Plant Circular RNA Database

Detail information of Os01g0356500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0356500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_001692
					
						Alias
						Os_ciR2230
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 14395507-14397542  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os01g0356500						
					
						Parent gene annotation
						
							Thiamin pyrophosphokinase, eukaryotic domain containing protein.
 (Os01t0356500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0356500_circ_g.1 Os01g0356500_circ_g.3 						
					
						Support reads
						5/9
					
						Tissues
						root/shoot, root, seed
					
						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
						Os01t0356500-01:3

General Information
CircRNA Name	Os01g0356500_circ_g.2
ID in PlantcircBase	osa_circ_001692
Alias	Os_ciR2230
Organism	Oryza sativa
Position	chr1: 14395507-14397542 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, find_circ
Parent gene	Os01g0356500
Parent gene annotation	Thiamin pyrophosphokinase, eukaryotic domain containing protein. (Os01t0356500-01)
Parent gene strand	-
Alternative splicing	Os01g0356500_circ_g.1 Os01g0356500_circ_g.3
Support reads	5/9
Tissues	root/shoot, root, seed
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	Os01t0356500-01:3

			
						 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  
						
							ATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGCGC
CCCAACATCTTAACCTCAAGAAGGTGATGTACCAAGctggctagagtagaactgtttcacttct
ggccttatagaatccatatctccctcaattatttctggaatatacctggatatcagcagccaat
tgtaagag

									
								

					

						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: 164
Transcript exons: 14395507-14395552,14397425-14397542
CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATGGAGAGTTGGCAGGCTG
ATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGCGC
CCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG
Transcript length: 358
Transcript exons: 14395507-14395579,14397171-14397267,14397355-14397542
CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATCTCCCTCAATTATTTCT
GGAATATACCTTTTTCGGGTGCTTTCATAGTCTGGATCATTAGTCATCTGAAACATCTCATCGA
ATATACGATTGGCACCTCCATCAGCACAGATTCTTAGCTTTGCATGAGTCCACAGGCGGGGCAC
GAATCGTGGAAGGTTCTGATTAAGAACAACTAGAGCATACTTCTTTGCTGGAGAGTTGGCAGGC
TGATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGC
GCCCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG
						
					

						Genomic sequence
						
							CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATCTCCCTCAATTATTTCT
GGAATATACCTGGATATCAGCAGCCAATTGTAAGAGTCAGGAAAATTTTACTCAATTATATTAG
TTCTAACAGTACGCAAGTATTCATCCTTAGGGGAGAGTAGAGCATGAACATTTATAGCTAGCTT
GGTCTTAGAAAACTGACCTTAAAATGCCATTCAGATATACATTATACATATTTCATAAAATATA
TAGTACTATTGAGGGCTTTTGGAGAACATACAAACTGTCGAGGTGGGTTGTTCTCTGTGTGACC
AGTGAACAGTTACCGAAAAATAAATAGGCACATGCCAAGCAATCACTAGTACCTAAATGCATTC
CATATGAAGAACACATCTAAGAGTACAATTACTATTATGGTATTACCTCTACTAGAAAAGTGCA
GATACGAACTTCTCATACAGAATAGAGGGAGCATATCCGAGTTGTTTAGTGAAATCTAATTACC
AAAGTAGTGTTAGTGACCAAGAATCTAATATAAACCGTGTTTGTAGAACTTCACTTTAATTAAG
AGATGGAACGATTCTGCAATCACTGAAGTAGTCTGAAAAATTTCAGTTTCCTTTAATCACAAAT
CACACATATGATCAAGTCATTTGAACCTTGGCCTGTATATGCCCATAGGTGCTGTTAATTTTTG
TAACTGTTTTAGGAACAAGTTGAGCATTTAGATCACAGAGCATGTCAAATGGAACTCCACTACT
GATTGATATCTCTAACAAGGAATAGAGTCTTGAGGTTAGAAATTACGAAAATAAGGTCTAGTAC
TTCAATCCAAACCACGTGAATGGACGAACAGGTGAGCCCTTTGGGCATTCAACATATTAGTGTA
TTAAATTTTATCTGTGGTCTCATTTATTTTTTTTAATGTACATGTTTCATATTTGGCTGTTTAC
AGTTTTACAACACACAGTTATTCAATGAGCTCAACTGGCATTACAATGTTGGCTTAGGACTTAT
GCCATCCAGATCCTAACACAACCCAATATCTTACCAAAAATAATCCAAACTACACTTCTTTTTT
TTTTCATGTACAACCCACCAAATACTCCCCGTCCCTTAATATAACAACCTAGGACATAATATAA
CAACCTAGGACCGGATGTGACACTACATAGTACAACAAATTTGAACATGCTACTATGAAGTGTC
CTAGATTGCTATAATATGGGACAAAGGGAGTAGTACCCTATTTATGTGCCTAACGTCCCATAAA
AGAACCTAAAGAGGAGTACATTACAAATAATATCGTAAAAAATGCTTATTTTGAGCACTTTCTG
TTTAAGTGTTACTACCCCTGTTCATAAAATAAGTAAATAATTTGTTTTTTTTTTGAAGTCTACG
AAATGCCACCTTGACCACTAAATTTTATCAACTTTCATTAAAAAAATACTGCATCGTTTTGATA
TAACCAAATTATATGATATAGATAACATATTTGGTCAAAACTAATATAGTTTGACATCAAGCAT
AATAAGTGCATATTTTTGTGATCAGAGGTAGCAACAGCTATCACTTATCATTAATCAATATCTG
CAAGGAATAATTTAAATTTAATAAACAACAAAATCCAAATGAAATGAGAAAGTTGTTACTCTAC
CTTTTTCGGGTGCTTTCATAGTCTGGATCATTAGTCATCTGAAACATCTCATCGAATATACGAT
TGGCACCTCCATCAGCACAGATTCTTAGCTTTGCTGCTCTATATCAAAATCACACGCAGAGGTT
TAAAGATACATGACTGATACAGAATGTCAAAAGAACAAATGAGCAGGGACAGCTACCATGAGTC
CACAGGCGGGGCACGAATCGTGGAAGGTTCTGATTAAGAACAACTAGAGCATACTTCTTTGCTG
GAGAGTTGGCAGGCTGATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCAT
ACTGCGTATTGCGCGCCCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG
						
