Plant Circular RNA Database

Detail information of Os01g0734399_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0734399_circ_g.3
					
						ID in PlantcircBase
						osa_circ_003787
					
						Alias
						Os_ciR5099
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 30631265-30632018  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0734399						
					
						Parent gene annotation
						
							Hypothetical protein. (Os01t0734399-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0734466_circ_igg.1 Os01g0734399_circ_g.1 Os01g0734399_circ_g.2 Os01g0734399_circ_g.4 Os01g0734399_circ_g.5 Os01g0734466_circ_g.1 						
					
						Support reads
						3
					
						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
						Os01t0734466-01:3
Os01t0734466-01:3
Os01t0734399-00:2

General Information
CircRNA Name	Os01g0734399_circ_g.3
ID in PlantcircBase	osa_circ_003787
Alias	Os_ciR5099
Organism	Oryza sativa
Position	chr1: 30631265-30632018 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	find_circ
Parent gene	Os01g0734399
Parent gene annotation	Hypothetical protein. (Os01t0734399-00)
Parent gene strand	-
Alternative splicing	Os01g0734466_circ_igg.1 Os01g0734399_circ_g.1 Os01g0734399_circ_g.2 Os01g0734399_circ_g.4 Os01g0734399_circ_g.5 Os01g0734466_circ_g.1
Support reads	3
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	Os01t0734466-01:3 Os01t0734466-01:3 Os01t0734399-00:2

			
						 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  
						
							GTAATGTTTTGACACTGCAAATGTCCAAGCCTCCCACGTTCCGTTACAAGAGTGGACAATATAT
GTTTGTTCAATGTCCAGCAGTGTCTCCCTTTGAATGactattgcagcagcaattgtggttggta
taatcctccatgcagggaaccaccttgtatgcgattttccacggttaataaaatcatcagatga
gaagtatg

						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: 596
Transcript exons: 30631265-30631648,30631733-30631828,30631903-30632018
ACTATTGCAGCAGCAATTGTGGTTGGTATAATCCTCCATGCAGGGAACCACCTTGTATGCGATT
TTCCACGGTTAATAAAATCATCAGATGAGAAGTATGCTCCTTTGGGCCAGTATTTTGGGGAAAT
AAAGCCAACATATTTTACATTGGTCAAAGGAGTGGAGGGCATCACTGGGGTAATCATGGTTGTA
TGCATGATAATTGCTTTTACTCTAGCAACCCGGTGGTTCCGCCGTAGCTTGGTTAAGCTTCCAA
GGCCATTTGACAAACTGACTGGCTTCAATGCCTTTTGGTATTCTCATCATCTGTTCATCATTGT
GTATATCGCGCTCATTGTTCATGGAGAGTGTCTATACCTTATTCATGTCTGGTACAGAAGAACG
ACATGGATGTATCTTTCAGTGCCTGTTTGCTTGTATGTAGGGGAGAGGATTCTAAGGTTCTTCA
GGTCTGGCAGTTATTCTGTCCGGCTATTGAAGGTGGCCATATATCCAGGTAATGTTTTGACACT
GCAAATGTCCAAGCCTCCCACGTTCCGTTACAAGAGTGGACAATATATGTTTGTTCAATGTCCA
GCAGTGTCTCCCTTTGAATG
						
						Genomic sequence
						
							ACTATTGCAGCAGCAATTGTGGTTGGTATAATCCTCCATGCAGGGAACCACCTTGTATGCGATT
TTCCACGGTTAATAAAATCATCAGATGAGAAGTATGCTCCTTTGGGCCAGTATTTTGGGGAAAT
AAAGCCAACATATTTTACATTGGTCAAAGGAGTGGAGGGCATCACTGGGGTAATCATGGTTGTA
TGCATGATAATTGCTTTTACTCTAGCAACCCGGTGGTTCCGCCGTAGCTTGGTTAAGCTTCCAA
GGCCATTTGACAAACTGACTGGCTTCAATGCCTTTTGGTATTCTCATCATCTGTTCATCATTGT
GTATATCGCGCTCATTGTTCATGGAGAGTGTCTATACCTTATTCATGTCTGGTACAGAAGAACG
GTAAGATATTTTTGAATTTATCTTCATTCATTGGTCTAAGATAATTCGAATTTCTAATGTCCTC
ATGCTTTTATTTCAATGCAGACATGGATGTATCTTTCAGTGCCTGTTTGCTTGTATGTAGGGGA
GAGGATTCTAAGGTTCTTCAGGTCTGGCAGTTATTCTGTCCGGCTATTGAAGGTCAATCCAAAG
ACATTACAAAATTGAGCATTGATACTTTGTGCCTTGTACTAATTCAGTAACTTTCTTAGCAGGT
GGCCATATATCCAGGTAATGTTTTGACACTGCAAATGTCCAAGCCTCCCACGTTCCGTTACAAG
AGTGGACAATATATGTTTGTTCAATGTCCAGCAGTGTCTCCCTTTGAATG

