Plant Circular RNA Database

Detail information of Os04g0435300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0435300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023894
					
						Alias
						Os_ciR1369
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 21653643-21655709  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os04g0435300						
					
						Parent gene annotation
						
							Hypothetical gene. (Os04t0435300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						10
					
						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
						Os04t0435300-01:4

General Information
CircRNA Name	Os04g0435300_circ_g.3
ID in PlantcircBase	osa_circ_023894
Alias	Os_ciR1369
Organism	Oryza sativa
Position	chr4: 21653643-21655709 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Os04g0435300
Parent gene annotation	Hypothetical gene. (Os04t0435300-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	10
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	Os04t0435300-01:4

			
						 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  
						
							TCTGATGAATAAACATGGTTGATGTCAATGAGCAGACGATTGGATCAGCTTGGACTGAACACGT
ACTATTTTCTGACTGCAAGTCCAAGGAGAGTAACAAtcttcagctatgcatcaagtaattagaa
tgcaagaagaacatggaaatgaaggaatcttgaatatcatcatttcgcctctgcaaagtttcag
agatatta

									
								

					

						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: 584
Transcript exons: 21653643-21653747,21654588-21654686,21654782-21655052,21
655601-21655709
TCTTCAGCTATGCATCAAGTAATTAGAATGCAAGAAGAACATGGAAATGAAGGAATCTTGAATA
TCATCATTTCGCCTCTGCAAAGTTTCAGAGATATTAATGATTAAATTGGTGTTAGCTGAAAGTA
AGAGGAACGAGCACCTAAGAACTATAGGAATGGGAGGCATCAGGAAAATCATCAGACCAAATCT
CCAATACCAGAGCTACAAGAAACAGAAGCTTGAACATTTTCTTCAGAGTACTAGAGTATATATA
GACCTATGCAGTGCAGGGCTGTGAAGGATAAATGAATTGAATCTGGTAGATGGTGCACAATAGG
ACACTGAAGTGAATGATCACATATATTGGCCAAGAAACATGTACAAGTCACTGTACAACATCTG
CAGGGATGTGATCTTCTGGGTACATCAGAAAGCTGATTGACATAATGAAGAGTAAGCAGAGAAC
AGTGCAGACACTTGGGATCTTTTGAGAGGACTGGATTCTGATGAATAAACATGGTTGATGTCAA
TGAGCAGACGATTGGATCAGCTTGGACTGAACACGTACTATTTTCTGACTGCAAGTCCAAGGAG
AGTAACAA
						
					

