Plant Circular RNA Database

Detail information of Os01g0575000_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0575000_circ_g.2
					
						ID in PlantcircBase
						osa_circ_002290
					
						Alias
						Os01circ15182/Os_ciR2141
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 22121500-22122046  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os01g0575000						
					
						Parent gene annotation
						
							Root hair defective 3 GTP-binding family protein. (Os01t0575000-
01);Root hair defective 3 GTP-binding family protein. (Os01t0575
000-02);Similar to Root hair defective 3 GTP-binding protein. (O
s01t0575000-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0575000_circ_g.3 Os01g0575000_circ_g.4 Os01g0575000_circ_g.5 Os01g0575000_circ_g.6 Os01g0575000_circ_g.7 						
					
						Support reads
						2/6/4/4
					
						Tissues
						leaf/root/root/shoot, 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
						Os01t0575000-02:3
Os01t0575000-01:3

General Information
CircRNA Name	Os01g0575000_circ_g.2
ID in PlantcircBase	osa_circ_002290
Alias	Os01circ15182/Os_ciR2141
Organism	Oryza sativa
Position	chr1: 22121500-22122046 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os01g0575000
Parent gene annotation	Root hair defective 3 GTP-binding family protein. (Os01t0575000- 01);Root hair defective 3 GTP-binding family protein. (Os01t0575 000-02);Similar to Root hair defective 3 GTP-binding protein. (O s01t0575000-03)
Parent gene strand	+
Alternative splicing	Os01g0575000_circ_g.3 Os01g0575000_circ_g.4 Os01g0575000_circ_g.5 Os01g0575000_circ_g.6 Os01g0575000_circ_g.7
Support reads	2/6/4/4
Tissues	leaf/root/root/shoot, 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	Os01t0575000-02:3 Os01t0575000-01:3

			
						 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   
						
							Yes							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   
						
							F: ATGGCGTTTTCAATGTTTCT
 R: ACGCCATCTCCATCAATAAG
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	Yes 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	F: ATGGCGTTTTCAATGTTTCT R: ACGCCATCTCCATCAATAAG PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							ACAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAATATTGAACCATGCACTCTTGTAATG
GATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAGaaatggacgcctgtttttcaacacagct
tattgatggagatggcgttttcaatgtttctggattggagaacttcatgaaggaagttaaaatg
ggcgaatg

						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: 317
Transcript exons: 22121500-22121646,22121756-22121820,22121942-22122046
AAATGGACGCCTGTTTTTCAACACAGCTTATTGATGGAGATGGCGTTTTCAATGTTTCTGGATT
GGAGAACTTCATGAAGGAAGTTAAAATGGGCGAATGTGGGCTTTCATATGCTGTTGTGTCAATA
ATGGGTCCACAAAGTAGTGGAAAGAGTACACTTTTAAATCACCTTTTCCGCACCAATTTCAGGG
AAATGGATGCCTTCAAAGGAAGGTCACAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAA
TATTGAACCATGCACTCTTGTAATGGATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAG
						
						Genomic sequence
						
							AAATGGACGCCTGTTTTTCAACACAGCTTATTGATGGAGATGGCGTTTTCAATGTTTCTGGATT
GGAGAACTTCATGAAGGAAGTTAAAATGGGCGAATGTGGGCTTTCATATGCTGTTGTGTCAATA
ATGGGTCCACAAAGTAGTGGTATGGTGTTTTTTTTTTCCTTTCATCATTTGCTCTATCTGTTTT
CAATGAATAATATATTTTATCCCAGCGCCATTGTTCATCAATTCCTTTTTACATTTTTTTCCAG
GAAAGAGTACACTTTTAAATCACCTTTTCCGCACCAATTTCAGGGAAATGGATGCCTTCAAAGG
AAGGCATGTTGTTATTCCTTTCTAGCCTTTAGTTCATGCCTTTTCTCATCAGAAACTTTATTGG
CTTTGATGGAATTGGTTCTTATTCTAAATCAAGTTCACTGCCATTTTCTGAATTCTTCAGGTCA
CAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAATATTGAACCATGCACTCTTGTAATGG
ATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAG

