Plant Circular RNA Database

Detail information of Os09g0394100_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os09g0394100_circ_g.1
					
						ID in PlantcircBase
						osa_circ_039086
					
						Alias
						Os_ciR1834
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 13627185-13627940  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0394100						
					
						Parent gene annotation
						
							Malonyl-CoA decarboxylase family protein. (Os09t0394100-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0394100_circ_g.2 Os09g0394100_circ_g.3 Os09g0394100_circ_g.4 						
					
						Support reads
						7/5
					
						Tissues
						root/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
						Os09t0394100-01:3

General Information
CircRNA Name	Os09g0394100_circ_g.1
ID in PlantcircBase	osa_circ_039086
Alias	Os_ciR1834
Organism	Oryza sativa
Position	chr9: 13627185-13627940 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0394100
Parent gene annotation	Malonyl-CoA decarboxylase family protein. (Os09t0394100-01)
Parent gene strand	-
Alternative splicing	Os09g0394100_circ_g.2 Os09g0394100_circ_g.3 Os09g0394100_circ_g.4
Support reads	7/5
Tissues	root/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	Os09t0394100-01:3

			
						 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  
						
							TGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCTTAGCAAGAAGCCATTG
CATGAAACCAGGGATTGGACTAAGAGTTGCAAAAATtgctccattttgcaagtgaaaatttgca
acagcatcaagagcttttcctcgttttttctccctggcgagatacctatagattatatgcaagg
actatcag

						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: 156
Transcript exons: 13627185-13627210,13627811-13627940
TGCTCCATTTTGCAAGTGAAAATTTGTGAAAGTGGAACTGGTTCCTTCTAATAAACTGCCATCC
TGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCTTAGCAAGAAGCCATTGCATGAAAC
CAGGGATTGGACTAAGAGTTGCAAAAAT
Transcript length: 375
Transcript exons: 13627185-13627257,13627339-13627461,13627762-13627940
TGCTCCATTTTGCAAGTGAAAATTTGCAACAGCATCAAGAGCTTTTCCTCGTTTTTTCTCCCTG
GCGAGATACCTTGCACACAAACGCATCAAAGGAGATTTCAGTGCAGAAGATAATTTGTCAGATT
TTACCCACTGACTTGATTTCAGTATATCTTGCAGTAGTTTGATTCCACTTTTTCCACCAGCATG
TTCAACCGCATCATGTATCATCCTCTCTTCCTCCGGAAAAAGGATGGATTCTCTGAAAGTGGAA
CTGGTTCCTTCTAATAAACTGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCA
GCTTAGCAAGAAGCCATTGCATGAAACCAGGGATTGGACTAAGAGTTGCAAAAAT
						
						Genomic sequence
						
							TGCTCCATTTTGCAAGTGAAAATTTGCAACAGCATCAAGAGCTTTTCCTCGTTTTTTCTCCCTG
GCGAGATACCTATAGATTATATGCAAGGACTATCAGTTGCAACTAATATATACTCTAAAAATAC
ACAGAAGAAGTGATGCTACTGGATACCTTGCACACAAACGCATCAAAGGAGATTTCAGTGCAGA
AGATAATTTGTCAGATTTTACCCACTGACTTGATTTCAGTATATCTTGCAGTAGTTTGATTCCA
CTTTTTCCACCAGCATGTTCACTGGAGCAAAAGTAGCAGCGCAGATGATTATAAATCACAAAGC
AGACCTTTACTCCTCTATTGACTGATCAAAATTTCACATGAACATGTAATGGAGTTAACTACAA
AAGAAAAAGAGACAGCATGTCCAGAATTAAGAGACTGATTTTTTTAGAAAACCAAAGTCTATGA
AAGAAAATGAAAACAAAGGTCAAGATAAAAAAAAACAAAAATACATTTTTTAATATAAGTACAG
AGAATATGAAAAAGGTTGAAATTACGTGAAGTACAATTTGCTATTTTTTTATGAAAGGAACATA
CACCGCATCATGTATCATCCTCTCTTCCTCCGGAAAAAGGATGGATTCTCTGAAAGTGGAACTG
GTTCCTTCTAATAAACTGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCT
TAGCAAGAAGCCATTGCATGAAACCAGGGATTGGACTAAGAGTTGCAAAAAT

