Plant Circular RNA Database

Detail information of Os05g0567400_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os05g0567400_circ_g.5
					
						ID in PlantcircBase
						osa_circ_029018
					
						Alias
						Os05circ18872
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 28247146-28248262  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Os05g0567400						
					
						Parent gene annotation
						
							Ribosomal RNA methyltransferase J domain containing protein. (Os
05t0567400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0567400_circ_g.2 Os05g0567400_circ_g.3 Os05g0567400_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						panicle
					
						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
						Os05t0567400-01:4

General Information
CircRNA Name	Os05g0567400_circ_g.5
ID in PlantcircBase	osa_circ_029018
Alias	Os05circ18872
Organism	Oryza sativa
Position	chr5: 28247146-28248262 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl
Parent gene	Os05g0567400
Parent gene annotation	Ribosomal RNA methyltransferase J domain containing protein. (Os 05t0567400-01)
Parent gene strand	+
Alternative splicing	Os05g0567400_circ_g.2 Os05g0567400_circ_g.3 Os05g0567400_circ_g.4
Support reads	2
Tissues	panicle
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	Os05t0567400-01:4

			
						 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  
						
							AGCTTATGAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAA
CGAGTAAATACTGATGCTGATGAAGAATTATTAGAGatggcggatacgcatacggaaagcacta
tcatcttctgaagtcactaaaaaaactgatgatactgcggtggaagtcaatgtcaaggatgatg
accaactt

									
								

					

						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: 541
Transcript exons: 28247146-28247329,28247419-28247508,28247879-28248012,28
248130-28248262
ATGGCGGATACGCATACGGAAAGCACTATCATCTTCTGAAGTCACTAAAAAAACTGATGATACT
GCGGTGGAAGTCAATGTCAAGGATGATGACCAACTTCTACAGGAAATGGAAGAATTGACGAGTG
TCATTGATAGAAAGAAGAAGAGAGAAAAGAAGCGTCAATCAAAGCGCCGTGCAAAGGATAAAGC
ACGCAAAGCAACAGGAATGCAAATAGATGCTACAGGAGATAATTACGGCGATCCTGATTTGTTT
TCTATAAGTGCTATCAAGGGCGGAAAAGAACTCCAAGCTATTGAATCGGCTGAGCTTAATGTAG
AAGATGCCCAAGGAGATAGTGAGAATGAGGATATTCAAACTCGTGAATACTCTGATGAGGAAAT
GGATTCTGACGAAGAACAGCAGAGGTATGATGCCCAACTTGAGGAAATGCTTGATGAAGCTTAT
GAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAACGAGTAA
ATACTGATGCTGATGAAGAATTATTAGAG
						
					

						Genomic sequence
						
							ATGGCGGATACGCATACGGAAAGCACTATCATCTTCTGAAGTCACTAAAAAAACTGATGATACT
GCGGTGGAAGTCAATGTCAAGGATGATGACCAACTTCTACAGGAAATGGAAGAATTGACGAGTG
TCATTGATAGAAAGAAGAAGAGAGAAAAGAAGCGTCAATCAAAGCGCCGTGCAAAGGTATATCA
GTCATGAGATATAGATGCTGCCATTGCCAAATGGGTGGTTAATTTGAGTTATGTGCTAATACAC
TGGTCTTTTCGTTCCAGGATAAAGCACGCAAAGCAACAGGAATGCAAATAGATGCTACAGGAGA
TAATTACGGCGATCCTGATTTGTTTTCTATAAGTGCTATCAAGGTTCATGCTGTTTCTGTAGTC
ATATCCTGTGTGGTTCTTAAGTATTTAGTACTAATATTTGTTTAAAATCATAGGACAGGTGTTC
ATTTGCATGGCTATAATTTTCCTGAATTTGAAAGTGTGCTTCTTTTCTTTGCACTTGAAATATG
CAACGTTCGTGCTCCTCAGTAAAGTTTCACTTTTATTGATCTCTCCATGCGACAATTTCTTAGT
GTGGTAGCCTTTATCAGTATTCACAAACTTAGTAAATTGATTTTCGTTATGTTACGCTTTCTCA
AAGTTACTTTCCAGTATGAGCTGTATAGTCTACACTTGTCTTGTGTAATACTTACTATCATCTA
AATAGATAGTTTGTGTCATTTTTCTGTAGGGCGGAAAAGAACTCCAAGCTATTGAATCGGCTGA
GCTTAATGTAGAAGATGCCCAAGGAGATAGTGAGAATGAGGATATTCAAACTCGTGAATACTCT
GATGAGGAAATGGATTCTGACGAAGAACAGCAGAGGTAAATTTCGAAATTAACACTCAATAAAA
CATACAATAAGCCGGTCATAAATTTTTACAGGTTTTATAATTTTACCGCAATCCCAAAAATGTG
TAACATGGTAATCTTCCCAACCAGGTATGATGCCCAACTTGAGGAAATGCTTGATGAAGCTTAT
GAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAACGAGTAA
ATACTGATGCTGATGAAGAATTATTAGAG
						
					

			
		