Sequences
Splice junction sequence	ACAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAATATTGAACCATGCACTCTTGTAATG GATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAGaaatggacgcctgtttttcaacacagct tattgatggagatggcgttttcaatgtttctggattggagaacttcatgaaggaagttaaaatg ggcgaatg
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: 317 Transcript exons: 22121500-22121646,22121756-22121820,22121942-22122046 AAATGGACGCCTGTTTTTCAACACAGCTTATTGATGGAGATGGCGTTTTCAATGTTTCTGGATT GGAGAACTTCATGAAGGAAGTTAAAATGGGCGAATGTGGGCTTTCATATGCTGTTGTGTCAATA ATGGGTCCACAAAGTAGTGGAAAGAGTACACTTTTAAATCACCTTTTCCGCACCAATTTCAGGG AAATGGATGCCTTCAAAGGAAGGTCACAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAA TATTGAACCATGCACTCTTGTAATGGATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAG
Genomic sequence	AAATGGACGCCTGTTTTTCAACACAGCTTATTGATGGAGATGGCGTTTTCAATGTTTCTGGATT GGAGAACTTCATGAAGGAAGTTAAAATGGGCGAATGTGGGCTTTCATATGCTGTTGTGTCAATA ATGGGTCCACAAAGTAGTGGTATGGTGTTTTTTTTTTCCTTTCATCATTTGCTCTATCTGTTTT CAATGAATAATATATTTTATCCCAGCGCCATTGTTCATCAATTCCTTTTTACATTTTTTTCCAG GAAAGAGTACACTTTTAAATCACCTTTTCCGCACCAATTTCAGGGAAATGGATGCCTTCAAAGG AAGGCATGTTGTTATTCCTTTCTAGCCTTTAGTTCATGCCTTTTCTCATCAGAAACTTTATTGG CTTTGATGGAATTGGTTCTTATTCTAAATCAAGTTCACTGCCATTTTCTGAATTCTTCAGGTCA CAGACTACCAAAGGTATATGGATGGCGAAGGCCCATAATATTGAACCATGCACTCTTGTAATGG ATTTGGAAGGCACGGATGGTCGAGAGAGGGGAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002158* osi_circ_010169 						
					
						PMCS
						0.462287416

Conservation Information
Conserved circRNAs	osi_circ_002158* osi_circ_010169
PMCS	0.462287416

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22121996-22121574(+)
22121503-22121574(+)
22121577-22121954(-)
						
						Potential amino acid sequence
						
							MHSCNGFGRHGWSREGREMDACFSTQLIDGDGVFNVSGLENFMKEVKMGECGLSYAVVSIMGPQ
SSGKSTLLNHLFRTNFREMDAFKGRSQTTKGIWMAKAHNIEPCTLVMDLEGTDGRERGEKWTPV
FQHSLLMEMAFSMFLDWRTS*(+)
MDACFSTQLIDGDGVFNVSGLENFMKEVKMGECGLSYAVVSIMGPQSSGKSTLLNHLFRTNFRE
MDAFKGRSQTTKGIWMAKAHNIEPCTLVMDLEGTDGRERGEKWTPVFQHSLLMEMAFSMFLDWR
TS*(+)
MKFSNPETLKTPSPSISCVEKQASISLPSLDHPCLPNPLQECMVQYYGPSPSIYLW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22121996-22121574(+) 22121503-22121574(+) 22121577-22121954(-)
Potential amino acid sequence	MHSCNGFGRHGWSREGREMDACFSTQLIDGDGVFNVSGLENFMKEVKMGECGLSYAVVSIMGPQ SSGKSTLLNHLFRTNFREMDAFKGRSQTTKGIWMAKAHNIEPCTLVMDLEGTDGRERGEKWTPV FQHSLLMEMAFSMFLDWRTS(+) MDACFSTQLIDGDGVFNVSGLENFMKEVKMGECGLSYAVVSIMGPQSSGKSTLLNHLFRTNFRE MDAFKGRSQTTKGIWMAKAHNIEPCTLVMDLEGTDGRERGEKWTPVFQHSLLMEMAFSMFLDWR TS(+) MKFSNPETLKTPSPSISCVEKQASISLPSLDHPCLPNPLQECMVQYYGPSPSIYLW*(-)
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 Os01g0575000_circ_g.2

Address

Any questions?

Supported by