Plant Circular RNA Database

Detail information of Os01g0629900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0629900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_002796
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 25155375-25156696  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0629900						
					
						Parent gene annotation
						
							Similar to Blast and wounding induced mitogen-activated protein 
kinase. (Os01t0629900-01);Similar to Mitogen-activated protein k
inase 10. (Os01t0629900-02);Similar to Mitogen-activated protein
 kinase 10. (Os01t0629900-03);Similar to Mitogen-activated prote
in kinase 10. (Os01t0629900-04)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0629900_circ_g.1 Os01g0629900_circ_g.2 Os01g0629900_circ_g.3 Os01g0629900_circ_g.5 						
					
						Support reads
						2
					
						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
						Os01t0630000-00:3
Os01t0629900-01:3
Os01t0630000-00:3

General Information
CircRNA Name	Os01g0629900_circ_g.4
ID in PlantcircBase	osa_circ_002796
Alias	NA
Organism	Oryza sativa
Position	chr1: 25155375-25156696 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0629900
Parent gene annotation	Similar to Blast and wounding induced mitogen-activated protein kinase. (Os01t0629900-01);Similar to Mitogen-activated protein k inase 10. (Os01t0629900-02);Similar to Mitogen-activated protein kinase 10. (Os01t0629900-03);Similar to Mitogen-activated prote in kinase 10. (Os01t0629900-04)
Parent gene strand	-
Alternative splicing	Os01g0629900_circ_g.1 Os01g0629900_circ_g.2 Os01g0629900_circ_g.3 Os01g0629900_circ_g.5
Support reads	2
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	Os01t0630000-00:3 Os01t0629900-01:3 Os01t0630000-00:3

			
						 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  
						
							CTGAGCACACCACCCCATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACTTGCATC
GCCATACTCCGTGAAAAAATCCGCCTCTGTAGAACTctttgaaaagaaggatccacagagctct
ggagccctgtaccatcttgttgcaacataatcctgcaggcaaatgaagagacatcagaggtgat
ccgcgtac

									
								

					

						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: 25155375-25155434,25155542-25155669,25156288-25156696
CTTTGAAAAGAAGGATCCACAGAGCTCTGGAGCCCTGTACCATCTTGTTGCAACATAATCCGTC
CAAAAGATTGTTGTCGGAGTATCATTGAATGCAACTCGCGCCAGTCCAAAATCACAAATTTTCA
GTTTGCAGTTGGAATTAGCTAATATATTCTTCGGCTTCAGGTCCCGGTGATAAACATTAGCAGT
GTGAATGTATTTCAGAGCCCGGAGTAGTTGGTAAAGAAAGAACTGATAATGCTCCTTCGTCAAG
TCATCATTAGCCTTTATAACTTGGTGAAGATCAGACTCCATAAGCTCAAAAACTACATAAATAT
CTTTGAAATCCCTCCTCGATGGAGGCAACATAATGTGCTTGATCTCAACTATGTCAGGATGTCT
TAGCAGCCTCAGAAGCTTGATCTCACGGAGAATCCGTGCAGCATCAGATATGTGTTCAAAGATA
TCGTGTATCTTCTTGATTGCCACTTTCTCTCCAGTGTGGACATCTATCGCTGAGCACACCACCC
CATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACTTGCATCGCCATACTCCGTGAA
AAAATCCGCCTCTGTAGAACT
						
					

