Plant Circular RNA Database

Detail information of Os05g0335401_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os05g0335401_circ_g.3
					
						ID in PlantcircBase
						osa_circ_027468
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 15682794-15684503  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0335401						
					
						Parent gene annotation
						
							Similar to haloacid dehalogenase-like hydrolase family protein. 
(Os05t0335401-01);Similar to haloacid dehalogenase-like hydrolas
e family protein. (Os05t0335401-02);Similar to haloacid dehaloge
nase-like hydrolase family protein. (Os05t0335401-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0333150_circ_ag.1 Os05g0333200_circ_g.1 Os05g0333200_circ_ag.1 Os05g0333500_circ_ag.1 Os05g0333500_circ_ag.2 Os05g0333500_circ_ag.3 Os05g0334000_circ_ag.1  Os05g0335100_circ_g.1 Os05g0335401_circ_g.1 Os05g0335401_circ_g.2 Os05g0335401_circ_g.4 Os05g0336000_circ_g.1 Os05g0339000_circ_g.1 Os05g0339000_circ_g.2 Os05g0339000_circ_g.3 Os05g0341300_circ_g.1 Os05g0341300_circ_g.2 Os05g0341300_circ_g.3 Os05g0341300_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os05t0335401-02:5
Os05t0335401-03:3
Os05t0335401-01:5

General Information
CircRNA Name	Os05g0335401_circ_g.3
ID in PlantcircBase	osa_circ_027468
Alias	NA
Organism	Oryza sativa
Position	chr5: 15682794-15684503 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0335401
Parent gene annotation	Similar to haloacid dehalogenase-like hydrolase family protein. (Os05t0335401-01);Similar to haloacid dehalogenase-like hydrolas e family protein. (Os05t0335401-02);Similar to haloacid dehaloge nase-like hydrolase family protein. (Os05t0335401-03)
Parent gene strand	-
Alternative splicing	Os05g0333150_circ_ag.1 Os05g0333200_circ_g.1 Os05g0333200_circ_ag.1 Os05g0333500_circ_ag.1 Os05g0333500_circ_ag.2 Os05g0333500_circ_ag.3 Os05g0334000_circ_ag.1 Os05g0335100_circ_g.1 Os05g0335401_circ_g.1 Os05g0335401_circ_g.2 Os05g0335401_circ_g.4 Os05g0336000_circ_g.1 Os05g0339000_circ_g.1 Os05g0339000_circ_g.2 Os05g0339000_circ_g.3 Os05g0341300_circ_g.1 Os05g0341300_circ_g.2 Os05g0341300_circ_g.3 Os05g0341300_circ_g.4
Support reads	1
Tissues	shoot
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	Os05t0335401-02:5 Os05t0335401-03:3 Os05t0335401-01:5

			
						 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  
						
							AATTAGCTGAATGAGCAGGCGTACATGTTTCCCGATCGAACATTTGTTCATCCCAGTCAATGAA
CTTTGCATATACACCTTTAGCCAGATCAAGAGTTACcttgatgacaacgaggaagaatagcttc
atcagctcctttagaaagaagaaggatcttcccactctggacatccttcaccacagcagacatt
cttttgcg

									
								

					

