Plant Circular RNA Database

Detail information of Os07g0476200_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0476200_circ_g.3
					
						ID in PlantcircBase
						osa_circ_033769
					
						Alias
						Os_ciR4958
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 17239850-17240793  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os07g0476200						
					
						Parent gene annotation
						
							Tetratricopeptide TPR-1 domain containing protein. (Os07t0476200
-01);Similar to PAF1 complex component. (Os07t0476200-02);Simila
r to PAF1 complex component. (Os07t0476200-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						4
					
						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  
						
							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
						Os07t0476200-02:5
Os07t0476200-01:5

General Information
CircRNA Name	Os07g0476200_circ_g.3
ID in PlantcircBase	osa_circ_033769
Alias	Os_ciR4958
Organism	Oryza sativa
Position	chr7: 17239850-17240793 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os07g0476200
Parent gene annotation	Tetratricopeptide TPR-1 domain containing protein. (Os07t0476200 -01);Similar to PAF1 complex component. (Os07t0476200-02);Simila r to PAF1 complex component. (Os07t0476200-03)
Parent gene strand	-
Alternative splicing	NA
Support reads	4
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	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	Os07t0476200-02:5 Os07t0476200-01:5

			
						 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  
						
							AGTTATCACCAACCTTATAGAGATCCAGTGAGTTCCTATAATAGTCCAGAGCTTTCTTGTGTTG
CTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGCcaaagaatggcaacacaaagtcctgtgg
cttactgatttcattgacagatgccatataataccttccagcagtctcaatatcaccctgaatt
tggtaaaa

									
								

					

						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: 568
Transcript exons: 17239850-17239934,17240066-17240280,17240358-17240421,17
240504-17240620,17240707-17240793
CAAAGAATGGCAACACAAAGTCCTGTGGCTTACTGATTTCATTGACAGATGCCATATAATACCT
TCCAGCAGTCTCAATATCACCCTTACTGTGGTACGATCTGGCTAAGTTATAGAAAGCATGTGAT
TTCAGCAGTCCATGATTACTTGAAGAGAGAGCAGTCTCCGTCAGTTGTTCAACCACAAAATGCT
GGCCAGTAAAGAAATAATGGTTTGCTAGGTGGTTGAGTGCCAATGTGCAATAAGGATAAATTTC
AAAAGCTCTTCTCATTTTCTCCATTCCTCTGCGAATTCCACCAGCTTCATTTGTTTGCAAGTCC
ATGATTGCCAGTGCTACTAAAGCATCAATATTTTCAGGGTCCAACTGCAGAACGCGTTGAAAAG
CTTGTCGAGCTTTATCTGACTGACCAAGTTTGTATCGGCAAAATGCTATACCAAGCCTTACAGC
AGCAGGACAGCTGGTATAGGCCCGCAGGGCTCTCTTATAGAGATCCAGTGAGTTCCTATAATAG
TCCAGAGCTTTCTTGTGTTGCTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGC
						
					

						Genomic sequence
						
							CAAAGAATGGCAACACAAAGTCCTGTGGCTTACTGATTTCATTGACAGATGCCATATAATACCT
TCCAGCAGTCTCAATATCACCCTGAATTTGGTAAAAGTTTGATTGAGGGTTATAAACAAGAGTA
GCAACCAAAAAAATCCAAGGTTTCAACAGAGAGAACAAGTAAAAGAATAACCAAATAGTCCCGT
GGGTGTATGAACAGAGTATATCACCTTACTGTGGTACGATCTGGCTAAGTTATAGAAAGCATGT
GATTTCAGCAGTCCATGATTACTTGAAGAGAGAGCAGTCTCCGTCAGTTGTTCAACCACAAAAT
GCTGGCCAGTAAAGAAATAATGGTTTGCTAGGTGGTTGAGTGCCAATGTGCAATAAGGATAAAT
TTCAAAAGCTCTTCTCATTTTCTCCATTCCTCTGCGAATTCCACCAGCTATACACAAGTTGCGA
GACTTCAGGGAAAATTTGTGAAAAAAGGATTCTTGTTAGTACTTAGGACAGAGCATTTACCTTC
ATTTGTTTGCAAGTCCATGATTGCCAGTGCTACTAAAGCATCAATATTTTCAGGGTCCAACTGT
GAAAGGTTAGTTTAGTTTAATCAATTAACCGAGGTAAATCTTCTATACAGCTATAAAAGTGACA
GAAATAGGGCTTGCCTGCAGAACGCGTTGAAAAGCTTGTCGAGCTTTATCTGACTGACCAAGTT
TGTATCGGCAAAATGCTATACCAAGCCTTACAGCAGCAGGACAGCTGGTATAGGCCCGCAGGGC
TCTCTACGAAGTTTATAAAAGTTAAAATATTATCACAGCAAATAATATGGCATTGTCAAAAGGA
ACTCAAGTGCTGAGTTATCACCAACCTTATAGAGATCCAGTGAGTTCCTATAATAGTCCAGAGC
TTTCTTGTGTTGCTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGC
						
					

			
		

