Plant Circular RNA Database

Detail information of Os05g0592500_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os05g0592500_circ_g.6
					
						ID in PlantcircBase
						osa_circ_029178
					
						Alias
						Os_ciR3995
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29522020-29524301  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os05g0592500						
					
						Parent gene annotation
						
							SIT4 phosphatase-associated protein family protein. (Os05t059250
0-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0592500_circ_g.3 Os05g0592500_circ_g.4 Os05g0592500_circ_g.5 Os05g0592500_circ_g.7 Os05g0592500_circ_g.8 Os05g0592500_circ_g.9 Os05g0592500_circ_g.10 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os05t0592500-01:9

General Information
CircRNA Name	Os05g0592500_circ_g.6
ID in PlantcircBase	osa_circ_029178
Alias	Os_ciR3995
Organism	Oryza sativa
Position	chr5: 29522020-29524301 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os05g0592500
Parent gene annotation	SIT4 phosphatase-associated protein family protein. (Os05t059250 0-01)
Parent gene strand	+
Alternative splicing	Os05g0592500_circ_g.3 Os05g0592500_circ_g.4 Os05g0592500_circ_g.5 Os05g0592500_circ_g.7 Os05g0592500_circ_g.8 Os05g0592500_circ_g.9 Os05g0592500_circ_g.10
Support reads	2/1
Tissues	root/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	Os05t0592500-01:9

			
						 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  
						
							AGGTGATTTGCTGAAGTTGTTGGATATTTCTTCTGCTGAAAATGTTTTACCTACAACATATGGA
TGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAGcttgcgagacaaggctcaagtggagcaa
ttgcttcgttacatcgtggaagaagtaccagaagattctgaaaagaaacgttcttttaagtatg
cattcttt

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT
TCTGAAAAGAAACGTTCTTTTAAGTATGCATTCTTTTGTCGTTTACCACCAAGTTTTGTAAAAT
AGCTTGTTGGTGAACCTTGCCTAACTTCAGTTATATAACTCAATGCAGGTTCCCATTCATTGCT
TGTGAGATATTTACCTGTGAAATTGACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGGTAA
ATATGTTCCCCTGACCCCTATTAACATATTCCTCTCGAGTATTTTATACTCCTCAGGCTGATAA
ACTTCATTCTAGCTGACCATCTCTTCCATTTCTTGTACTTGATGCAGTTAATGGATTTGCTTTT
CTCATTTGTAAGACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTACTA
TTTTTCTCCTGTGTTGGTTGTCTCTGAATCATTCTTTGACTTTTAAAGCTATCTGCAGTGGTTT
AACTTTAATGTGCTATTATAAATTTGGACACTATTCTTCACACTGTTCATCAGCATACATGGCT
TGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATGCTGAGAAAGACTTCCCC
TCTAATGAACTATGTCCAGGTATTGCTCATCTTTCTTACTTAAACATAGGTTGTCGCCAGTATG
CTATTATTCTTGGTAATTATGAGCACATTTACTCATATTTTTTGTTTGACAACCTGAAACAACT
TAGACTGGATTTGTAGTACTCTCCTCTGAAGCCTGATAGGTCATGAGCTACATTCTGTACGTGT
AATTGTGGGTGTAATTTTGTGTGCATCCTGAAGTTTAAAGCTTTTTCTTGCTGATTGGATCTAG
AAGTACCATGTGATAGAAAATGTTTTAGAACTATTGGTTCTTCAGTATTGTTTATATTTGCGAT
CTGCATTCCACTCATTTTATGTTTATAGGTTGCATTCTGTTGTATTTATTCTTTAAGCGGTTTG
CACCAATCAAAATGTTAATTCTTACATGTAAGGTTGTGATAAGATACAAGCTTACGAATGCCTG
CGTATTTTCCAATTATGGGTGCTCATATTTGTACCCCTTTCATTGTGTAGGAGCACCCAGACAT
TGTTGTCCATCTTGTTGATCTCATCGGCACCACCTCAATAATGGAGGTCAGCTGTTGTTAAATC
CGTTCCATTCCTATTTTTTGCATGTTCATTTCATTTATTGATGCCATGATACTGCTTGTAAAAC
AGGTTCTGATTCGACTGATAGGTGCTGATGAGACCATATACTCGAATTATGCTGACACATTGCA
GTGGTTAGAAAATACAGATGTACTGGAAATGATTGTGGATAAATTTAGCTCATCTGTAAGTTTC
AAAGCTTGAGCACTTACTGACATGCTAAGTACTATAAAATGCCACTAGTTAATACTTAATACTA
GTTACTCTCAGTATGGTGCATCTAGAAATATCTGATAAAATATATTGAATATTTTGACTAGAAA
AGTGCTTATATATCATACACTATTTTAACCAAGCAGGATTCCCCTGAAGTACACGCCAATGCTG
CAGAAATTCTTTCTGCAGTGACTCGATGCGCCCCTCCTGCTCTCGCTGCAAAAATATGCAGCCC
AAGGTTTGTGTTTTAGGTTTTACTTAATATTTGATCAGAATCGTAAAATGCCGCACAGACAATT
TCCTATGTCAACTATCATATGCATTTTTTTTTGTTTGTTTGTTGCATGCCATTTCAGTTTTGTT
GGGAGATTATTTCGTCATGCTCTTCAAGAATCACGCCCCAAATCTGTCCTGGTTCATTCATTAT
CAGTATGTATATCTTTGTTGGATCCAAAAAGACTAGCGTCAGCCTCATACCAAGCATTTAGAAG
TAACTTGAGCCATGGGACATTGGTTACTGCTAGTCCAGAGACAGTTGATGGTATGCTGGAGAGC
CTAGGTGAGTGCTCTTCTTTTTTTTTTTTGATAGTATTATTAGGCTACTGCTACCTAAGTAGTT
TCTCTCTTAGGATCTTAGTTCTATATACTGTAGACAACATCTGTCTTATGGTATATTGTGTTTT
TGGTGATTTTTTTTAGAGAATCTTTAATATGCATTTCTTCTGCTTACTGATCTATCTGAAATCA
CATCGTAGGTGATTTGCTGAAGTTGTTGGATATTTCTTCTGCTGAAAATGTTTTACCTACAACA
TATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAG
						
