Plant Circular RNA Database

Detail information of Os08g0223766_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os08g0223766_circ_g.3
					
						ID in PlantcircBase
						osa_circ_036379
					
						Alias
						Os08circ05101/Os_ciR1228
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr8: 7497952-7498613  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os08g0223766						
					
						Parent gene annotation
						
							Similar to H0702G05.10 protein. (Os08t0223766-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os08g0223766_circ_igg.1 Os08g0223766_circ_igg.2 Os08g0223766_circ_g.1 Os08g0223766_circ_g.2 Os08g0223766_circ_g.4 Os08g0223766_circ_g.5 Os08g0223766_circ_g.6 Os08g0223766_circ_ag.1 Os08g0223833_circ_g.1 Os08g0223833_circ_g.2 						
					
						Support reads
						2/17/3/6
					
						Tissues
						leaf and panicle/root/root/shoot, root, seed, pistil
					
						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
						Os08t0223766-00:3

General Information
CircRNA Name	Os08g0223766_circ_g.3
ID in PlantcircBase	osa_circ_036379
Alias	Os08circ05101/Os_ciR1228
Organism	Oryza sativa
Position	chr8: 7497952-7498613 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os08g0223766
Parent gene annotation	Similar to H0702G05.10 protein. (Os08t0223766-00)
Parent gene strand	+
Alternative splicing	Os08g0223766_circ_igg.1 Os08g0223766_circ_igg.2 Os08g0223766_circ_g.1 Os08g0223766_circ_g.2 Os08g0223766_circ_g.4 Os08g0223766_circ_g.5 Os08g0223766_circ_g.6 Os08g0223766_circ_ag.1 Os08g0223833_circ_g.1 Os08g0223833_circ_g.2
Support reads	2/17/3/6
Tissues	leaf and panicle/root/root/shoot, root, seed, pistil
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	Os08t0223766-00:3

			
						 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  
						
							GGCCGAGTTGCGTGTTGAACTCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCA
TCTCAGATTTGGCGGTTATACTGGGCCAGCCATCAGgtgctcttgagaaaggtggtgtgggtgc
tcttgaacttgttgctatggacatgaaagccaggttagctcttcctggaacttctcggtggttc
ggttctac

						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: 254
Transcript exons: 7497952-7498012,7498221-7498284,7498485-7498613
GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGAAC
GCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTAGAGGAAAGAATGATGAAT
ATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTGTTGAACTCCTTTCAGCAATTGAAT
ATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCGGTTATACTGGGCCAGCCATCAG
Transcript length: 272
Transcript exons: 7497952-7498613
GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGGGG
TATGTATGTTTGCAGAACGCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTA
GAGGAAAGAATGATGAATATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTGTTGAAC
TCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCGGTTATA
CTGGGCCAGCCATCAG
						
						Genomic sequence
						
							GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGGTT
AGCTCTTCCTGGAACTTCTCGGTGGTTCGGTTCTACCTTTTACACACATCGTAGTTGACATGAA
GAGCCCTTATGCATTGGGTGTATATACAAATTGCTCTTTCTGTACATAGGTAAGCCAATTACCT
CGTTGATACATTTCCTCTTCTAATAATGATTGGTATACCTCTTGTTCAACTTGTCCCAGGGGTA
TGTATGTTTGCAGAACGCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTAGA
GGAAAGAATGATGGTAAGATTGATGCTCCTTATTTTCTGCTTTTATTTTGGTGGTATGATTAGT
TTACTTTGAACCATTTTAAAAATCTTTATAGTTTACAATGTGATTTCACATAACATTAAAAACC
AATGTTATGTTTAGCCTTTTCTAATCATTTTTTGTGTAGTGCTGGTGTTGATTTTTATTTCACA
TTTTGTTATCTCATGATGCAGAATATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTG
TTGAACTCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCG
GTTATACTGGGCCAGCCATCAG

Sequences
Splice junction sequence	GGCCGAGTTGCGTGTTGAACTCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCA TCTCAGATTTGGCGGTTATACTGGGCCAGCCATCAGgtgctcttgagaaaggtggtgtgggtgc tcttgaacttgttgctatggacatgaaagccaggttagctcttcctggaacttctcggtggttc ggttctac
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: 254 Transcript exons: 7497952-7498012,7498221-7498284,7498485-7498613 GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGAAC GCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTAGAGGAAAGAATGATGAAT ATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTGTTGAACTCCTTTCAGCAATTGAAT ATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCGGTTATACTGGGCCAGCCATCAG Transcript length: 272 Transcript exons: 7497952-7498613 GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGGGG TATGTATGTTTGCAGAACGCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTA GAGGAAAGAATGATGAATATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTGTTGAAC TCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCGGTTATA CTGGGCCAGCCATCAG
Genomic sequence	GTGCTCTTGAGAAAGGTGGTGTGGGTGCTCTTGAACTTGTTGCTATGGACATGAAAGCCAGGTT AGCTCTTCCTGGAACTTCTCGGTGGTTCGGTTCTACCTTTTACACACATCGTAGTTGACATGAA GAGCCCTTATGCATTGGGTGTATATACAAATTGCTCTTTCTGTACATAGGTAAGCCAATTACCT CGTTGATACATTTCCTCTTCTAATAATGATTGGTATACCTCTTGTTCAACTTGTCCCAGGGGTA TGTATGTTTGCAGAACGCTAAGTTATAAGGGTGCTGCTTTTGCTACCGTGGAAGCTCCTCTAGA GGAAAGAATGATGGTAAGATTGATGCTCCTTATTTTCTGCTTTTATTTTGGTGGTATGATTAGT TTACTTTGAACCATTTTAAAAATCTTTATAGTTTACAATGTGATTTCACATAACATTAAAAACC AATGTTATGTTTAGCCTTTTCTAATCATTTTTTGTGTAGTGCTGGTGTTGATTTTTATTTCACA TTTTGTTATCTCATGATGCAGAATATGTATAGGAAAGCAGCTGAATTTTGGGCCGAGTTGCGTG TTGAACTCCTTTCAGCAATTGAATATTATGCAGAAGACAAGGGCAATTCATCTCAGATTTGGCG GTTATACTGGGCCAGCCATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007607* osi_circ_018354 						
					
						PMCS
						0.471483368

Conservation Information
Conserved circRNAs	osi_circ_007607* osi_circ_018354
PMCS	0.471483368

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7498556-7497958(+)
7497997-7498002(+)
7498005-7498252(-)
						
						Potential amino acid sequence
						
							MQKTRAIHLRFGGYTGPAIRCS*(+)
MDMKARTLSYKGAAFATVEAPLEERMMNMYRKAAEFWAELRVELLSAIEYYAEDKGNSSQIWRL
YWASHQVLLRKVVWVLLNLLLWT*(+)
MSIATSSRAPTPPFSRAPDGWPSITAKSEMNCPCLLHNIQLLKGVQHATRPKIQLLSYTYSSFF
PLEELPR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7498556-7497958(+) 7497997-7498002(+) 7498005-7498252(-)
Potential amino acid sequence	MQKTRAIHLRFGGYTGPAIRCS(+) MDMKARTLSYKGAAFATVEAPLEERMMNMYRKAAEFWAELRVELLSAIEYYAEDKGNSSQIWRL YWASHQVLLRKVVWVLLNLLLWT(+) MSIATSSRAPTPPFSRAPDGWPSITAKSEMNCPCLLHNIQLLKGVQHATRPKIQLLSYTYSSFF PLEELPR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os08g0223766_circ_g.3

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