						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: 589
Transcript exons: 15682794-15682958,15683074-15683183,15683264-15683360,15
684173-15684313,15684428-15684503
CTTGATGACAACGAGGAAGAATAGCTTCATCAGCTCCTTTAGAAAGAAGAAGGATCTTCCCACT
CTGGACATCCTTCACCACAGCAGACATTCTTTTGCGATCGGAAGTAAACTCCAAAATATCCAAC
AAATCATAATAGAACTTACAACCGTTGAAAGAAATCTCAGCAGTGTTGCTGTCTTTACTCACAA
GCACCGTATTTAGTTTTGATGCAGCAGTGACCAAAGCTTCCTCGTCTTGTGATTGTGCTTGGTA
TGTTATAGTACCACCATTGCTTTTGATAGGAACAACTGTACTGCAAAGAGCCATCACCGTGAGA
AATTTGACAATATCAGGATCGTTACACGAAACAGCATCTAGAAGTCTGGCATCTTTTAAAGCAT
CCCCATTGTTTTCTCCATAGAGTATCACTCATGCAACATCTTCTGAAAATCATTCTGTTTTCTG
TCAGTGTTCCAGTTCCGTCACTCAAAATATACTCAACCTGTCCAAGGTCTTCACTAATAGTTGT
GATGTTTCCCGATCGAACATTTGTTCATCCCAGTCAATGAACTTTGCATATACACCTTTAGCCA
GATCAAGAGTTAC
						
					

						Genomic sequence
						
							CTTGATGACAACGAGGAAGAATAGCTTCATCAGCTCCTTTAGAAAGAAGAAGGATCTTCCCACT
CTGGACATCCTTCACCACAGCAGACATTCTTTTGCGATCGGAAGTAAACTCCAAAATATCCAAC
AAATCATAATAGAACTTACAACCGTTGAAAGAAATCTCTGTAGAAATAGAAAATAGTGAAATGA
ATGCAAAAATCAGTCTGAGATAAGAAAAAGCAACCTAGTTAGAGCAATTCATTGTCATATCATC
TTAATCTAACAAAAATATACCAACCAGCAGTGTTGCTGTCTTTACTCACAAGCACCGTATTTAG
TTTTGATGCAGCAGTGACCAAAGCTTCCTCGTCTTGTGATTGTGCTTGGTATGTTATAGTACCA
CCATTGCTGAAATTAGGAACAAGGAATAACTAAACAGCAGGCATTTTCAAAGTACAGTACTGTA
ACATGAAGAAGATGCCACTTACCTTTTGATAGGAACAACTGTACTGCAAAGAGCCATCACCGTG
AGAAATTTGACAATATCAGGATCGTTACACGAAACAGCATCTAGAAGTCTGGCATCTAATTAGA
GAGGAAAAACAATTAGTTAGAGAGCAAAACAAAATATTGACCAATAAATGATATATCAATATTG
ATAATATAATTGAACAAATCCATGAAAAAATTCTGTGTAGTTCCTGCGACCTAGAAAAAAGGTA
TCATGCAGTATAGTCTGAAAGGATGAAGCAAAGATTAGTGTGTTAGATGTAATGCATGAACAAT
TCACCTACTTAAAAAGCACATGAGTTAATACCCAGGCACATTTATAGAAGGTAAAATCTCCAAA
AAAAATGATTAACCCAGGCACCTAAGGAGATGTTTGGATGATGCCTAGGGATGCCACAAGCTTA
GCCAAATTGTGGCATGAAGAAAAAGTGTGGCTAGAAAATAGTTGGCCACAGGTGTGGTATAGTT
AGCTCTAAAACTGAGTATGACAAGTGGGACCTAAGGCTAATGAAGTGTGGGACGACACAATTGT
GAGAATGAAACAAATATACACCTAAGAAACCGTGGCATGACTAAAGTGTGGTGTGGCAAAGTGA
GGGAATGAACCAAACACCCCCTTTATTATCCCTGACACCTTCACATAAGCTGAGCCAGAAACAG
AAGGTTGATTGAGTTTACAATGCATTGTAAGGACTTAACAAATGGGGAGCATCTATTGTTGCTG
TTTGCAAATTCCTATTTAACTCAACACTCGTGAATCAACATTTCACATGCCACTGAAGAAAGTC
AGACAGTTCATGACCAGATGTGCAAACAAATAACATTGTATTACACTAAGCCCAGAGAAAAGAG
AATTTCTCCTGGTAGCTAGAACATAAGTGGATAACCTTTTAAAGCATCCCCATTGTTTTCTCCA
TAGAGTATCACTCATGCAACATCTTCTGAAAATCATTCTGTTTTCTGTCAGTGTTCCAGTTCCG
TCACTCAAAATATACTCAACCTGTCCAAGGTCTTCACTAATAGTTGTGCTGAAAGAGACACTTA
TGTAAGCTGTACTAAAAAATAAATAGGTTGGATGAAAAATCTAAATTCACATATATGGAAATAA
TATGGCACATAATTAGCTGAATGAGCAGGCGTACATGTTTCCCGATCGAACATTTGTTCATCCC
AGTCAATGAACTTTGCATATACACCTTTAGCCAGATCAAGAGTTAC
						
