Plant Circular RNA Database

Detail information of Os05g0592500_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os05g0592500_circ_g.5
					
						ID in PlantcircBase
						osa_circ_029177
					
						Alias
						Os05circ20545/Os_ciR182, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29522020-29522678  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI-long
					
						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.6 Os05g0592500_circ_g.7 Os05g0592500_circ_g.8 Os05g0592500_circ_g.9 Os05g0592500_circ_g.10 						
					
						Support reads
						10/267/43/45
					
						Tissues
						leaf and panicle/root/root/shoot, root, seed, 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
						Os05t0592500-01:4

General Information
CircRNA Name	Os05g0592500_circ_g.5
ID in PlantcircBase	osa_circ_029177
Alias	Os05circ20545/Os_ciR182,
Organism	Oryza sativa
Position	chr5: 29522020-29522678 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI-long
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.6 Os05g0592500_circ_g.7 Os05g0592500_circ_g.8 Os05g0592500_circ_g.9 Os05g0592500_circ_g.10
Support reads	10/267/43/45
Tissues	leaf and panicle/root/root/shoot, root, seed, 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	Os05t0592500-01:4

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: CCTGGTCATCCACATAGCACA
 R: TCTTCCACGATGTAACGAAGCA
PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							Yes							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   
						
							F: CGTGGAAGAAGTACCAGAAG
 R: TTCCACGATGTAACGAAGCA
PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	Yes 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	F: CCTGGTCATCCACATAGCACA R: TCTTCCACGATGTAACGAAGCA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	Yes 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	F: CGTGGAAGAAGTACCAGAAG R: TTCCACGATGTAACGAAGCA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							CATCAGCATACATGGCTTGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATG
CTGAGAAAGACTTCCCCTCTAATGAACTATGTCCAGcttgcgagacaaggctcaagtggagcaa
ttgcttcgttacatcgtggaagaagtaccagaagattctgaaaagaaacgttcttttaagtatg
cattcttt

						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: 292
Transcript exons: 29522020-29522106,29522196-29522271,29522387-29522461,29
522625-29522678
CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT
TCTGAAAAGAAACGTTCTTTTAAGTTCCCATTCATTGCTTGTGAGATATTTACCTGTGAAATTG
ACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGTTAATGGATTTGCTTTTCTCATTTGTAAG
ACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTGGTAATATGTTTGATG
CTGAGAAAGACTTCCCCTCTAATGAACTATGTCCAG
						
						Genomic sequence
						
							CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT
TCTGAAAAGAAACGTTCTTTTAAGTATGCATTCTTTTGTCGTTTACCACCAAGTTTTGTAAAAT
AGCTTGTTGGTGAACCTTGCCTAACTTCAGTTATATAACTCAATGCAGGTTCCCATTCATTGCT
TGTGAGATATTTACCTGTGAAATTGACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGGTAA
ATATGTTCCCCTGACCCCTATTAACATATTCCTCTCGAGTATTTTATACTCCTCAGGCTGATAA
ACTTCATTCTAGCTGACCATCTCTTCCATTTCTTGTACTTGATGCAGTTAATGGATTTGCTTTT
CTCATTTGTAAGACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTACTA
TTTTTCTCCTGTGTTGGTTGTCTCTGAATCATTCTTTGACTTTTAAAGCTATCTGCAGTGGTTT
AACTTTAATGTGCTATTATAAATTTGGACACTATTCTTCACACTGTTCATCAGCATACATGGCT
TGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATGCTGAGAAAGACTTCCCC
TCTAATGAACTATGTCCAG

Sequences
Splice junction sequence	CATCAGCATACATGGCTTGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATG CTGAGAAAGACTTCCCCTCTAATGAACTATGTCCAGcttgcgagacaaggctcaagtggagcaa ttgcttcgttacatcgtggaagaagtaccagaagattctgaaaagaaacgttcttttaagtatg cattcttt
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: 292 Transcript exons: 29522020-29522106,29522196-29522271,29522387-29522461,29 522625-29522678 CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT TCTGAAAAGAAACGTTCTTTTAAGTTCCCATTCATTGCTTGTGAGATATTTACCTGTGAAATTG ACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGTTAATGGATTTGCTTTTCTCATTTGTAAG ACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTGGTAATATGTTTGATG CTGAGAAAGACTTCCCCTCTAATGAACTATGTCCAG
Genomic sequence	CTTGCGAGACAAGGCTCAAGTGGAGCAATTGCTTCGTTACATCGTGGAAGAAGTACCAGAAGAT TCTGAAAAGAAACGTTCTTTTAAGTATGCATTCTTTTGTCGTTTACCACCAAGTTTTGTAAAAT AGCTTGTTGGTGAACCTTGCCTAACTTCAGTTATATAACTCAATGCAGGTTCCCATTCATTGCT TGTGAGATATTTACCTGTGAAATTGACATCATCTTGAGGACCTTAGTAGAGGATGAAGAGGTAA ATATGTTCCCCTGACCCCTATTAACATATTCCTCTCGAGTATTTTATACTCCTCAGGCTGATAA ACTTCATTCTAGCTGACCATCTCTTCCATTTCTTGTACTTGATGCAGTTAATGGATTTGCTTTT CTCATTTGTAAGACCTGGTCATCCACATAGCACATTGTTAGCTGGATACTTCAGTAAGGTACTA TTTTTCTCCTGTGTTGGTTGTCTCTGAATCATTCTTTGACTTTTAAAGCTATCTGCAGTGGTTT AACTTTAATGTGCTATTATAAATTTGGACACTATTCTTCACACTGTTCATCAGCATACATGGCT TGTGGTCTCAGTTTGATCTCGTACTGTAGGTGGTAATATGTTTGATGCTGAGAAAGACTTCCCC TCTAATGAACTATGTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015858 						
					
						PMCS
						0.3544261

Conservation Information
Conserved circRNAs	osi_circ_015858
PMCS	0.3544261

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29522634-29522245(+)
29522391-29522085(+)
29522672-29522085(+)
						
						Potential amino acid sequence
						
							MFDAEKDFPSNELCPACETRLKWSNCFVTSWKKYQKILKRNVLLSSHSLLVRYLPVKLTSS*(+
)
MDLLFSFVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQLARQGSSGAIASLHRGRSTRRF
*(+)
MSSLRDKAQVEQLLRYIVEEVPEDSEKKRSFKFPFIACEIFTCEIDIILRTLVEDEELMDLLFS
FVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQLARQGSSGAIASLHRGRSTRRF*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29522634-29522245(+) 29522391-29522085(+) 29522672-29522085(+)
Potential amino acid sequence	MFDAEKDFPSNELCPACETRLKWSNCFVTSWKKYQKILKRNVLLSSHSLLVRYLPVKLTSS(+ ) MDLLFSFVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQLARQGSSGAIASLHRGRSTRRF (+) MSSLRDKAQVEQLLRYIVEEVPEDSEKKRSFKFPFIACEIFTCEIDIILRTLVEDEELMDLLFS FVRPGHPHSTLLAGYFSKVVICLMLRKTSPLMNYVQLARQGSSGAIASLHRGRSTRRF*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017; this study

circRNA

Detail information of Os05g0592500_circ_g.5

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