						Genomic sequence
						
							TCTTCAGCTATGCATCAAGTAATTAGAATGCAAGAAGAACATGGAAATGAAGGAATCTTGAATA
TCATCATTTCGCCTCTGCAAAGTTTCAGAGATATTAATGATGTAAGTATTTTATTTAATTTTTA
GTGAGGCATATATATAGGTGCTGCCATTCCCTTTCTGATTGAGAATTAAAAGGTGCATATAGAT
GCTAATATATGTTTTGTCCAATTCTTTGTTATGTTCATGTGATGGGGAGTATCTCAGTAGTGTC
GTTCAATCCATTCGGATCATTTTGCATATTATAGATGCTAAGTGCTTAGTGCTGATATATACTC
CATAAATGATATAGAGTTTATATAAAATAAACAGCATACACGCATGTCTCTATGCTGAGCTGCT
TAGTTACATCATGTGCATTTGTGCTCTCTTATCTATCTTGACTATGGGTTCATCACTGAAGAAC
TAGTGATGAGTATGTGCCATTTCTGGATCAAAGAGAAGTAGTGTCATTTAGATGTTATCAAGTA
TGAATACAGTTTCAAACTAGTAGGGAATGTGGAATTTTTAGACATGTTTAGGAGTGCAGGATTT
TTTTAATTGAACCATCTCTCTGAAACGTTAGATAATTAGAGCCCAATTTCTATGCACTACACTC
CATTTTCTCTTGTTCTTCATGATTCACTCTAAAATGTCCATTTTCCAGTGTCCCCCTTTTGTTT
TCTCTGCGGAAACAATTGAGCAAGTCAAAAGGAAGAGGAAGGAGTGATTAAGAATAATAGGAAT
GGGAGGCATTGGGAAACACTCAGCCAAATTTCCACCTCTATTGTCAGAGATGGAAACTAAAGGT
TTAGGTTTCCTCCATGTTCCCATTCCAACCATTCTTAGACCCTCTTTCTTCCTCTTCCCGACTC
ACTGCCAAGGCATCTAAATGTGGACATGGATACATTTTGTTTTCTCTAGTAAATTGGTGTTAGC
TGAAAGTAAGAGGAACGAGCACCTAAGAACTATAGGAATGGGAGGCATCAGGAAAATCATCAGA
CCAAATCTCCAATACCAGAGGTTAGAGCTTAATTTGGCTTTCCTTCATGTTCCCATTCCTACTG
CTCTTAGAGTCTCTCTTCCTCTTCCTGGCTCACCCTCTTTTTGGCACACAGCTACAAGAAACAG
AAGCTTGAACATTTTCTTCAGAGTACTAGAGTATATATAGACCTATGCAGTGCAGGGCTGTGAA
GGATAAATGAATTGAATCTGGTAGATGGTGCACAATAGGACACTGAAGTGAATGATCACATATA
TTGGCCAAGAAACATGTACAAGTCACTGTACAACATCTGCAGGGATGTGATCTTCTGGGTACAT
CAGAAAGCTGATTGACATAATGAAGAGTAAGCAGAGAACAGTGCAGACACTTGGGATCTTTTGA
GAGTAAGAATTCAGAGTGGAGAAAGAGTCAATGTGAATCTGAATTTAAAGTGGATCCTGTGTGA
GTGTGGAACATTGCACGTTTCTTTTCTGATACAGATACTTAGCAAAGTTACTTGTACTCAAGTA
TTAAGCCGTAGCAACACATATGCTGTAACATTAAATTCACTAATGCTATCTGACAAAATAATCA
CCAGGACTTGAATAGCTAAGCAGTTTTGTCAATCTCTCTTTTGGGTGCTTCACTGTCTTTGGAA
ACTTAAATGCTCAGGATATAACGGTGATGTGGCCATGTTATAGGTCATATTAACTTCCAAAACG
TTTTATCTGACAGTATTAACCTTCAATTTCTCATAGGTTTCATCTATCAAATTTTGCTAGATTT
CAGAATAGGCACCTTGTTCTACACTTATACATCTTTTCAGAATGCCCACCTAGTAAATAGTTTT
TGCAAGAACAAACGACATGTTTAGAACAAAACACCATCCATACATCAATACCATGTTCACTTTT
GCATGCACTGATTAATACATAATTTGTTTGGCTTTCAGGGACTGGATTCTGATGAATAAACATG
GTTGATGTCAATGAGCAGACGATTGGATCAGCTTGGACTGAACACGTACTATTTTCTGACTGCA
AGTCCAAGGAGAGTAACAA
						
					

			
		