Sequences
Splice junction sequence	TGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCTTAGCAAGAAGCCATTG CATGAAACCAGGGATTGGACTAAGAGTTGCAAAAATtgctccattttgcaagtgaaaatttgca acagcatcaagagcttttcctcgttttttctccctggcgagatacctatagattatatgcaagg actatcag
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: 156 Transcript exons: 13627185-13627210,13627811-13627940 TGCTCCATTTTGCAAGTGAAAATTTGTGAAAGTGGAACTGGTTCCTTCTAATAAACTGCCATCC TGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCTTAGCAAGAAGCCATTGCATGAAAC CAGGGATTGGACTAAGAGTTGCAAAAAT Transcript length: 375 Transcript exons: 13627185-13627257,13627339-13627461,13627762-13627940 TGCTCCATTTTGCAAGTGAAAATTTGCAACAGCATCAAGAGCTTTTCCTCGTTTTTTCTCCCTG GCGAGATACCTTGCACACAAACGCATCAAAGGAGATTTCAGTGCAGAAGATAATTTGTCAGATT TTACCCACTGACTTGATTTCAGTATATCTTGCAGTAGTTTGATTCCACTTTTTCCACCAGCATG TTCAACCGCATCATGTATCATCCTCTCTTCCTCCGGAAAAAGGATGGATTCTCTGAAAGTGGAA CTGGTTCCTTCTAATAAACTGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCA GCTTAGCAAGAAGCCATTGCATGAAACCAGGGATTGGACTAAGAGTTGCAAAAAT
Genomic sequence	TGCTCCATTTTGCAAGTGAAAATTTGCAACAGCATCAAGAGCTTTTCCTCGTTTTTTCTCCCTG GCGAGATACCTATAGATTATATGCAAGGACTATCAGTTGCAACTAATATATACTCTAAAAATAC ACAGAAGAAGTGATGCTACTGGATACCTTGCACACAAACGCATCAAAGGAGATTTCAGTGCAGA AGATAATTTGTCAGATTTTACCCACTGACTTGATTTCAGTATATCTTGCAGTAGTTTGATTCCA CTTTTTCCACCAGCATGTTCACTGGAGCAAAAGTAGCAGCGCAGATGATTATAAATCACAAAGC AGACCTTTACTCCTCTATTGACTGATCAAAATTTCACATGAACATGTAATGGAGTTAACTACAA AAGAAAAAGAGACAGCATGTCCAGAATTAAGAGACTGATTTTTTTAGAAAACCAAAGTCTATGA AAGAAAATGAAAACAAAGGTCAAGATAAAAAAAAACAAAAATACATTTTTTAATATAAGTACAG AGAATATGAAAAAGGTTGAAATTACGTGAAGTACAATTTGCTATTTTTTTATGAAAGGAACATA CACCGCATCATGTATCATCCTCTCTTCCTCCGGAAAAAGGATGGATTCTCTGAAAGTGGAACTG GTTCCTTCTAATAAACTGCCATCCTGTGATTCTGCCTCTGCTAACTTTATTTGGGATGCCAGCT TAGCAAGAAGCCATTGCATGAAACCAGGGATTGGACTAAGAGTTGCAAAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018462 ptr_circ_000117* 						
					
						PMCS
						0.301765961

Conservation Information
Conserved circRNAs	osi_circ_018462 ptr_circ_000117*
PMCS	0.301765961

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13627802-13627200(+)
13627909-13627187(-)
13627221-13627873(-)
						
						Potential amino acid sequence
						
							MDSLKVELVPSNKLPSCDSASANFIWDASLARSHCMKPGIGLRVAKIAPFCK*(+)
MQWLLAKLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDI
LKSSQWVKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQW
LLAKLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKS
SQWVKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQWLLA
KLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKSSQW
VKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQWLLAKLA
SQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKSSQWVKS
DKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGA(-)
MLLQIFTCKMEQFLQLLVQSLVSCNGFLLSWHPK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13627802-13627200(+) 13627909-13627187(-) 13627221-13627873(-)
Potential amino acid sequence	MDSLKVELVPSNKLPSCDSASANFIWDASLARSHCMKPGIGLRVAKIAPFCK(+) MQWLLAKLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDI LKSSQWVKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQW LLAKLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKS SQWVKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQWLLA KLASQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKSSQW VKSDKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGAIFATLSPIPGFMQWLLAKLA SQIKLAEAESQDGSLLEGTSSTFRESILFPEEERMIHDAVEHAGGKSGIKLLQDILKSSQWVKS DKLSSALKSPLMRLCARYLAREKKRGKALDAVANFHLQNGA(-) MLLQIFTCKMEQFLQLLVQSLVSCNGFLLSWHPK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os09g0394100_circ_g.1

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