Plant Circular RNA Database

Detail information of Os03g0737200_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0737200_circ_g.2
					
						ID in PlantcircBase
						osa_circ_021744
					
						Alias
						Os03circ25779/Os_ciR517
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 30220075-30221304  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os03g0737200						
					
						Parent gene annotation
						
							E3-ubiquitin ligase, Modulation of the cold stress response (Os0
3t0737200-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0737200_circ_g.1 Os03g0737200_circ_g.3 Os03g0737200_circ_g.4 Os03g0737200_circ_g.5 Os03g0737200_circ_g.6 						
					
						Support reads
						9/64
					
						Tissues
						leaf and panicle/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
						Os03t0737200-01:2

General Information
CircRNA Name	Os03g0737200_circ_g.2
ID in PlantcircBase	osa_circ_021744
Alias	Os03circ25779/Os_ciR517
Organism	Oryza sativa
Position	chr3: 30220075-30221304 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os03g0737200
Parent gene annotation	E3-ubiquitin ligase, Modulation of the cold stress response (Os0 3t0737200-01)
Parent gene strand	-
Alternative splicing	Os03g0737200_circ_g.1 Os03g0737200_circ_g.3 Os03g0737200_circ_g.4 Os03g0737200_circ_g.5 Os03g0737200_circ_g.6
Support reads	9/64
Tissues	leaf and panicle/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	Os03t0737200-01:2

			
						 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  
						
							GTGATCATAACTTCAACAACACTGGAAATTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGG
ATAACTTAGACATCATCATCTCTAATCCAGATCTATaatcgcttgctttgcaatcaccatatca
gatgatccatgcaggaagagtacatcaactgcctctcgcaagtccttaaatgggtatttatcaa
cactgaac

									
								

					

						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: 225
Transcript exons: 30220075-30220237,30221243-30221304
AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG
ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCTGCACAGCAAACTTCTGCAGTTGGGATA
ACTTAGACATCATCATCTCTAATCCAGATCTAT
Transcript length: 247
Transcript exons: 30220075-30220226,30221210-30221304
AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG
ATGACTGTTCACTCTGCAAACAGACATAACTTCAACAACACTGGAAATTCCTGCCAACTGCACA
GCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCCAGATCTAT
Transcript length: 262
Transcript exons: 30220075-30220236,30221205-30221304
AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG
ATGACTGTTCACTCTGCAAACAGACAATTTCCACGTGATCATAACTTCAACAACACTGGAAATT
CCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCCAG
ATCTAT
Transcript length: 286
Transcript exons: 30220075-30220158,30220197-30220297,30221168-30221268
AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATAGATGATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCT
TCCTCGCTACCACTATTGCTTTCTTGAATCCCAAGGTTCTGTAGTGCCTGCTCAATGGTCATTA
ACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACACTGGAAATTCCTG
CCAACTGCACAGCAAACTTCTGCAGTTGGG
Transcript length: 584
Transcript exons: 30220075-30220482,30221129-30221304
AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG
ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCTTCCTCGCTACCACTATTGCTTTCTTG
AATCCCAAGGTTCTGTAGTGCCTGCTCAATGAAAAGTATCCCCTGGTTGGCTTCATTGTACGCA
GATGATTTATCAGAGAATTCAGGCCATTTCCGTTCTTTTGCATCTGCCTTTCTTTTAATCACAT
CAGAACTCCAAGATGCTAAGTTAGTGTGCCTTGAGGGTATGTCCTCAAGAAATTTATGCCTGAT
GCACCACATCATGGCCTCCAAATGCTGTTTCGCCTTCAGCGTGCTTTCCATAAGTTGATGAAGG
TCATTAACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACACTGGAAA
TTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCC
AGATCTAT
						
					