Sequences
Splice junction sequence	TCTGATGAATAAACATGGTTGATGTCAATGAGCAGACGATTGGATCAGCTTGGACTGAACACGT ACTATTTTCTGACTGCAAGTCCAAGGAGAGTAACAAtcttcagctatgcatcaagtaattagaa tgcaagaagaacatggaaatgaaggaatcttgaatatcatcatttcgcctctgcaaagtttcag agatatta
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: 584 Transcript exons: 21653643-21653747,21654588-21654686,21654782-21655052,21 655601-21655709 TCTTCAGCTATGCATCAAGTAATTAGAATGCAAGAAGAACATGGAAATGAAGGAATCTTGAATA TCATCATTTCGCCTCTGCAAAGTTTCAGAGATATTAATGATTAAATTGGTGTTAGCTGAAAGTA AGAGGAACGAGCACCTAAGAACTATAGGAATGGGAGGCATCAGGAAAATCATCAGACCAAATCT CCAATACCAGAGCTACAAGAAACAGAAGCTTGAACATTTTCTTCAGAGTACTAGAGTATATATA GACCTATGCAGTGCAGGGCTGTGAAGGATAAATGAATTGAATCTGGTAGATGGTGCACAATAGG ACACTGAAGTGAATGATCACATATATTGGCCAAGAAACATGTACAAGTCACTGTACAACATCTG CAGGGATGTGATCTTCTGGGTACATCAGAAAGCTGATTGACATAATGAAGAGTAAGCAGAGAAC AGTGCAGACACTTGGGATCTTTTGAGAGGACTGGATTCTGATGAATAAACATGGTTGATGTCAA TGAGCAGACGATTGGATCAGCTTGGACTGAACACGTACTATTTTCTGACTGCAAGTCCAAGGAG AGTAACAA
Genomic sequence	TCTTCAGCTATGCATCAAGTAATTAGAATGCAAGAAGAACATGGAAATGAAGGAATCTTGAATA TCATCATTTCGCCTCTGCAAAGTTTCAGAGATATTAATGATGTAAGTATTTTATTTAATTTTTA GTGAGGCATATATATAGGTGCTGCCATTCCCTTTCTGATTGAGAATTAAAAGGTGCATATAGAT GCTAATATATGTTTTGTCCAATTCTTTGTTATGTTCATGTGATGGGGAGTATCTCAGTAGTGTC GTTCAATCCATTCGGATCATTTTGCATATTATAGATGCTAAGTGCTTAGTGCTGATATATACTC CATAAATGATATAGAGTTTATATAAAATAAACAGCATACACGCATGTCTCTATGCTGAGCTGCT TAGTTACATCATGTGCATTTGTGCTCTCTTATCTATCTTGACTATGGGTTCATCACTGAAGAAC TAGTGATGAGTATGTGCCATTTCTGGATCAAAGAGAAGTAGTGTCATTTAGATGTTATCAAGTA TGAATACAGTTTCAAACTAGTAGGGAATGTGGAATTTTTAGACATGTTTAGGAGTGCAGGATTT TTTTAATTGAACCATCTCTCTGAAACGTTAGATAATTAGAGCCCAATTTCTATGCACTACACTC CATTTTCTCTTGTTCTTCATGATTCACTCTAAAATGTCCATTTTCCAGTGTCCCCCTTTTGTTT TCTCTGCGGAAACAATTGAGCAAGTCAAAAGGAAGAGGAAGGAGTGATTAAGAATAATAGGAAT GGGAGGCATTGGGAAACACTCAGCCAAATTTCCACCTCTATTGTCAGAGATGGAAACTAAAGGT TTAGGTTTCCTCCATGTTCCCATTCCAACCATTCTTAGACCCTCTTTCTTCCTCTTCCCGACTC ACTGCCAAGGCATCTAAATGTGGACATGGATACATTTTGTTTTCTCTAGTAAATTGGTGTTAGC TGAAAGTAAGAGGAACGAGCACCTAAGAACTATAGGAATGGGAGGCATCAGGAAAATCATCAGA CCAAATCTCCAATACCAGAGGTTAGAGCTTAATTTGGCTTTCCTTCATGTTCCCATTCCTACTG CTCTTAGAGTCTCTCTTCCTCTTCCTGGCTCACCCTCTTTTTGGCACACAGCTACAAGAAACAG AAGCTTGAACATTTTCTTCAGAGTACTAGAGTATATATAGACCTATGCAGTGCAGGGCTGTGAA GGATAAATGAATTGAATCTGGTAGATGGTGCACAATAGGACACTGAAGTGAATGATCACATATA TTGGCCAAGAAACATGTACAAGTCACTGTACAACATCTGCAGGGATGTGATCTTCTGGGTACAT CAGAAAGCTGATTGACATAATGAAGAGTAAGCAGAGAACAGTGCAGACACTTGGGATCTTTTGA GAGTAAGAATTCAGAGTGGAGAAAGAGTCAATGTGAATCTGAATTTAAAGTGGATCCTGTGTGA GTGTGGAACATTGCACGTTTCTTTTCTGATACAGATACTTAGCAAAGTTACTTGTACTCAAGTA TTAAGCCGTAGCAACACATATGCTGTAACATTAAATTCACTAATGCTATCTGACAAAATAATCA CCAGGACTTGAATAGCTAAGCAGTTTTGTCAATCTCTCTTTTGGGTGCTTCACTGTCTTTGGAA ACTTAAATGCTCAGGATATAACGGTGATGTGGCCATGTTATAGGTCATATTAACTTCCAAAACG TTTTATCTGACAGTATTAACCTTCAATTTCTCATAGGTTTCATCTATCAAATTTTGCTAGATTT CAGAATAGGCACCTTGTTCTACACTTATACATCTTTTCAGAATGCCCACCTAGTAAATAGTTTT TGCAAGAACAAACGACATGTTTAGAACAAAACACCATCCATACATCAATACCATGTTCACTTTT GCATGCACTGATTAATACATAATTTGTTTGGCTTTCAGGGACTGGATTCTGATGAATAAACATG GTTGATGTCAATGAGCAGACGATTGGATCAGCTTGGACTGAACACGTACTATTTTCTGACTGCA AGTCCAAGGAGAGTAACAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005469* osi_circ_014385 						
					
						PMCS
						0.221020404

Conservation Information
Conserved circRNAs	osi_circ_005469* osi_circ_014385
PMCS	0.221020404

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21655625-21653661(+)
21655632-21653665(+)
						
						Potential amino acid sequence
						
							MVDVNEQTIGSAWTEHVLFSDCKSKESNNLQLCIK*(+)
MSMSRRLDQLGLNTYYFLTASPRRVTIFSYASSN*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21655625-21653661(+) 21655632-21653665(+)
Potential amino acid sequence	MVDVNEQTIGSAWTEHVLFSDCKSKESNNLQLCIK(+) MSMSRRLDQLGLNTYYFLTASPRRVTIFSYASSN(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os04g0435300_circ_g.3

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