					

			
		

Sequences
Splice junction sequence	AGGTGATTTGCTGAAGTTGTTGGATATTTCTTCTGCTGAAAATGTTTTACCTACAACATATGGA TGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAGcttgcgagacaaggctcaagtggagcaa ttgcttcgttacatcgtggaagaagtaccagaagattctgaaaagaaacgttcttttaagtatg cattcttt
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT TCTGAAAAGAAACGTTCTTTTAAGTATGCATTCTTTTGTCGTTTACCACCAAGTTTTGTAAAAT AGCTTGTTGGTGAACCTTGCCTAACTTCAGTTATATAACTCAATGCAGGTTCCCATTCATTGCT TGTGAGATATTTACCTGTGAAATTGACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGGTAA ATATGTTCCCCTGACCCCTATTAACATATTCCTCTCGAGTATTTTATACTCCTCAGGCTGATAA ACTTCATTCTAGCTGACCATCTCTTCCATTTCTTGTACTTGATGCAGTTAATGGATTTGCTTTT CTCATTTGTAAGACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTACTA TTTTTCTCCTGTGTTGGTTGTCTCTGAATCATTCTTTGACTTTTAAAGCTATCTGCAGTGGTTT AACTTTAATGTGCTATTATAAATTTGGACACTATTCTTCACACTGTTCATCAGCATACATGGCT TGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATGCTGAGAAAGACTTCCCC TCTAATGAACTATGTCCAGGTATTGCTCATCTTTCTTACTTAAACATAGGTTGTCGCCAGTATG CTATTATTCTTGGTAATTATGAGCACATTTACTCATATTTTTTGTTTGACAACCTGAAACAACT TAGACTGGATTTGTAGTACTCTCCTCTGAAGCCTGATAGGTCATGAGCTACATTCTGTACGTGT AATTGTGGGTGTAATTTTGTGTGCATCCTGAAGTTTAAAGCTTTTTCTTGCTGATTGGATCTAG AAGTACCATGTGATAGAAAATGTTTTAGAACTATTGGTTCTTCAGTATTGTTTATATTTGCGAT CTGCATTCCACTCATTTTATGTTTATAGGTTGCATTCTGTTGTATTTATTCTTTAAGCGGTTTG CACCAATCAAAATGTTAATTCTTACATGTAAGGTTGTGATAAGATACAAGCTTACGAATGCCTG CGTATTTTCCAATTATGGGTGCTCATATTTGTACCCCTTTCATTGTGTAGGAGCACCCAGACAT TGTTGTCCATCTTGTTGATCTCATCGGCACCACCTCAATAATGGAGGTCAGCTGTTGTTAAATC CGTTCCATTCCTATTTTTTGCATGTTCATTTCATTTATTGATGCCATGATACTGCTTGTAAAAC AGGTTCTGATTCGACTGATAGGTGCTGATGAGACCATATACTCGAATTATGCTGACACATTGCA GTGGTTAGAAAATACAGATGTACTGGAAATGATTGTGGATAAATTTAGCTCATCTGTAAGTTTC AAAGCTTGAGCACTTACTGACATGCTAAGTACTATAAAATGCCACTAGTTAATACTTAATACTA GTTACTCTCAGTATGGTGCATCTAGAAATATCTGATAAAATATATTGAATATTTTGACTAGAAA