					

			
		

Sequences
Splice junction sequence	AATTAGCTGAATGAGCAGGCGTACATGTTTCCCGATCGAACATTTGTTCATCCCAGTCAATGAA CTTTGCATATACACCTTTAGCCAGATCAAGAGTTACcttgatgacaacgaggaagaatagcttc atcagctcctttagaaagaagaaggatcttcccactctggacatccttcaccacagcagacatt cttttgcg
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: 589 Transcript exons: 15682794-15682958,15683074-15683183,15683264-15683360,15 684173-15684313,15684428-15684503 CTTGATGACAACGAGGAAGAATAGCTTCATCAGCTCCTTTAGAAAGAAGAAGGATCTTCCCACT CTGGACATCCTTCACCACAGCAGACATTCTTTTGCGATCGGAAGTAAACTCCAAAATATCCAAC AAATCATAATAGAACTTACAACCGTTGAAAGAAATCTCAGCAGTGTTGCTGTCTTTACTCACAA GCACCGTATTTAGTTTTGATGCAGCAGTGACCAAAGCTTCCTCGTCTTGTGATTGTGCTTGGTA TGTTATAGTACCACCATTGCTTTTGATAGGAACAACTGTACTGCAAAGAGCCATCACCGTGAGA AATTTGACAATATCAGGATCGTTACACGAAACAGCATCTAGAAGTCTGGCATCTTTTAAAGCAT CCCCATTGTTTTCTCCATAGAGTATCACTCATGCAACATCTTCTGAAAATCATTCTGTTTTCTG TCAGTGTTCCAGTTCCGTCACTCAAAATATACTCAACCTGTCCAAGGTCTTCACTAATAGTTGT GATGTTTCCCGATCGAACATTTGTTCATCCCAGTCAATGAACTTTGCATATACACCTTTAGCCA GATCAAGAGTTAC
Genomic sequence	CTTGATGACAACGAGGAAGAATAGCTTCATCAGCTCCTTTAGAAAGAAGAAGGATCTTCCCACT CTGGACATCCTTCACCACAGCAGACATTCTTTTGCGATCGGAAGTAAACTCCAAAATATCCAAC AAATCATAATAGAACTTACAACCGTTGAAAGAAATCTCTGTAGAAATAGAAAATAGTGAAATGA ATGCAAAAATCAGTCTGAGATAAGAAAAAGCAACCTAGTTAGAGCAATTCATTGTCATATCATC TTAATCTAACAAAAATATACCAACCAGCAGTGTTGCTGTCTTTACTCACAAGCACCGTATTTAG TTTTGATGCAGCAGTGACCAAAGCTTCCTCGTCTTGTGATTGTGCTTGGTATGTTATAGTACCA CCATTGCTGAAATTAGGAACAAGGAATAACTAAACAGCAGGCATTTTCAAAGTACAGTACTGTA ACATGAAGAAGATGCCACTTACCTTTTGATAGGAACAACTGTACTGCAAAGAGCCATCACCGTG AGAAATTTGACAATATCAGGATCGTTACACGAAACAGCATCTAGAAGTCTGGCATCTAATTAGA GAGGAAAAACAATTAGTTAGAGAGCAAAACAAAATATTGACCAATAAATGATATATCAATATTG ATAATATAATTGAACAAATCCATGAAAAAATTCTGTGTAGTTCCTGCGACCTAGAAAAAAGGTA TCATGCAGTATAGTCTGAAAGGATGAAGCAAAGATTAGTGTGTTAGATGTAATGCATGAACAAT TCACCTACTTAAAAAGCACATGAGTTAATACCCAGGCACATTTATAGAAGGTAAAATCTCCAAA AAAAATGATTAACCCAGGCACCTAAGGAGATGTTTGGATGATGCCTAGGGATGCCACAAGCTTA GCCAAATTGTGGCATGAAGAAAAAGTGTGGCTAGAAAATAGTTGGCCACAGGTGTGGTATAGTT AGCTCTAAAACTGAGTATGACAAGTGGGACCTAAGGCTAATGAAGTGTGGGACGACACAATTGT GAGAATGAAACAAATATACACCTAAGAAACCGTGGCATGACTAAAGTGTGGTGTGGCAAAGTGA GGGAATGAACCAAACACCCCCTTTATTATCCCTGACACCTTCACATAAGCTGAGCCAGAAACAG AAGGTTGATTGAGTTTACAATGCATTGTAAGGACTTAACAAATGGGGAGCATCTATTGTTGCTG TTTGCAAATTCCTATTTAACTCAACACTCGTGAATCAACATTTCACATGCCACTGAAGAAAGTC AGACAGTTCATGACCAGATGTGCAAACAAATAACATTGTATTACACTAAGCCCAGAGAAAAGAG AATTTCTCCTGGTAGCTAGAACATAAGTGGATAACCTTTTAAAGCATCCCCATTGTTTTCTCCA TAGAGTATCACTCATGCAACATCTTCTGAAAATCATTCTGTTTTCTGTCAGTGTTCCAGTTCCG TCACTCAAAATATACTCAACCTGTCCAAGGTCTTCACTAATAGTTGTGCTGAAAGAGACACTTA TGTAAGCTGTACTAAAAAATAAATAGGTTGGATGAAAAATCTAAATTCACATATATGGAAATAA TATGGCACATAATTAGCTGAATGAGCAGGCGTACATGTTTCCCGATCGAACATTTGTTCATCCC AGTCAATGAACTTTGCATATACACCTTTAGCCAGATCAAGAGTTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.227117661