					

			
		

Sequences
Splice junction sequence	ATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGCGC CCCAACATCTTAACCTCAAGAAGGTGATGTACCAAGctggctagagtagaactgtttcacttct ggccttatagaatccatatctccctcaattatttctggaatatacctggatatcagcagccaat tgtaagag
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: 164 Transcript exons: 14395507-14395552,14397425-14397542 CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATGGAGAGTTGGCAGGCTG ATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGCGC CCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG Transcript length: 358 Transcript exons: 14395507-14395579,14397171-14397267,14397355-14397542 CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATCTCCCTCAATTATTTCT GGAATATACCTTTTTCGGGTGCTTTCATAGTCTGGATCATTAGTCATCTGAAACATCTCATCGA ATATACGATTGGCACCTCCATCAGCACAGATTCTTAGCTTTGCATGAGTCCACAGGCGGGGCAC GAATCGTGGAAGGTTCTGATTAAGAACAACTAGAGCATACTTCTTTGCTGGAGAGTTGGCAGGC TGATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCATACTGCGTATTGCGC GCCCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG
Genomic sequence	CTGGCTAGAGTAGAACTGTTTCACTTCTGGCCTTATAGAATCCATATCTCCCTCAATTATTTCT GGAATATACCTGGATATCAGCAGCCAATTGTAAGAGTCAGGAAAATTTTACTCAATTATATTAG TTCTAACAGTACGCAAGTATTCATCCTTAGGGGAGAGTAGAGCATGAACATTTATAGCTAGCTT GGTCTTAGAAAACTGACCTTAAAATGCCATTCAGATATACATTATACATATTTCATAAAATATA TAGTACTATTGAGGGCTTTTGGAGAACATACAAACTGTCGAGGTGGGTTGTTCTCTGTGTGACC AGTGAACAGTTACCGAAAAATAAATAGGCACATGCCAAGCAATCACTAGTACCTAAATGCATTC CATATGAAGAACACATCTAAGAGTACAATTACTATTATGGTATTACCTCTACTAGAAAAGTGCA GATACGAACTTCTCATACAGAATAGAGGGAGCATATCCGAGTTGTTTAGTGAAATCTAATTACC AAAGTAGTGTTAGTGACCAAGAATCTAATATAAACCGTGTTTGTAGAACTTCACTTTAATTAAG AGATGGAACGATTCTGCAATCACTGAAGTAGTCTGAAAAATTTCAGTTTCCTTTAATCACAAAT CACACATATGATCAAGTCATTTGAACCTTGGCCTGTATATGCCCATAGGTGCTGTTAATTTTTG TAACTGTTTTAGGAACAAGTTGAGCATTTAGATCACAGAGCATGTCAAATGGAACTCCACTACT GATTGATATCTCTAACAAGGAATAGAGTCTTGAGGTTAGAAATTACGAAAATAAGGTCTAGTAC TTCAATCCAAACCACGTGAATGGACGAACAGGTGAGCCCTTTGGGCATTCAACATATTAGTGTA TTAAATTTTATCTGTGGTCTCATTTATTTTTTTTAATGTACATGTTTCATATTTGGCTGTTTAC