Plant Circular RNA Database

Detail information of Os12g0162500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os12g0162500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_010549
					
						Alias
						Os_ciR4628
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 3153945-3156047  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							Os12g0162500						
					
						Parent gene annotation
						
							Similar to BZIP-like protein. (Os12t0162500-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						4/5/5
					
						Tissues
						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
						Os12t0162500-01:2

General Information
CircRNA Name	Os12g0162500_circ_g.2
ID in PlantcircBase	osa_circ_010549
Alias	Os_ciR4628
Organism	Oryza sativa
Position	chr12: 3153945-3156047 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	Os12g0162500
Parent gene annotation	Similar to BZIP-like protein. (Os12t0162500-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	4/5/5
Tissues	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	Os12t0162500-01:2

			
						 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  
						
							TCACTTGAAACCCAGAGGGATACATCTGGTTTAACTGCCGAGAATAGAGAGCTCAAGCTACGGT
TGCAGTCCATGGAAGAGCAAGCTAAACTACGTGATGaattctggcgaacaggcagtcggctgca
aggtccaaggaaaggaagatcaagtacactagcgagctggagaggaaggtgcagacactgcaga
ccgaggcc

									
								

					

						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: 218
Transcript exons: 3153945-3154077,3155963-3156047
AATTCTGGCGAACAGGCAGTCGGCTGCAAGGTCCAAGGAAAGGAAGATCAAGTACACTAGCGAG
CTGGAGAGGAAGGTGCAGACACTGCAGACCGAGGCCACCACGCTGTCTGCACAGCTCACGCTTC
TCCAGAGGGATACATCTGGTTTAACTGCCGAGAATAGAGAGCTCAAGCTACGGTTGCAGTCCAT
GGAAGAGCAAGCTAAACTACGTGATG
						
					

						Genomic sequence
						
							AATTCTGGCGAACAGGCAGTCGGCTGCAAGGTCCAAGGAAAGGAAGATCAAGTACACTAGCGAG
CTGGAGAGGAAGGTGCAGACACTGCAGACCGAGGCCACCACGCTGTCTGCACAGCTCACGCTTC
TCCAGGTATGGAACTTTGTTTATTCCGAGCGCCAGATAAGCCTCCTATATTGTCTTATCTAATC
AGCTTAGTTTGTTAGTCAATTGTTTTGTTTGACATGTATTAGTTGTGCAAAGTTAGAGTAGGTT
ACACGAAACTTTAATGTTTTGACTCAATGATTGTCATGCATGTGAAGAACTGCTGTAAGCAAAG
CTACTGCTTGAACCTTTTTATGTTTTTAGAAGCATAATAGTATGTTGCTGTATCTTGTCCCTTT
CCTTCTAGCTAAAGCGGCTTATTGATTGTTTCAAGCATGTGTGCTAAGTTGTGGATCTTACTTG
GGGTGTCAAAACGAGCTATTTGTGTTACTATGATAATGTGTTGAAGAAAGTGTGCAGGAATAAC
ACGTAATAATAGCATGTAGCTTTGCATTGCATAACATTCTATGAATTTCATTTTTTTTATACAA
TTCTGTTGTGGGCCAGCTTTATTTAAAACCAAATAACAGTTTATAAGTTAGTACACAATAAATA
ATTTGTCTGCATTGAATGCGGCAGTTCGTTTCCTTTTGGGTTAGCAACTTAGTGTCCTACAGTA
AACTTCCAGTATCTGAGCTCAGAGCTGCAGAAAGTTTAGGAAGTGGAATTTTTAAAGCATGATA
GTCACTAGAATGGAAATGTACAAATAAGAACTTTGTTAGTAGACCATTTATTCTACACATATTT
TAGGACACTTCATAAGCTAAAGCATAACTTAGTTCTTTTTTATTTCAAACTGATGTTCCTTATG
GCACCTTATGCATCTAGCACCTGAATTTATTAGATTGATAGTTGCCTAGATATATGTGGCTTTG
TAAAAACTAGTGATAGCACTAGTATTCCATGGATGTCAAATGGACAGTGAGATGTATGGTAAAT
CATTTTTTTGTTAGTAATATCAAGATATTCTGAATTTTGTTATGGCACTTTGCATGGTGCACAA
TGTAGGACAAGCTGTAGTGTATGAACACAATGGAGAACATAATAATAGATTTGACAAGAGCACA
ACATTTTTTTTCCTTTATCATTACCTTGTTGCCTGTGTAATTGTTGTAGATGCGACAATAAGAG
TAGGAATTGAAGCACCTAATGGTTTAAGAGGTATAAGTATGTTTGTAGCGTGAACGATCGATCA
CTCACCAAAAATTGGGCTAGTGATGAACCATTTTAGAGTGCAGTTTGATTGATGGAATCAGACG
GGTCATGTTAGGATGGAGAAATAAGTGACCACAGATTGTAACATATGATGTCTCACTTTCAAGA
AAACATGCTAGTGCTTATCATATAATTAGAACAAAGCAGTCATCCAGAAATCCCATGAATAAAT
GATATTCTAAAATGCGCCTACTTTTATCATGATCCTTCTGAAGTCAGCTTATTTTTTGTGACGA
TAACAGACATTTTTGCTTTATCTTTTTTGAGCAATGAAATAATGTCAGTGGCTTGTATGTTCTT
TGGAATCTTATATTCCTTCAACCCTTTATGCAGTTCTGTTTGTTCATTGTATAATTTATTTGAT
GAGATTCAGAGAACTAGAGTGCCATCTAATTATTTATTTCCCTATGAATACATAGTTTTTTTTA
CTTAATGTTGTCAACTTTTACGTACAGAGGATATGGATGCTAACTTAATATTGCTCATTTTAGT
ACATAATTTGTTGCACGTAGCATTTGCGTAAATTTAGTCCGTAGATTGTCAAGCTTTGAATCAT
CCTATCGCACAACACCATTTTTTGCATGCTGCTGATAGTATCTGGTAGGCAAATTACTCGCCAA
TCCTGTAAGCCAACAGTTTCTTTTGTTCTGTTTGTGTATGTGATGTGTGCCATCTGGTAGTCTC
GAATCTGATTTTTTGCAATTCACTTGAAACCCAGAGGGATACATCTGGTTTAACTGCCGAGAAT
AGAGAGCTCAAGCTACGGTTGCAGTCCATGGAAGAGCAAGCTAAACTACGTGATG
						
