Plant Circular RNA Database

Detail information of Os05g0509300_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os05g0509300_circ_g.1
					
						ID in PlantcircBase
						osa_circ_028471
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 25219780-25221077  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0509300						
					
						Parent gene annotation
						
							Pseudouridine synthase, TruD domain containing protein. (Os05t05
09300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0509300_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						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
						Os05t0509300-01:5

General Information
CircRNA Name	Os05g0509300_circ_g.1
ID in PlantcircBase	osa_circ_028471
Alias	NA
Organism	Oryza sativa
Position	chr5: 25219780-25221077 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0509300
Parent gene annotation	Pseudouridine synthase, TruD domain containing protein. (Os05t05 09300-01)
Parent gene strand	+
Alternative splicing	Os05g0509300_circ_g.2
Support reads	1
Tissues	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	Os05t0509300-01:5

			
						 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  
						
							GCATTTCTTCAGGGGTGTTGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGGGCTTA
GGAAAGAATGGATTTATCAACTACTATGGGTTGCAGgtttcacctttgcaaagagaacaaggac
acacaagaagcgttaggagtaattgggaaaatgttaggacttcaggtatacctcggttgctaac
tcataaca

									
								

					

						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: 361
Transcript exons: 25219780-25219852,25219971-25220027,25220531-25220610,25
220698-25220760,25220990-25221077
GTTTCACCTTTGCAAAGAGAACAAGGACACACAAGAAGCGTTAGGAGTAATTGGGAAAATGTTA
GGACTTCAGTCACGTTCATTCGGGTTTGCAGGGACAAAAGATAAACGTGCTGTTACAACACAAC
AGGTGACTGTTTTCAAGATATCAGCCAACAGATTGGCTGCACTTAATAATCGACTATTTGGAAT
TAAAGTTGGAAACTTTAGTTATGTGAAGGAGGGACTTGTTCTTGGTCAACTAATGGGAAATCGA
TTTACAATTACTCTGAGGGGTGTTGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGG
GCTTAGGAAAGAATGGATTTATCAACTACTATGGGTTGCAG
						
					

						Genomic sequence
						
							GTTTCACCTTTGCAAAGAGAACAAGGACACACAAGAAGCGTTAGGAGTAATTGGGAAAATGTTA
GGACTTCAGGTATACCTCGGTTGCTAACTCATAACATTGTGTTCTTGTTTCTACTGAATGCTTT
GATTCTTCTTTTTTACCTTCCTTCGCATTCCTAGTTGATTTCTATACCTTTTGCAATTTGCAGT
CACGTTCATTCGGGTTTGCAGGGACAAAAGATAAACGTGCTGTTACAACACAACAGGTACTTAT
TCCTCATGTGCATACCATCTCACTCAATTTTCTTTACATAAATCGTGTTTTTGTACAATTTGTT
TAAAAGTTCGCATACAAGTATGCAAGAAATACTGGTATAATTTTAATTAAGGCATAATTTATGG
TATTATGATGTTACAACCAGATGAGATAAGTGAAGCTGCTCTGGTTTGGAATACTACATGTAGT
ATTGTCTTGGCAAAGGAGTTTTGTGAAATGAAACTACAAGATCATTTTTCTTTAACTAGTACCG
TTCATAGTTTTTAGTCTTTTCACCTTTAGTTTGTATTGCTTGGCTTTGTTCTCATCTCTAGCCT
ACCCAGCTTGGTTGAGATTAAAGGCTGGTGTTGTTGCTGTATTTTGCATAGTGATTTTTAGTCT
ATTTGACAGATTTGTTTATGTTATCTCACTCCTTTTTCATGGTTGTGATCCTCTGCATGTAATT
ACGTTTTCTTGCAATGGTTACTTTTCTGATTGTTTTCCCCTGGTTAGGTGACTGTTTTCAAGAT
ATCAGCCAACAGATTGGCTGCACTTAATAATCGACTATTTGGAATTAAAGTTGGAAACTTTAGG
TAGGTGATAAAATGCATTATCCTCTTTGTTGATATCATTGCAATGTAATTATTCTAAATACTAA
TTATTTTTGCATTCCTTTCTAGTTATGTGAAGGAGGGACTTGTTCTTGGTCAACTAATGGGAAA
TCGATTTACAATTACTCTGAGGTACTTGTTTTTTATTTCTCCTTTTAGTTTAATGTAAAAAACT
AAAAATGTTCTCTAGTGCTCTAAAAAATGATTTGCACTAATCTTAGAGCTCATGGAGGGCCTGA
TTTGCAGCTACATATTACTTCACTACAAACAGTACTATATTTCACATGCACCAAACCTCTTCTT
TTCTTGGTTCAAGAAAACCAAACAAATGGAGAGCTGATATTTTCCTGCATTTCTTCAGGGGTGT
TGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGGGCTTAGGAAAGAATGGATTTATC
AACTACTATGGGTTGCAG
						
					

			
		