						Genomic sequence
						
							AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT
CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG
ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCTTCCTCGCTACCACTATTGCTTTCTTG
AATCCCAAGGTTCTGTAGTGCCTGCTCAATGAAAAGTATCCCCTGGTTGGCTTCATTGTACGCA
GATGATTTATCAGAGAATTCAGGCCATTTCCGTTCTTTTGCATCTGCCTTTCTTTTAATCACAT
CAGAACTCCAAGATGCTAAGTTAGTGTGCCTTGAGGGTATGTCCTCAAGAAATTTATGCCTGAT
GCACCACATCATGGCCTCCAAATGCTGTAAAAAAAAGCTCCAAAATGGACACTTCATTCAGACA
TAATGACAGTAAGAAACATCTGGCTACTTCTCTTTTCATGCATTCAGTGATAAACAAATGGTAG
GGATATACATAAAAAATATATACGAAGCATTTCAACATTGATTTTCTCATTTTCTTGAGAAATT
GTCCCATGTCCTAGTCCCTAGACCTAGTATAGCATCGCGATGGAAGAGAAAAGCAGTGCACAGA
CATCTTATCACCTACTGGAGAGATATATTCAGTTTCGGAGAAGTAGTGCACAGACATTTAACTA
AAATAACGATGTTTCTTCCACCTTTGACACTGGGAGCTATAGTTTTACCACTAGAAACTAATCA
AACAGAACTAAATCATATATGATACTTCTCCATCGTTTTGTTCAGTAAATACTGAACCACCCAG
AGCGATTAGTAGTGCTCCACCACCATGACTGTGAATATTCCAATATGAACTCTTAAGTGACCTA
AGTAGCTCTAGCTTCTTGGCAAAACAACACTAGTAGAACCATTCCATGAAATATCATAATGCAT
GGGCACCCATTGTGCTGCCTAGAGTAGTTTATTCTATTAGCTTGATCATTGTGGCAGTGAAAAA
TTTATAGCAGAAGTGGAGTTAAGACAAAACCTGTTTCGCCTTCAGCGTGCTTTCCATAAGTTGA
TGAAGGTCATTAACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACAC
TGGAAATTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTC
TAATCCAGATCTAT
						
					

			
		