					

			
		

Sequences
Splice junction sequence	TCACTTGAAACCCAGAGGGATACATCTGGTTTAACTGCCGAGAATAGAGAGCTCAAGCTACGGT TGCAGTCCATGGAAGAGCAAGCTAAACTACGTGATGaattctggcgaacaggcagtcggctgca aggtccaaggaaaggaagatcaagtacactagcgagctggagaggaaggtgcagacactgcaga ccgaggcc
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: 218 Transcript exons: 3153945-3154077,3155963-3156047 AATTCTGGCGAACAGGCAGTCGGCTGCAAGGTCCAAGGAAAGGAAGATCAAGTACACTAGCGAG CTGGAGAGGAAGGTGCAGACACTGCAGACCGAGGCCACCACGCTGTCTGCACAGCTCACGCTTC TCCAGAGGGATACATCTGGTTTAACTGCCGAGAATAGAGAGCTCAAGCTACGGTTGCAGTCCAT GGAAGAGCAAGCTAAACTACGTGATG
Genomic sequence	AATTCTGGCGAACAGGCAGTCGGCTGCAAGGTCCAAGGAAAGGAAGATCAAGTACACTAGCGAG CTGGAGAGGAAGGTGCAGACACTGCAGACCGAGGCCACCACGCTGTCTGCACAGCTCACGCTTC TCCAGGTATGGAACTTTGTTTATTCCGAGCGCCAGATAAGCCTCCTATATTGTCTTATCTAATC AGCTTAGTTTGTTAGTCAATTGTTTTGTTTGACATGTATTAGTTGTGCAAAGTTAGAGTAGGTT ACACGAAACTTTAATGTTTTGACTCAATGATTGTCATGCATGTGAAGAACTGCTGTAAGCAAAG CTACTGCTTGAACCTTTTTATGTTTTTAGAAGCATAATAGTATGTTGCTGTATCTTGTCCCTTT CCTTCTAGCTAAAGCGGCTTATTGATTGTTTCAAGCATGTGTGCTAAGTTGTGGATCTTACTTG GGGTGTCAAAACGAGCTATTTGTGTTACTATGATAATGTGTTGAAGAAAGTGTGCAGGAATAAC ACGTAATAATAGCATGTAGCTTTGCATTGCATAACATTCTATGAATTTCATTTTTTTTATACAA TTCTGTTGTGGGCCAGCTTTATTTAAAACCAAATAACAGTTTATAAGTTAGTACACAATAAATA ATTTGTCTGCATTGAATGCGGCAGTTCGTTTCCTTTTGGGTTAGCAACTTAGTGTCCTACAGTA AACTTCCAGTATCTGAGCTCAGAGCTGCAGAAAGTTTAGGAAGTGGAATTTTTAAAGCATGATA GTCACTAGAATGGAAATGTACAAATAAGAACTTTGTTAGTAGACCATTTATTCTACACATATTT TAGGACACTTCATAAGCTAAAGCATAACTTAGTTCTTTTTTATTTCAAACTGATGTTCCTTATG GCACCTTATGCATCTAGCACCTGAATTTATTAGATTGATAGTTGCCTAGATATATGTGGCTTTG TAAAAACTAGTGATAGCACTAGTATTCCATGGATGTCAAATGGACAGTGAGATGTATGGTAAAT CATTTTTTTGTTAGTAATATCAAGATATTCTGAATTTTGTTATGGCACTTTGCATGGTGCACAA TGTAGGACAAGCTGTAGTGTATGAACACAATGGAGAACATAATAATAGATTTGACAAGAGCACA ACATTTTTTTTCCTTTATCATTACCTTGTTGCCTGTGTAATTGTTGTAGATGCGACAATAAGAG