AGTGCTTATATATCATACACTATTTTAACCAAGCAGGATTCCCCTGAAGTACACGCCAATGCTG CAGAAATTCTTTCTGCAGTGACTCGATGCGCCCCTCCTGCTCTCGCTGCAAAAATATGCAGCCC AAGGTTTGTGTTTTAGGTTTTACTTAATATTTGATCAGAATCGTAAAATGCCGCACAGACAATT TCCTATGTCAACTATCATATGCATTTTTTTTTGTTTGTTTGTTGCATGCCATTTCAGTTTTGTT GGGAGATTATTTCGTCATGCTCTTCAAGAATCACGCCCCAAATCTGTCCTGGTTCATTCATTAT CAGTATGTATATCTTTGTTGGATCCAAAAAGACTAGCGTCAGCCTCATACCAAGCATTTAGAAG TAACTTGAGCCATGGGACATTGGTTACTGCTAGTCCAGAGACAGTTGATGGTATGCTGGAGAGC CTAGGTGAGTGCTCTTCTTTTTTTTTTTTGATAGTATTATTAGGCTACTGCTACCTAAGTAGTT TCTCTCTTAGGATCTTAGTTCTATATACTGTAGACAACATCTGTCTTATGGTATATTGTGTTTT TGGTGATTTTTTTTAGAGAATCTTTAATATGCATTTCTTCTGCTTACTGATCTATCTGAAATCA CATCGTAGGTGATTTGCTGAAGTTGTTGGATATTTCTTCTGCTGAAAATGTTTTACCTACAACA TATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.112457165

Conservation Information
Conserved circRNAs	NA
PMCS	0.112457165

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29524266-29522245(+)
29522391-29522085(+)
						
						Potential amino acid sequence
						
							MFAAPSWKTPLEACETRLKWSNCFVTSWKKYQKILKRNVLLSSHSLLVRYLPVKLTSS*(+)
MDLLFSFVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQEHPDIVVHLVDLIGTTSIMEVL
IRLIGADETIYSNYADTLQWLENTDVLEMIVDKFSSSDSPEVHANAAEILSAVTRCAPPALAAK
ICSPSFVGRLFRHALQESRPKSVLVHSLSVCISLLDPKRLASASYQAFRSNLSHGTLVTASPET
VDGMLESLGDLLKLLDISSAENVLPTTYGCLQPPLGKHRLKLARQGSSGAIASLHRGRSTRRF*
(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29524266-29522245(+) 29522391-29522085(+)
Potential amino acid sequence	MFAAPSWKTPLEACETRLKWSNCFVTSWKKYQKILKRNVLLSSHSLLVRYLPVKLTSS(+) MDLLFSFVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQEHPDIVVHLVDLIGTTSIMEVL IRLIGADETIYSNYADTLQWLENTDVLEMIVDKFSSSDSPEVHANAAEILSAVTRCAPPALAAK ICSPSFVGRLFRHALQESRPKSVLVHSLSVCISLLDPKRLASASYQAFRSNLSHGTLVTASPET VDGMLESLGDLLKLLDISSAENVLPTTYGCLQPPLGKHRLKLARQGSSGAIASLHRGRSTRRF (+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os05g0592500_circ_g.6

Address

Any questions?

Supported by