						Genomic sequence
						
							CTTTGAAAAGAAGGATCCACAGAGCTCTGGAGCCCTGTACCATCTTGTTGCAACATAATCCTGC
AGGCAAATGAAGAGACATCAGAGGTGATCCGCGTACACAAATAAGCCAGAAGCCAAAGGTTTAG
ACAAAACTAAGTTAAAGATAGATATTTCCATGAGCATACCGTCCAAAAGATTGTTGTCGGAGTA
TCATTGAATGCAACTCGCGCCAGTCCAAAATCACAAATTTTCAGTTTGCAGTTGGAATTAGCTA
ATATATTCTTCGGCTTCAGGTCCCGGTGATAAACATTAGCTGCAGTCACGTGGACTTAGTATAA
GCAAAGCTTGCAAAAGGAAAAAGTAGCACATCTGCATAGAACATTTATGCACATTCTGCTGATA
AGAGAATTGGAAAAATGGTAGTGTTGTTCAGAGATTACAGCATAAGCAACCAACCAATATGCAA
GTCATAAGCAGATTATTTAATACAAGAACTCTAAAATAATGAGGAAGTAACACATTATCTATCA
AGAATACCTGGGATCCTGCGCATTTTCTACCCTTAAAGGTTGCAAAAACAGAGTGATCTTTTTG
AAGCATTGAATTCAATAGGGCCCCAATAGGGCCCATATGTTTTGCACCTCTCCCCATACCCACC
CAAGGCACTTGTTGACACTTGAGACCAGTTGTTTTACGCTATAAATCTGCAAATCATGCTAATC
CCATAATTTTATATGGAAATTGCATGAATATCCTACAAGAATCTTACGTAGTACACTAACCAAA
AAGGAAGGTATCCAAAGGTAATAATAATATATCTAATCAGGAGACACTGACTCAATGCAGGTTC
ACTAGAGCACATACATTGTGTGATTCACGTTACATATGATCTTCAAAGCAAAACAATGGACTGA
AAGTGACAGTTCCCTACCAGTGTGAATGTATTTCAGAGCCCGGAGTAGTTGGTAAAGAAAGAAC
TGATAATGCTCCTTCGTCAAGTCATCATTAGCCTTTATAACTTGGTGAAGATCAGACTCCATAA
GCTCAAAAACTACATAAATATCTTTGAAATCCCTCCTCGATGGAGGCAACATAATGTGCTTGAT
CTCAACTATGTCAGGATGTCTTAGCAGCCTCAGAAGCTTGATCTCACGGAGAATCCGTGCAGCA
TCAGATATGTGTTCAAAGATATCGTGTATCTTCTTGATTGCCACTTTCTCTCCAGTGTGGACAT
CTATCGCTGAGCACACCACCCCATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACT
TGCATCGCCATACTCCGTGAAAAAATCCGCCTCTGTAGAACT
						
					

			
		

Sequences
Splice junction sequence	CTGAGCACACCACCCCATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACTTGCATC GCCATACTCCGTGAAAAAATCCGCCTCTGTAGAACTctttgaaaagaaggatccacagagctct ggagccctgtaccatcttgttgcaacataatcctgcaggcaaatgaagagacatcagaggtgat ccgcgtac
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: 25155375-25155434,25155542-25155669,25156288-25156696 CTTTGAAAAGAAGGATCCACAGAGCTCTGGAGCCCTGTACCATCTTGTTGCAACATAATCCGTC CAAAAGATTGTTGTCGGAGTATCATTGAATGCAACTCGCGCCAGTCCAAAATCACAAATTTTCA GTTTGCAGTTGGAATTAGCTAATATATTCTTCGGCTTCAGGTCCCGGTGATAAACATTAGCAGT GTGAATGTATTTCAGAGCCCGGAGTAGTTGGTAAAGAAAGAACTGATAATGCTCCTTCGTCAAG TCATCATTAGCCTTTATAACTTGGTGAAGATCAGACTCCATAAGCTCAAAAACTACATAAATAT CTTTGAAATCCCTCCTCGATGGAGGCAACATAATGTGCTTGATCTCAACTATGTCAGGATGTCT TAGCAGCCTCAGAAGCTTGATCTCACGGAGAATCCGTGCAGCATCAGATATGTGTTCAAAGATA TCGTGTATCTTCTTGATTGCCACTTTCTCTCCAGTGTGGACATCTATCGCTGAGCACACCACCC CATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACTTGCATCGCCATACTCCGTGAA AAAATCCGCCTCTGTAGAACT
Genomic sequence	CTTTGAAAAGAAGGATCCACAGAGCTCTGGAGCCCTGTACCATCTTGTTGCAACATAATCCTGC AGGCAAATGAAGAGACATCAGAGGTGATCCGCGTACACAAATAAGCCAGAAGCCAAAGGTTTAG ACAAAACTAAGTTAAAGATAGATATTTCCATGAGCATACCGTCCAAAAGATTGTTGTCGGAGTA TCATTGAATGCAACTCGCGCCAGTCCAAAATCACAAATTTTCAGTTTGCAGTTGGAATTAGCTA ATATATTCTTCGGCTTCAGGTCCCGGTGATAAACATTAGCTGCAGTCACGTGGACTTAGTATAA GCAAAGCTTGCAAAAGGAAAAAGTAGCACATCTGCATAGAACATTTATGCACATTCTGCTGATA AGAGAATTGGAAAAATGGTAGTGTTGTTCAGAGATTACAGCATAAGCAACCAACCAATATGCAA GTCATAAGCAGATTATTTAATACAAGAACTCTAAAATAATGAGGAAGTAACACATTATCTATCA AGAATACCTGGGATCCTGCGCATTTTCTACCCTTAAAGGTTGCAAAAACAGAGTGATCTTTTTG AAGCATTGAATTCAATAGGGCCCCAATAGGGCCCATATGTTTTGCACCTCTCCCCATACCCACC CAAGGCACTTGTTGACACTTGAGACCAGTTGTTTTACGCTATAAATCTGCAAATCATGCTAATC CCATAATTTTATATGGAAATTGCATGAATATCCTACAAGAATCTTACGTAGTACACTAACCAAA AAGGAAGGTATCCAAAGGTAATAATAATATATCTAATCAGGAGACACTGACTCAATGCAGGTTC ACTAGAGCACATACATTGTGTGATTCACGTTACATATGATCTTCAAAGCAAAACAATGGACTGA AAGTGACAGTTCCCTACCAGTGTGAATGTATTTCAGAGCCCGGAGTAGTTGGTAAAGAAAGAAC TGATAATGCTCCTTCGTCAAGTCATCATTAGCCTTTATAACTTGGTGAAGATCAGACTCCATAA GCTCAAAAACTACATAAATATCTTTGAAATCCCTCCTCGATGGAGGCAACATAATGTGCTTGAT CTCAACTATGTCAGGATGTCTTAGCAGCCTCAGAAGCTTGATCTCACGGAGAATCCGTGCAGCA TCAGATATGTGTTCAAAGATATCGTGTATCTTCTTGATTGCCACTTTCTCTCCAGTGTGGACAT CTATCGCTGAGCACACCACCCCATAGCTTCCCTTACCAATAACTTCCTGAATCTTGTATCGACT TGCATCGCCATACTCCGTGAAAAAATCCGCCTCTGTAGAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010379 						
					