TAGGAATTGAAGCACCTAATGGTTTAAGAGGTATAAGTATGTTTGTAGCGTGAACGATCGATCA CTCACCAAAAATTGGGCTAGTGATGAACCATTTTAGAGTGCAGTTTGATTGATGGAATCAGACG GGTCATGTTAGGATGGAGAAATAAGTGACCACAGATTGTAACATATGATGTCTCACTTTCAAGA AAACATGCTAGTGCTTATCATATAATTAGAACAAAGCAGTCATCCAGAAATCCCATGAATAAAT GATATTCTAAAATGCGCCTACTTTTATCATGATCCTTCTGAAGTCAGCTTATTTTTTGTGACGA TAACAGACATTTTTGCTTTATCTTTTTTGAGCAATGAAATAATGTCAGTGGCTTGTATGTTCTT TGGAATCTTATATTCCTTCAACCCTTTATGCAGTTCTGTTTGTTCATTGTATAATTTATTTGAT GAGATTCAGAGAACTAGAGTGCCATCTAATTATTTATTTCCCTATGAATACATAGTTTTTTTTA CTTAATGTTGTCAACTTTTACGTACAGAGGATATGGATGCTAACTTAATATTGCTCATTTTAGT ACATAATTTGTTGCACGTAGCATTTGCGTAAATTTAGTCCGTAGATTGTCAAGCTTTGAATCAT CCTATCGCACAACACCATTTTTTGCATGCTGCTGATAGTATCTGGTAGGCAAATTACTCGCCAA TCCTGTAAGCCAACAGTTTCTTTTGTTCTGTTTGTGTATGTGATGTGTGCCATCTGGTAGTCTC GAATCTGATTTTTTGCAATTCACTTGAAACCCAGAGGGATACATCTGGTTTAACTGCCGAGAAT AGAGAGCTCAAGCTACGGTTGCAGTCCATGGAAGAGCAAGCTAAACTACGTGATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.215104537

Conservation Information
Conserved circRNAs	NA
PMCS	0.215104537

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3156021-3155978(+)
3156046-3154001(+)
3156023-3156035(-)
						
						Potential amino acid sequence
						
							MEEQAKLRDEFWRTGSRLQGPRKGRSSTLASWRGRCRHCRPRPPRCLHSSRFSRGIHLV*(+)
MNSGEQAVGCKVQGKEDQVH*(+)
MDCNRSLSSLFSAVKPDVSLWRSVSCADSVVASVCSVCTFLSSSLVYLIFLSLDLAADCLFARI
HHVV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3156021-3155978(+) 3156046-3154001(+) 3156023-3156035(-)
Potential amino acid sequence	MEEQAKLRDEFWRTGSRLQGPRKGRSSTLASWRGRCRHCRPRPPRCLHSSRFSRGIHLV(+) MNSGEQAVGCKVQGKEDQVH(+) MDCNRSLSSLFSAVKPDVSLWRSVSCADSVVASVCSVCTFLSSSLVYLIFLSLDLAADCLFARI HHVV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os12g0162500_circ_g.2

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