Conservation Information
Conserved circRNAs	NA
PMCS	0.227117661

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							15684464-15683110(+)
15683300-15684495(-)
15682867-15684272(-)
						
						Potential amino acid sequence
						
							MNFAYTPLARSRVTLMTTRKNSFISSFRKKKDLPTLDILHHSRHSFAIGSKLQNIQQIIIELTT
VERNLSSVAVFTHKHRI*(+)
MALCSTVVPIKSNGGTITYQAQSQDEEALVTAASKLNTVLVSKDSNTAEISFNGCKFYYDLLDI
LEFTSDRKRMSAVVKDVQSGKILLLSKGADEAILPRCHQGNS*(-)
MSRVGRSFFFLKELMKLFFLVVIKVTLDLAKGVYAKFIDWDEQMFDRETSQLLVKTLDRLSIF*
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	15684464-15683110(+) 15683300-15684495(-) 15682867-15684272(-)
Potential amino acid sequence	MNFAYTPLARSRVTLMTTRKNSFISSFRKKKDLPTLDILHHSRHSFAIGSKLQNIQQIIIELTT VERNLSSVAVFTHKHRI(+) MALCSTVVPIKSNGGTITYQAQSQDEEALVTAASKLNTVLVSKDSNTAEISFNGCKFYYDLLDI LEFTSDRKRMSAVVKDVQSGKILLLSKGADEAILPRCHQGNS(-) MSRVGRSFFFLKELMKLFFLVVIKVTLDLAKGVYAKFIDWDEQMFDRETSQLLVKTLDRLSIF* (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0335401_circ_g.3

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