Sequences
Splice junction sequence	GCATTTCTTCAGGGGTGTTGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGGGCTTA GGAAAGAATGGATTTATCAACTACTATGGGTTGCAGgtttcacctttgcaaagagaacaaggac acacaagaagcgttaggagtaattgggaaaatgttaggacttcaggtatacctcggttgctaac tcataaca
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: 361 Transcript exons: 25219780-25219852,25219971-25220027,25220531-25220610,25 220698-25220760,25220990-25221077 GTTTCACCTTTGCAAAGAGAACAAGGACACACAAGAAGCGTTAGGAGTAATTGGGAAAATGTTA GGACTTCAGTCACGTTCATTCGGGTTTGCAGGGACAAAAGATAAACGTGCTGTTACAACACAAC AGGTGACTGTTTTCAAGATATCAGCCAACAGATTGGCTGCACTTAATAATCGACTATTTGGAAT TAAAGTTGGAAACTTTAGTTATGTGAAGGAGGGACTTGTTCTTGGTCAACTAATGGGAAATCGA TTTACAATTACTCTGAGGGGTGTTGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGG GCTTAGGAAAGAATGGATTTATCAACTACTATGGGTTGCAG
Genomic sequence	GTTTCACCTTTGCAAAGAGAACAAGGACACACAAGAAGCGTTAGGAGTAATTGGGAAAATGTTA GGACTTCAGGTATACCTCGGTTGCTAACTCATAACATTGTGTTCTTGTTTCTACTGAATGCTTT GATTCTTCTTTTTTACCTTCCTTCGCATTCCTAGTTGATTTCTATACCTTTTGCAATTTGCAGT CACGTTCATTCGGGTTTGCAGGGACAAAAGATAAACGTGCTGTTACAACACAACAGGTACTTAT TCCTCATGTGCATACCATCTCACTCAATTTTCTTTACATAAATCGTGTTTTTGTACAATTTGTT TAAAAGTTCGCATACAAGTATGCAAGAAATACTGGTATAATTTTAATTAAGGCATAATTTATGG TATTATGATGTTACAACCAGATGAGATAAGTGAAGCTGCTCTGGTTTGGAATACTACATGTAGT ATTGTCTTGGCAAAGGAGTTTTGTGAAATGAAACTACAAGATCATTTTTCTTTAACTAGTACCG TTCATAGTTTTTAGTCTTTTCACCTTTAGTTTGTATTGCTTGGCTTTGTTCTCATCTCTAGCCT ACCCAGCTTGGTTGAGATTAAAGGCTGGTGTTGTTGCTGTATTTTGCATAGTGATTTTTAGTCT ATTTGACAGATTTGTTTATGTTATCTCACTCCTTTTTCATGGTTGTGATCCTCTGCATGTAATT ACGTTTTCTTGCAATGGTTACTTTTCTGATTGTTTTCCCCTGGTTAGGTGACTGTTTTCAAGAT ATCAGCCAACAGATTGGCTGCACTTAATAATCGACTATTTGGAATTAAAGTTGGAAACTTTAGG TAGGTGATAAAATGCATTATCCTCTTTGTTGATATCATTGCAATGTAATTATTCTAAATACTAA TTATTTTTGCATTCCTTTCTAGTTATGTGAAGGAGGGACTTGTTCTTGGTCAACTAATGGGAAA TCGATTTACAATTACTCTGAGGTACTTGTTTTTTATTTCTCCTTTTAGTTTAATGTAAAAAACT AAAAATGTTCTCTAGTGCTCTAAAAAATGATTTGCACTAATCTTAGAGCTCATGGAGGGCCTGA TTTGCAGCTACATATTACTTCACTACAAACAGTACTATATTTCACATGCACCAAACCTCTTCTT TTCTTGGTTCAAGAAAACCAAACAAATGGAGAGCTGATATTTTCCTGCATTTCTTCAGGGGTGT TGTTGCAGAATCAGAAGACATAATAAAGGCTTCTGTGGAGGGCTTAGGAAAGAATGGATTTATC AACTACTATGGGTTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.217421713

Conservation Information
Conserved circRNAs	NA
PMCS	0.217421713

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25219839-25220002(+)
25221050-25220002(+)
25219982-25221067(-)
						
						Potential amino acid sequence
						
							MLGLQSRSFGFAGTKDKRAVTTQQVTVFKISANRLAALNNRLFGIKVGNFSYVKEGLVLGQLMG
NRFTITLRGVVAESEDIIKASVEGLGKNGFINYYGLQVSPLQREQGHTRSVRSNWENVRTSVTF
IRVCRDKR*(+)
MDLSTTMGCRFHLCKENKDTQEALGVIGKMLGLQSRSFGFAGTKDKRAVTTQQVTVFKISANRL
AALNNRLFGIKVGNFSYVKEGLVLGQLMGNRFTITLRGVVAESEDIIKASVEGLGKNGFINYYG
LQVSPLQREQGHTRSVRSNWENVRTSVTFIRVCRDKR*(+)
MNVTEVLTFSQLLLTLLVCPCSLCKGETCNP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25219839-25220002(+) 25221050-25220002(+) 25219982-25221067(-)
Potential amino acid sequence	MLGLQSRSFGFAGTKDKRAVTTQQVTVFKISANRLAALNNRLFGIKVGNFSYVKEGLVLGQLMG NRFTITLRGVVAESEDIIKASVEGLGKNGFINYYGLQVSPLQREQGHTRSVRSNWENVRTSVTF IRVCRDKR(+) MDLSTTMGCRFHLCKENKDTQEALGVIGKMLGLQSRSFGFAGTKDKRAVTTQQVTVFKISANRL AALNNRLFGIKVGNFSYVKEGLVLGQLMGNRFTITLRGVVAESEDIIKASVEGLGKNGFINYYG LQVSPLQREQGHTRSVRSNWENVRTSVTFIRVCRDKR(+) MNVTEVLTFSQLLLTLLVCPCSLCKGETCNP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0509300_circ_g.1

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