Sequences
Splice junction sequence	AGTTATCACCAACCTTATAGAGATCCAGTGAGTTCCTATAATAGTCCAGAGCTTTCTTGTGTTG CTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGCcaaagaatggcaacacaaagtcctgtgg cttactgatttcattgacagatgccatataataccttccagcagtctcaatatcaccctgaatt tggtaaaa
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: 568 Transcript exons: 17239850-17239934,17240066-17240280,17240358-17240421,17 240504-17240620,17240707-17240793 CAAAGAATGGCAACACAAAGTCCTGTGGCTTACTGATTTCATTGACAGATGCCATATAATACCT TCCAGCAGTCTCAATATCACCCTTACTGTGGTACGATCTGGCTAAGTTATAGAAAGCATGTGAT TTCAGCAGTCCATGATTACTTGAAGAGAGAGCAGTCTCCGTCAGTTGTTCAACCACAAAATGCT GGCCAGTAAAGAAATAATGGTTTGCTAGGTGGTTGAGTGCCAATGTGCAATAAGGATAAATTTC AAAAGCTCTTCTCATTTTCTCCATTCCTCTGCGAATTCCACCAGCTTCATTTGTTTGCAAGTCC ATGATTGCCAGTGCTACTAAAGCATCAATATTTTCAGGGTCCAACTGCAGAACGCGTTGAAAAG CTTGTCGAGCTTTATCTGACTGACCAAGTTTGTATCGGCAAAATGCTATACCAAGCCTTACAGC AGCAGGACAGCTGGTATAGGCCCGCAGGGCTCTCTTATAGAGATCCAGTGAGTTCCTATAATAG TCCAGAGCTTTCTTGTGTTGCTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGC
Genomic sequence	CAAAGAATGGCAACACAAAGTCCTGTGGCTTACTGATTTCATTGACAGATGCCATATAATACCT TCCAGCAGTCTCAATATCACCCTGAATTTGGTAAAAGTTTGATTGAGGGTTATAAACAAGAGTA GCAACCAAAAAAATCCAAGGTTTCAACAGAGAGAACAAGTAAAAGAATAACCAAATAGTCCCGT GGGTGTATGAACAGAGTATATCACCTTACTGTGGTACGATCTGGCTAAGTTATAGAAAGCATGT GATTTCAGCAGTCCATGATTACTTGAAGAGAGAGCAGTCTCCGTCAGTTGTTCAACCACAAAAT GCTGGCCAGTAAAGAAATAATGGTTTGCTAGGTGGTTGAGTGCCAATGTGCAATAAGGATAAAT TTCAAAAGCTCTTCTCATTTTCTCCATTCCTCTGCGAATTCCACCAGCTATACACAAGTTGCGA GACTTCAGGGAAAATTTGTGAAAAAAGGATTCTTGTTAGTACTTAGGACAGAGCATTTACCTTC ATTTGTTTGCAAGTCCATGATTGCCAGTGCTACTAAAGCATCAATATTTTCAGGGTCCAACTGT GAAAGGTTAGTTTAGTTTAATCAATTAACCGAGGTAAATCTTCTATACAGCTATAAAAGTGACA GAAATAGGGCTTGCCTGCAGAACGCGTTGAAAAGCTTGTCGAGCTTTATCTGACTGACCAAGTT TGTATCGGCAAAATGCTATACCAAGCCTTACAGCAGCAGGACAGCTGGTATAGGCCCGCAGGGC TCTCTACGAAGTTTATAAAAGTTAAAATATTATCACAGCAAATAATATGGCATTGTCAAAAGGA ACTCAAGTGCTGAGTTATCACCAACCTTATAGAGATCCAGTGAGTTCCTATAATAGTCCAGAGC TTTCTTGTGTTGCTGCTCTGAGTCACCCATCAGGAAATAAACAGAGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.365586785

Conservation Information
Conserved circRNAs	NA
PMCS	0.365586785

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17240567-17239905(+)
17240777-17240770(-)
17239893-17240770(-)
						
						Potential amino acid sequence
						
							MLYQALQQQDSWYRPAGLSYRDPVSSYNSPELSCVAALSHPSGNKQRPKNGNTKSCGLLISLTD
AI*(+)
MGDSEQQHKKALDYYRNSLDLYKRALRAYTSCPAAVRLGIAFCRYKLGQSDKARQAFQRVLQLD
PENIDALVALAIMDLQTNEAGGIRRGMEKMRRAFEIYPYCTLALNHLANHYFFTGQHFVVEQLT
ETALSSSNHGLLKSHAFYNLARSYHSKGDIETAGRYYMASVNEISKPQDFVLPFFGLCLFPDG*
(-)
MKSVSHRTLCCHSLASVYFLMGDSEQQHKKALDYYRNSLDLYKRALRAYTSCPAAVRLGIAFCR
YKLGQSDKARQAFQRVLQLDPENIDALVALAIMDLQTNEAGGIRRGMEKMRRAFEIYPYCTLAL
NHLANHYFFTGQHFVVEQLTETALSSSNHGLLKSHAFYNLARSYHSKGDIETAGRYYMASVNEI
SKPQDFVLPFFGLCLFPDG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17240567-17239905(+) 17240777-17240770(-) 17239893-17240770(-)
Potential amino acid sequence	MLYQALQQQDSWYRPAGLSYRDPVSSYNSPELSCVAALSHPSGNKQRPKNGNTKSCGLLISLTD AI(+) MGDSEQQHKKALDYYRNSLDLYKRALRAYTSCPAAVRLGIAFCRYKLGQSDKARQAFQRVLQLD PENIDALVALAIMDLQTNEAGGIRRGMEKMRRAFEIYPYCTLALNHLANHYFFTGQHFVVEQLT ETALSSSNHGLLKSHAFYNLARSYHSKGDIETAGRYYMASVNEISKPQDFVLPFFGLCLFPDG (-) MKSVSHRTLCCHSLASVYFLMGDSEQQHKKALDYYRNSLDLYKRALRAYTSCPAAVRLGIAFCR YKLGQSDKARQAFQRVLQLDPENIDALVALAIMDLQTNEAGGIRRGMEKMRRAFEIYPYCTLAL NHLANHYFFTGQHFVVEQLTETALSSSNHGLLKSHAFYNLARSYHSKGDIETAGRYYMASVNEI SKPQDFVLPFFGLCLFPDG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os07g0476200_circ_g.3

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