						PMCS
						0.495949059

Conservation Information
Conserved circRNAs	osi_circ_010379
PMCS	0.495949059

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25156452-25155377(-)
25155572-25156593(-)
25155419-25156625(-)
						
						Potential amino acid sequence
						
							MLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALKYIHTANVYHRDLKP
KNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSFFSKSSTEADFFTEY
GDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARILREIKLLRLLRHPD
IVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALKYIHTANV
YHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSFFSKSSTE
ADFFTEYGDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARILREIKLL
RLLRHPDIVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALK
YIHTANVYHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSF
FSKSSTEADFFTEYGDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARI
LREIKLLRLLRHPDIVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLY
QLLRALKYIHTANVYHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRA
PELCGSFFSK(-)
MILRQQSFGRIMLQQDGTGLQSSVDPSFQRVLQRRIFSRSMAMQVDTRFRKLLVREAMGWCAQR
*(-)
MVQGSRALWILLFKEFYRGGFFHGVWRCKSIQDSGSYW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25156452-25155377(-) 25155572-25156593(-) 25155419-25156625(-)
Potential amino acid sequence	MLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALKYIHTANVYHRDLKP KNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSFFSKSSTEADFFTEY GDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARILREIKLLRLLRHPD IVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALKYIHTANV YHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSFFSKSSTE ADFFTEYGDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARILREIKLL RLLRHPDIVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLYQLLRALK YIHTANVYHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSF FSKSSTEADFFTEYGDASRYKIQEVIGKGSYGVVCSAIDVHTGEKVAIKKIHDIFEHISDAARI LREIKLLRLLRHPDIVEIKHIMLPPSRRDFKDIYVVFELMESDLHQVIKANDDLTKEHYQFFLY QLLRALKYIHTANVYHRDLKPKNILANSNCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRA PELCGSFFSK(-) MILRQQSFGRIMLQQDGTGLQSSVDPSFQRVLQRRIFSRSMAMQVDTRFRKLLVREAMGWCAQR (-) MVQGSRALWILLFKEFYRGGFFHGVWRCKSIQDSGSYW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0629900_circ_g.4

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