Plant Circular RNA Database

Detail information of Os12g0106000_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0106000_circ_g.4
					
						ID in PlantcircBase
						osa_circ_010283
					
						Alias
						NA, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 322211-322625  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI-long
					
						Parent gene
						
							Os12g0106000						
					
						Parent gene annotation
						
							Ferritin, Iron storage protein, Iron homeostasis (Os12t0106000-0
1)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os12g0106000_circ_g.1 Os12g0106000_circ_g.2 Os12g0106000_circ_g.3 						
					
						Support reads
						3
					
						Tissues
						shoot, root, leaf
					
						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
						Os12t0106000-01:3

General Information
CircRNA Name	Os12g0106000_circ_g.4
ID in PlantcircBase	osa_circ_010283
Alias	NA,
Organism	Oryza sativa
Position	chr12: 322211-322625 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI-long
Parent gene	Os12g0106000
Parent gene annotation	Ferritin, Iron storage protein, Iron homeostasis (Os12t0106000-0 1)
Parent gene strand	-
Alternative splicing	Os12g0106000_circ_g.1 Os12g0106000_circ_g.2 Os12g0106000_circ_g.3
Support reads	3
Tissues	shoot, root, leaf
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	Os12t0106000-01:3

			
						 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  
						
							GGTGGTGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAA
AGGGAGTGGTACGCGTACGATGCATTGAACTCCACAcatacaaggcatcccctttctcaggatg
gtcgaactctgtcaagggtgtgacgatggactggagccgcaccctgcctccacgcatgttctga
caaagaag

						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: 153
Transcript exons: 322211-322279,322542-322625
CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG
CCGCATTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAAAGGGAGTGGTA
CGCGTACGATGCATTGAACTCCACA
Transcript length: 233
Transcript exons: 322211-322298,322401-322461,322542-322625
CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG
CCGCACCCTGCCTCCACGCATGTTCTGGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCA
TCGCTGGATTCTTTGAAGAATTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGG
CGAAAAGGGAGTGGTACGCGTACGATGCATTGAACTCCACA

Transcript length: 313
Transcript exons: 322211-322298,322401-322625
CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG
CCGCACCCTGCCTCCACGCATGTTCTGGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCA
TCGCTGGATTCTTTGAAGAATCTGAAGGAACAGAATTTATCGATACATGGGTGACAATTTTCCT
ACTTGGTGATGGCTAATGAGGGGTGGTGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTG
TCACGGTCAAAGTAGGCGAAAAGGGAGTGGTACGCGTACGATGCATTGAACTCCACA
						
						Genomic sequence
						
							CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG
CCGCACCCTGCCTCCACGCATGTTCTGACAAAGAAGAACATGGCAGTTTTAGCATTTGGGCGCA
TGATTATAGTGGTACAGCCTACAGTTTTCCTGGTGTGCCAAACGAAGCAGAGGTAAAGTTACCT
GGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCATCGCTGGATTCTTTGAAGAATCTGAA
GGAACAGAATTTATCGATACATGGGTGACAATTTTCCTACTTGGTGATGGCTAATGAGGGGTGG
TGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAAAGGGA
GTGGTACGCGTACGATGCATTGAACTCCACA

Sequences
Splice junction sequence	GGTGGTGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAA AGGGAGTGGTACGCGTACGATGCATTGAACTCCACAcatacaaggcatcccctttctcaggatg gtcgaactctgtcaagggtgtgacgatggactggagccgcaccctgcctccacgcatgttctga caaagaag
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: 153 Transcript exons: 322211-322279,322542-322625 CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG CCGCATTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAAAGGGAGTGGTA CGCGTACGATGCATTGAACTCCACA Transcript length: 233 Transcript exons: 322211-322298,322401-322461,322542-322625 CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG CCGCACCCTGCCTCCACGCATGTTCTGGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCA TCGCTGGATTCTTTGAAGAATTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGG CGAAAAGGGAGTGGTACGCGTACGATGCATTGAACTCCACA Transcript length: 313 Transcript exons: 322211-322298,322401-322625 CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG CCGCACCCTGCCTCCACGCATGTTCTGGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCA TCGCTGGATTCTTTGAAGAATCTGAAGGAACAGAATTTATCGATACATGGGTGACAATTTTCCT ACTTGGTGATGGCTAATGAGGGGTGGTGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTG TCACGGTCAAAGTAGGCGAAAAGGGAGTGGTACGCGTACGATGCATTGAACTCCACA
Genomic sequence	CATACAAGGCATCCCCTTTCTCAGGATGGTCGAACTCTGTCAAGGGTGTGACGATGGACTGGAG CCGCACCCTGCCTCCACGCATGTTCTGACAAAGAAGAACATGGCAGTTTTAGCATTTGGGCGCA TGATTATAGTGGTACAGCCTACAGTTTTCCTGGTGTGCCAAACGAAGCAGAGGTAAAGTTACCT GGTACTTCATGAGTTTCTCTGCGTGATCCCTCTCCTCATCGCTGGATTCTTTGAAGAATCTGAA GGAACAGAATTTATCGATACATGGGTGACAATTTTCCTACTTGGTGATGGCTAATGAGGGGTGG TGATGGCTTACTTGGCGAATCCCTTGAGAGCAACGTTGTCACGGTCAAAGTAGGCGAAAAGGGA GTGGTACGCGTACGATGCATTGAACTCCACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010202 osi_circ_009318 						
					
						PMCS
						0.377069679

Conservation Information
Conserved circRNAs	osi_circ_010202 osi_circ_009318
PMCS	0.377069679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							322237-322425(+)
322414-322411(-)
322224-322577(-)
						
						Potential amino acid sequence
						
							MVELCQGCDDGLEPHPASTHVLVLHEFLCVIPLLIAGFFEEFGESLESNVVTVKVGEKGVVRVR
CIELHTYKASPFSGWSNSVKGVTMDWSRTLPPRMFWYFMSFSA*(+)
MKYQNMRGGRVRLQSIVTPLTEFDHPEKGDALYVWSSMHRTRTTPFSPTLTVTTLLSRDSPNSS
KNPAMRRGITQRNS*(-)
MPCMCGVQCIVRVPLPFRLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	322237-322425(+) 322414-322411(-) 322224-322577(-)
Potential amino acid sequence	MVELCQGCDDGLEPHPASTHVLVLHEFLCVIPLLIAGFFEEFGESLESNVVTVKVGEKGVVRVR CIELHTYKASPFSGWSNSVKGVTMDWSRTLPPRMFWYFMSFSA(+) MKYQNMRGGRVRLQSIVTPLTEFDHPEKGDALYVWSSMHRTRTTPFSPTLTVTTLLSRDSPNSS KNPAMRRGITQRNS(-) MPCMCGVQCIVRVPLPFRLL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017; this study

circRNA

Detail information of Os12g0106000_circ_g.4

Address

Any questions?

Supported by