTELPIFTLYASHLLVQTHFSVHQISQLLLLDGPEQKGDPSTELQ*(+)
MRLHQQMGRIQRENGQFCAIKEVQVISDDPHSKERLKQLNQEIDMLRQLSHPNIVQYYGSEMTD
DALSIYLEFVSGGSIHKLLREYGPFKEPVIRNYTGQILSGLAYLHGRNTVHRDIKGANILVGPN
GEVKLADFGMAKHISSFAEIRSFKGSPYWMAPEVIMNGRGYHLPVDIWSLGCTIIEMATAKPPW
HKYEGVAAIFKIANSKEIPEIPDSFSEEGKSFLQMCLKRDPASRFTATQLMDHPFVQDHPAVRA
AKSGALRNAFAPADGTHTT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21756344-21754170(+) 21754094-21756400(-)
Potential amino acid sequence	MWIIRNNLDLLNRTELPIFTLYASHLLVQTHFSVHQISQLLLLDGPEQKGDPSTELQ(+) MRLHQQMGRIQRENGQFCAIKEVQVISDDPHSKERLKQLNQEIDMLRQLSHPNIVQYYGSEMTD DALSIYLEFVSGGSIHKLLREYGPFKEPVIRNYTGQILSGLAYLHGRNTVHRDIKGANILVGPN GEVKLADFGMAKHISSFAEIRSFKGSPYWMAPEVIMNGRGYHLPVDIWSLGCTIIEMATAKPPW HKYEGVAAIFKIANSKEIPEIPDSFSEEGKSFLQMCLKRDPASRFTATQLMDHPFVQDHPAVRA AKSGALRNAFAPADGTHTT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0437600_circ_g.2

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