Sequences
Splice junction sequence	GTGATCATAACTTCAACAACACTGGAAATTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGG ATAACTTAGACATCATCATCTCTAATCCAGATCTATaatcgcttgctttgcaatcaccatatca gatgatccatgcaggaagagtacatcaactgcctctcgcaagtccttaaatgggtatttatcaa cactgaac
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: 225 Transcript exons: 30220075-30220237,30221243-30221304 AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCTGCACAGCAAACTTCTGCAGTTGGGATA ACTTAGACATCATCATCTCTAATCCAGATCTAT Transcript length: 247 Transcript exons: 30220075-30220226,30221210-30221304 AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG ATGACTGTTCACTCTGCAAACAGACATAACTTCAACAACACTGGAAATTCCTGCCAACTGCACA GCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCCAGATCTAT Transcript length: 262 Transcript exons: 30220075-30220236,30221205-30221304 AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG ATGACTGTTCACTCTGCAAACAGACAATTTCCACGTGATCATAACTTCAACAACACTGGAAATT CCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCCAG ATCTAT Transcript length: 286 Transcript exons: 30220075-30220158,30220197-30220297,30221168-30221268 AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATAGATGATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCT TCCTCGCTACCACTATTGCTTTCTTGAATCCCAAGGTTCTGTAGTGCCTGCTCAATGGTCATTA ACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACACTGGAAATTCCTG CCAACTGCACAGCAAACTTCTGCAGTTGGG Transcript length: 584 Transcript exons: 30220075-30220482,30221129-30221304 AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCTTCCTCGCTACCACTATTGCTTTCTTG AATCCCAAGGTTCTGTAGTGCCTGCTCAATGAAAAGTATCCCCTGGTTGGCTTCATTGTACGCA GATGATTTATCAGAGAATTCAGGCCATTTCCGTTCTTTTGCATCTGCCTTTCTTTTAATCACAT CAGAACTCCAAGATGCTAAGTTAGTGTGCCTTGAGGGTATGTCCTCAAGAAATTTATGCCTGAT GCACCACATCATGGCCTCCAAATGCTGTTTCGCCTTCAGCGTGCTTTCCATAAGTTGATGAAGG TCATTAACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACACTGGAAA TTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTCTAATCC AGATCTAT
Genomic sequence	AATCGCTTGCTTTGCAATCACCATATCAGATGATCCATGCAGGAAGAGTACATCAACTGCCTCT CGCAAGTCCTTAAATGGGTATTTATCAACACTGAACTGATCAATTGTGGAACAGAACATAGATG ATGACTGTTCACTCTGCAAACAGACAATTTCCACTCCTTCCTCGCTACCACTATTGCTTTCTTG AATCCCAAGGTTCTGTAGTGCCTGCTCAATGAAAAGTATCCCCTGGTTGGCTTCATTGTACGCA GATGATTTATCAGAGAATTCAGGCCATTTCCGTTCTTTTGCATCTGCCTTTCTTTTAATCACAT CAGAACTCCAAGATGCTAAGTTAGTGTGCCTTGAGGGTATGTCCTCAAGAAATTTATGCCTGAT GCACCACATCATGGCCTCCAAATGCTGTAAAAAAAAGCTCCAAAATGGACACTTCATTCAGACA TAATGACAGTAAGAAACATCTGGCTACTTCTCTTTTCATGCATTCAGTGATAAACAAATGGTAG GGATATACATAAAAAATATATACGAAGCATTTCAACATTGATTTTCTCATTTTCTTGAGAAATT GTCCCATGTCCTAGTCCCTAGACCTAGTATAGCATCGCGATGGAAGAGAAAAGCAGTGCACAGA CATCTTATCACCTACTGGAGAGATATATTCAGTTTCGGAGAAGTAGTGCACAGACATTTAACTA AAATAACGATGTTTCTTCCACCTTTGACACTGGGAGCTATAGTTTTACCACTAGAAACTAATCA AACAGAACTAAATCATATATGATACTTCTCCATCGTTTTGTTCAGTAAATACTGAACCACCCAG AGCGATTAGTAGTGCTCCACCACCATGACTGTGAATATTCCAATATGAACTCTTAAGTGACCTA AGTAGCTCTAGCTTCTTGGCAAAACAACACTAGTAGAACCATTCCATGAAATATCATAATGCAT GGGCACCCATTGTGCTGCCTAGAGTAGTTTATTCTATTAGCTTGATCATTGTGGCAGTGAAAAA TTTATAGCAGAAGTGGAGTTAAGACAAAACCTGTTTCGCCTTCAGCGTGCTTTCCATAAGTTGA TGAAGGTCATTAACATGAGCTGAAACTGCTTCACTAAAAGATGTGATCATAACTTCAACAACAC TGGAAATTCCTGCCAACTGCACAGCAAACTTCTGCAGTTGGGATAACTTAGACATCATCATCTC TAATCCAGATCTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005085* osi_circ_013607 						
					
						PMCS
						0.467981592

Conservation Information
Conserved circRNAs	osi_circ_005085* osi_circ_013607
PMCS	0.467981592

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30221289-30221292(-)
						
						Potential amino acid sequence
						
							MMMSKLSQLQKFAVQLAGISSVVEVMITSFSEAVSAHVNDLHQLMESTLKAKQHLEAMMWCIRH
KFLEDIPSRHTNLASWSSDVIKRKADAKERKWPEFSDKSSAYNEANQGILFIEQALQNLGIQES
NSGSEEGVEIVCLQSEQSSSMFCSTIDQFSVDKYPFKDLREAVDVLFLHGSSDMVIAKQAIIDL
D*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30221289-30221292(-)
Potential amino acid sequence	MMMSKLSQLQKFAVQLAGISSVVEVMITSFSEAVSAHVNDLHQLMESTLKAKQHLEAMMWCIRH KFLEDIPSRHTNLASWSSDVIKRKADAKERKWPEFSDKSSAYNEANQGILFIEQALQNLGIQES NSGSEEGVEIVCLQSEQSSSMFCSTIDQFSVDKYPFKDLREAVDVLFLHGSSDMVIAKQAIIDL D*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015

circRNA

Detail information of Os03g0737200_circ_g.2

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