Sequences
Splice junction sequence	GTAATGTTTTGACACTGCAAATGTCCAAGCCTCCCACGTTCCGTTACAAGAGTGGACAATATAT GTTTGTTCAATGTCCAGCAGTGTCTCCCTTTGAATGactattgcagcagcaattgtggttggta taatcctccatgcagggaaccaccttgtatgcgattttccacggttaataaaatcatcagatga gaagtatg
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: 596 Transcript exons: 30631265-30631648,30631733-30631828,30631903-30632018 ACTATTGCAGCAGCAATTGTGGTTGGTATAATCCTCCATGCAGGGAACCACCTTGTATGCGATT TTCCACGGTTAATAAAATCATCAGATGAGAAGTATGCTCCTTTGGGCCAGTATTTTGGGGAAAT AAAGCCAACATATTTTACATTGGTCAAAGGAGTGGAGGGCATCACTGGGGTAATCATGGTTGTA TGCATGATAATTGCTTTTACTCTAGCAACCCGGTGGTTCCGCCGTAGCTTGGTTAAGCTTCCAA GGCCATTTGACAAACTGACTGGCTTCAATGCCTTTTGGTATTCTCATCATCTGTTCATCATTGT GTATATCGCGCTCATTGTTCATGGAGAGTGTCTATACCTTATTCATGTCTGGTACAGAAGAACG ACATGGATGTATCTTTCAGTGCCTGTTTGCTTGTATGTAGGGGAGAGGATTCTAAGGTTCTTCA GGTCTGGCAGTTATTCTGTCCGGCTATTGAAGGTGGCCATATATCCAGGTAATGTTTTGACACT GCAAATGTCCAAGCCTCCCACGTTCCGTTACAAGAGTGGACAATATATGTTTGTTCAATGTCCA GCAGTGTCTCCCTTTGAATG
Genomic sequence	ACTATTGCAGCAGCAATTGTGGTTGGTATAATCCTCCATGCAGGGAACCACCTTGTATGCGATT TTCCACGGTTAATAAAATCATCAGATGAGAAGTATGCTCCTTTGGGCCAGTATTTTGGGGAAAT AAAGCCAACATATTTTACATTGGTCAAAGGAGTGGAGGGCATCACTGGGGTAATCATGGTTGTA TGCATGATAATTGCTTTTACTCTAGCAACCCGGTGGTTCCGCCGTAGCTTGGTTAAGCTTCCAA GGCCATTTGACAAACTGACTGGCTTCAATGCCTTTTGGTATTCTCATCATCTGTTCATCATTGT GTATATCGCGCTCATTGTTCATGGAGAGTGTCTATACCTTATTCATGTCTGGTACAGAAGAACG GTAAGATATTTTTGAATTTATCTTCATTCATTGGTCTAAGATAATTCGAATTTCTAATGTCCTC ATGCTTTTATTTCAATGCAGACATGGATGTATCTTTCAGTGCCTGTTTGCTTGTATGTAGGGGA GAGGATTCTAAGGTTCTTCAGGTCTGGCAGTTATTCTGTCCGGCTATTGAAGGTCAATCCAAAG ACATTACAAAATTGAGCATTGATACTTTGTGCCTTGTACTAATTCAGTAACTTTCTTAGCAGGT GGCCATATATCCAGGTAATGTTTTGACACTGCAAATGTCCAAGCCTCCCACGTTCCGTTACAAG AGTGGACAATATATGTTTGTTCAATGTCCAGCAGTGTCTCCCTTTGAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.432610588

Conservation Information
Conserved circRNAs	NA
PMCS	0.432610588

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30632017-30632016(+)
30631463-30631796(-)
30631305-30631991(-)
						
						Potential amino acid sequence
						
							MTIAAAIVVGIILHAGNHLVCDFPRLIKSSDEKYAPLGQYFGEIKPTYFTLVKGVEGITGVIMV
VCMIIAFTLATRWFRRSLVKLPRPFDKLTGFNAFWYSHHLFIIVYIALIVHGECLYLIHVWYRR
TTWMYLSVPVCLYVGERILRFFRSGSYSVRLLKVAIYPGNVLTLQMSKPPTFRYKSGQYMFVQC
PAVSPFE*(+)
MHTTMITPVMPSTPLTNVKYVGFISPKYWPKGAYFSSDDFINRGKSHTRWFPAWRIIPTTIAAA
IVIQRETLLDIEQTYIVHSCNGTWEAWTFAVSKHYLDIWPPSIAGQNNCQT*(-)
MEDYTNHNCCCNSHSKGDTAGH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30632017-30632016(+) 30631463-30631796(-) 30631305-30631991(-)
Potential amino acid sequence	MTIAAAIVVGIILHAGNHLVCDFPRLIKSSDEKYAPLGQYFGEIKPTYFTLVKGVEGITGVIMV VCMIIAFTLATRWFRRSLVKLPRPFDKLTGFNAFWYSHHLFIIVYIALIVHGECLYLIHVWYRR TTWMYLSVPVCLYVGERILRFFRSGSYSVRLLKVAIYPGNVLTLQMSKPPTFRYKSGQYMFVQC PAVSPFE(+) MHTTMITPVMPSTPLTNVKYVGFISPKYWPKGAYFSSDDFINRGKSHTRWFPAWRIIPTTIAAA IVIQRETLLDIEQTYIVHSCNGTWEAWTFAVSKHYLDIWPPSIAGQNNCQT(-) MEDYTNHNCCCNSHSKGDTAGH*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0734399_circ_g.3

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