Plant Circular RNA Database

Detail information of Os12g0641100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os12g0641100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_012546
					
						Alias
						Os_ciR4199
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 27495989-27496769  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os12g0641100						
					
						Parent gene annotation
						
							Similar to Na+/H+ antiporter. (Os12t0641100-01);Similar to Na+/H
+ antiporter. (Os12t0641100-02);Plasma membrane Na+/H+ antiporte
r, Salt stress (Os12t0641100-03);Plasma membrane Na+/H+ antiport
er, Salt tolerance (Os12t0641100-04)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						8/8
					
						Tissues
						root/root
					
						Exon boundary  
						
							No-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
						Os12t0641100-02:2
Os12t0641100-04:2
Os12t0641100-03:3

General Information
CircRNA Name	Os12g0641100_circ_g.2
ID in PlantcircBase	osa_circ_012546
Alias	Os_ciR4199
Organism	Oryza sativa
Position	chr12: 27495989-27496769 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os12g0641100
Parent gene annotation	Similar to Na+/H+ antiporter. (Os12t0641100-01);Similar to Na+/H + antiporter. (Os12t0641100-02);Plasma membrane Na+/H+ antiporte r, Salt stress (Os12t0641100-03);Plasma membrane Na+/H+ antiport er, Salt tolerance (Os12t0641100-04)
Parent gene strand	-
Alternative splicing	NA
Support reads	8/8
Tissues	root/root
Exon boundary	No-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	Os12t0641100-02:2 Os12t0641100-04:2 Os12t0641100-03:3

			
						 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  
						
							GCCTCTATTTCGGGCCTCCCTATCTCAACGAACAAAATCCTTGCTCTAGCCTCCACCTGATAGC
TGGGTGCTGTATAACAGTAGTCAATGCGGTTTATAGttgggttgcgacgttgatcatcgatcag
cagcgctggagggctgacggaaggtgagcatgctgggagaatcgactctgacaatcacctcttc
cccggccg

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TTGGGTTGCGACGTTGATCATCGATCAGCAGCGCTGGAGGGCTGACGGAAGGTGAGCATGCTGG
GAGAATCGACTCTGACAATCACCTCTTCCCCGGCCGACTCATCGCTCGAGTTGTCCTCGTCCTC
TTCTATTGCCTTGCGTTGTCGCCGCCGCCGCCGTCCTGCCTCCTCCGGCTCCGGCGGCAGAGAA
GCACCAGCAGCAGCAGCCTGCCTTGCCGTCGTCATGTTGGCACCCTCGGACTGCACAGACAGCA
GGGGCCTCTGCGTGTTGGACGACCTCGAAGGCACTCTTGGGTACGACGAGCTGTGCGCTTTATT
AGAGCTTGCTTTCGTGTGACGATGCCTCTGCCTCCTCTGACCCTGACCCTGACCGGACTTCATG
TCATTGATCTGCAAACCAAATCCATCAGCTGACTTTGATCAGAAATACTACTGTATGTAAAACC
ATAATTTTGCTTTCCTTATTCTACGTACCATGCTCCCGTACATGCTCAGCTGCAATGCTCTTGC
AGAGAAGCTTGCTGGATGGTCTCTGATTTCAGTTAAGCTGGCACCATTCTGAGCTCCCCTGGAT
TTTCTGAAGCTTTCCGGCCAGCTGAGCAAACCGCTGTGCTCCTTGCTTTGTGTCCGAGGCAGTT
CAAGGGTTTGAGATATCAATGACGCACTCCTTTGCAGATCCGCCTCTATTTCGGGCCTCCCTAT
CTCAACGAACAAAATCCTTGCTCTAGCCTCCACCTGATAGCTGGGTGCTGTATAACAGTAGTCA
ATGCGGTTTATAG

Sequences
Splice junction sequence	GCCTCTATTTCGGGCCTCCCTATCTCAACGAACAAAATCCTTGCTCTAGCCTCCACCTGATAGC TGGGTGCTGTATAACAGTAGTCAATGCGGTTTATAGttgggttgcgacgttgatcatcgatcag cagcgctggagggctgacggaaggtgagcatgctgggagaatcgactctgacaatcacctcttc cccggccg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTGGGTTGCGACGTTGATCATCGATCAGCAGCGCTGGAGGGCTGACGGAAGGTGAGCATGCTGG GAGAATCGACTCTGACAATCACCTCTTCCCCGGCCGACTCATCGCTCGAGTTGTCCTCGTCCTC TTCTATTGCCTTGCGTTGTCGCCGCCGCCGCCGTCCTGCCTCCTCCGGCTCCGGCGGCAGAGAA GCACCAGCAGCAGCAGCCTGCCTTGCCGTCGTCATGTTGGCACCCTCGGACTGCACAGACAGCA GGGGCCTCTGCGTGTTGGACGACCTCGAAGGCACTCTTGGGTACGACGAGCTGTGCGCTTTATT AGAGCTTGCTTTCGTGTGACGATGCCTCTGCCTCCTCTGACCCTGACCCTGACCGGACTTCATG TCATTGATCTGCAAACCAAATCCATCAGCTGACTTTGATCAGAAATACTACTGTATGTAAAACC ATAATTTTGCTTTCCTTATTCTACGTACCATGCTCCCGTACATGCTCAGCTGCAATGCTCTTGC AGAGAAGCTTGCTGGATGGTCTCTGATTTCAGTTAAGCTGGCACCATTCTGAGCTCCCCTGGAT TTTCTGAAGCTTTCCGGCCAGCTGAGCAAACCGCTGTGCTCCTTGCTTTGTGTCCGAGGCAGTT CAAGGGTTTGAGATATCAATGACGCACTCCTTTGCAGATCCGCCTCTATTTCGGGCCTCCCTAT CTCAACGAACAAAATCCTTGCTCTAGCCTCCACCTGATAGCTGGGTGCTGTATAACAGTAGTCA ATGCGGTTTATAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.225268128

Conservation Information
Conserved circRNAs	NA
PMCS	0.225268128

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
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 Os12g0641100_circ_g.2

Address

Any questions?

Supported by