Sequences
Splice junction sequence	AGCTTATGAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAA CGAGTAAATACTGATGCTGATGAAGAATTATTAGAGatggcggatacgcatacggaaagcacta tcatcttctgaagtcactaaaaaaactgatgatactgcggtggaagtcaatgtcaaggatgatg accaactt
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: 541 Transcript exons: 28247146-28247329,28247419-28247508,28247879-28248012,28 248130-28248262 ATGGCGGATACGCATACGGAAAGCACTATCATCTTCTGAAGTCACTAAAAAAACTGATGATACT GCGGTGGAAGTCAATGTCAAGGATGATGACCAACTTCTACAGGAAATGGAAGAATTGACGAGTG TCATTGATAGAAAGAAGAAGAGAGAAAAGAAGCGTCAATCAAAGCGCCGTGCAAAGGATAAAGC ACGCAAAGCAACAGGAATGCAAATAGATGCTACAGGAGATAATTACGGCGATCCTGATTTGTTT TCTATAAGTGCTATCAAGGGCGGAAAAGAACTCCAAGCTATTGAATCGGCTGAGCTTAATGTAG AAGATGCCCAAGGAGATAGTGAGAATGAGGATATTCAAACTCGTGAATACTCTGATGAGGAAAT GGATTCTGACGAAGAACAGCAGAGGTATGATGCCCAACTTGAGGAAATGCTTGATGAAGCTTAT GAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAACGAGTAA ATACTGATGCTGATGAAGAATTATTAGAG
Genomic sequence	ATGGCGGATACGCATACGGAAAGCACTATCATCTTCTGAAGTCACTAAAAAAACTGATGATACT GCGGTGGAAGTCAATGTCAAGGATGATGACCAACTTCTACAGGAAATGGAAGAATTGACGAGTG TCATTGATAGAAAGAAGAAGAGAGAAAAGAAGCGTCAATCAAAGCGCCGTGCAAAGGTATATCA GTCATGAGATATAGATGCTGCCATTGCCAAATGGGTGGTTAATTTGAGTTATGTGCTAATACAC TGGTCTTTTCGTTCCAGGATAAAGCACGCAAAGCAACAGGAATGCAAATAGATGCTACAGGAGA TAATTACGGCGATCCTGATTTGTTTTCTATAAGTGCTATCAAGGTTCATGCTGTTTCTGTAGTC ATATCCTGTGTGGTTCTTAAGTATTTAGTACTAATATTTGTTTAAAATCATAGGACAGGTGTTC ATTTGCATGGCTATAATTTTCCTGAATTTGAAAGTGTGCTTCTTTTCTTTGCACTTGAAATATG CAACGTTCGTGCTCCTCAGTAAAGTTTCACTTTTATTGATCTCTCCATGCGACAATTTCTTAGT GTGGTAGCCTTTATCAGTATTCACAAACTTAGTAAATTGATTTTCGTTATGTTACGCTTTCTCA AAGTTACTTTCCAGTATGAGCTGTATAGTCTACACTTGTCTTGTGTAATACTTACTATCATCTA AATAGATAGTTTGTGTCATTTTTCTGTAGGGCGGAAAAGAACTCCAAGCTATTGAATCGGCTGA GCTTAATGTAGAAGATGCCCAAGGAGATAGTGAGAATGAGGATATTCAAACTCGTGAATACTCT GATGAGGAAATGGATTCTGACGAAGAACAGCAGAGGTAAATTTCGAAATTAACACTCAATAAAA CATACAATAAGCCGGTCATAAATTTTTACAGGTTTTATAATTTTACCGCAATCCCAAAAATGTG TAACATGGTAATCTTCCCAACCAGGTATGATGCCCAACTTGAGGAAATGCTTGATGAAGCTTAT GAGCGTTATGTAACTAAAAAGGGTGGTGAAGTGAAACAAGAACGCAAGCGTGCAAAACGAGTAA ATACTGATGCTGATGAAGAATTATTAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.266652111

Conservation Information
Conserved circRNAs	NA
PMCS	0.266652111

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28247256-28247181(+)
28247279-28248259(-)
28247179-28248177(-)
						
						Potential amino acid sequence
						
							MEELTSVIDRKKKREKKRQSKRRAKDKARKATGMQIDATGDNYGDPDLFSISAIKGGKELQAIE
SAELNVEDAQGDSENEDIQTREYSDEEMDSDEEQQRYDAQLEEMLDEAYERYVTKKGGEVKQER
KRAKRVNTDADEELLEMADTHTESTIIF*(+)
MTLVNSSISCRSWSSSLTLTSTAVSSVFLVTSEDDSAFRMRIRHL*(-)
MIVLSVCVSAISNNSSSASVFTRFARLRSCFTSPPFLVT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28247256-28247181(+) 28247279-28248259(-) 28247179-28248177(-)
Potential amino acid sequence	MEELTSVIDRKKKREKKRQSKRRAKDKARKATGMQIDATGDNYGDPDLFSISAIKGGKELQAIE SAELNVEDAQGDSENEDIQTREYSDEEMDSDEEQQRYDAQLEEMLDEAYERYVTKKGGEVKQER KRAKRVNTDADEELLEMADTHTESTIIF(+) MTLVNSSISCRSWSSSLTLTSTAVSSVFLVTSEDDSAFRMRIRHL(-) MIVLSVCVSAISNNSSSASVFTRFARLRSCFTSPPFLVT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Os05g0567400_circ_g.5

Address

Any questions?

Supported by