AGTTTTACAACACACAGTTATTCAATGAGCTCAACTGGCATTACAATGTTGGCTTAGGACTTAT GCCATCCAGATCCTAACACAACCCAATATCTTACCAAAAATAATCCAAACTACACTTCTTTTTT TTTTCATGTACAACCCACCAAATACTCCCCGTCCCTTAATATAACAACCTAGGACATAATATAA CAACCTAGGACCGGATGTGACACTACATAGTACAACAAATTTGAACATGCTACTATGAAGTGTC CTAGATTGCTATAATATGGGACAAAGGGAGTAGTACCCTATTTATGTGCCTAACGTCCCATAAA AGAACCTAAAGAGGAGTACATTACAAATAATATCGTAAAAAATGCTTATTTTGAGCACTTTCTG TTTAAGTGTTACTACCCCTGTTCATAAAATAAGTAAATAATTTGTTTTTTTTTTGAAGTCTACG AAATGCCACCTTGACCACTAAATTTTATCAACTTTCATTAAAAAAATACTGCATCGTTTTGATA TAACCAAATTATATGATATAGATAACATATTTGGTCAAAACTAATATAGTTTGACATCAAGCAT AATAAGTGCATATTTTTGTGATCAGAGGTAGCAACAGCTATCACTTATCATTAATCAATATCTG CAAGGAATAATTTAAATTTAATAAACAACAAAATCCAAATGAAATGAGAAAGTTGTTACTCTAC CTTTTTCGGGTGCTTTCATAGTCTGGATCATTAGTCATCTGAAACATCTCATCGAATATACGAT TGGCACCTCCATCAGCACAGATTCTTAGCTTTGCTGCTCTATATCAAAATCACACGCAGAGGTT TAAAGATACATGACTGATACAGAATGTCAAAAGAACAAATGAGCAGGGACAGCTACCATGAGTC CACAGGCGGGGCACGAATCGTGGAAGGTTCTGATTAAGAACAACTAGAGCATACTTCTTTGCTG GAGAGTTGGCAGGCTGATGCAACTTTGGAAGAAGGAAGGTTGAAGAATGCACCATAACCTCCAT ACTGCGTATTGCGCGCCCCAACATCTTAACCTCAAGAAGGTGATGTACCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002044* osi_circ_009417 						
					
						PMCS
						0.31343161

Conservation Information
Conserved circRNAs	osi_circ_002044* osi_circ_009417
PMCS	0.31343161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14397474-14395511(+)
14397516-14397524(-)
						
						Potential amino acid sequence
						
							MHHNLHTAYCAPQHLNLKKVMYQAG*(+)
MLGRAIRSMEVMVHSSTFLLPKLHQPANSPAKKYALVVLNQNLPRFVPRLWTHAKLRICADGGA
NRIFDEMFQMTNDPDYESTRKRYIPEIIEGDMDSIRPEVKQFYSSQLGTSPS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14397474-14395511(+) 14397516-14397524(-)
Potential amino acid sequence	MHHNLHTAYCAPQHLNLKKVMYQAG(+) MLGRAIRSMEVMVHSSTFLLPKLHQPANSPAKKYALVVLNQNLPRFVPRLWTHAKLRICADGGA NRIFDEMFQMTNDPDYESTRKRYIPEIIEGDMDSIRPEVKQFYSSQLGTSPS(-)
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 Os01g0356500_circ_g.2

Address

Any questions?

Supported by