Plant Circular RNA Database

Detail information of Os01g0616100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0616100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_002618
					
						Alias
						Os_ciR5908
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 24430955-24433212  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0616100						
					
						Parent gene annotation
						
							Similar to kinase family protein. (Os01t0616100-01);Hypothetical
 conserved gene. (Os01t0616100-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0616100_circ_g.3 Os01g0616100_circ_g.4 Os01g0616100_circ_g.5 Os01g0616100_circ_g.6 Os01g0616100_circ_g.7 						
					
						Support reads
						2/1
					
						Tissues
						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
						Os01t0616100-01:5

General Information
CircRNA Name	Os01g0616100_circ_g.2
ID in PlantcircBase	osa_circ_002618
Alias	Os_ciR5908
Organism	Oryza sativa
Position	chr1: 24430955-24433212 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0616100
Parent gene annotation	Similar to kinase family protein. (Os01t0616100-01);Hypothetical conserved gene. (Os01t0616100-02)
Parent gene strand	+
Alternative splicing	Os01g0616100_circ_g.3 Os01g0616100_circ_g.4 Os01g0616100_circ_g.5 Os01g0616100_circ_g.6 Os01g0616100_circ_g.7
Support reads	2/1
Tissues	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	Os01t0616100-01:5

			
						 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  
						
							TGAGCTTTCAACACTGCCGGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTT
TTGCTCGTGAAGCATGCGGATCTTATTATTCACAAGtatatgaattccttgacgtatttaacaa
gtgaagccttttctaatattcctgctgatttagtggtggatttgcaaaggatgctatcagttga
tgtagcat

									
								

					

						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: 477
Transcript exons: 24430955-24431081,24431225-24431286,24431527-24431613,24
432592-24432678,24433099-24433212
TATATGAATTCCTTGACGTATTTAACAAGTGAAGCCTTTTCTAATATTCCTGCTGATTTAGTGG
TGGATTTGCAAAGGATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGG
CTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTTGAG
AGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATT
CCCGAGTTCTTCGGTATAAAGTTCTTCCACCTCTCTGTGCTGAGTTACGCAACATGGTCATGCA
GCCAATGATTTTGCCCATGGTTCTAACAATAGCGGAATCTCAGGACAAAGGTGATTTTGAGCTT
TCAACACTGCCGGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTTTTGCTCG
TGAAGCATGCGGATCTTATTATTCACAAG
						
					

						Genomic sequence
						
							TATATGAATTCCTTGACGTATTTAACAAGTGAAGCCTTTTCTAATATTCCTGCTGATTTAGTGG
TGGATTTGCAAAGGATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGG
TAAATTATCACTTATCATTTCTTTATCTTGGGCATAAGATCTTCCAGAATGGAGTTTTTGGATG
TTCTATTTGATTGGAGATCACCAGGTTACCTATACTTACATGAAATTCTTTTGAAATGTTGCAC
CTTCTGTCTGATAGGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTT
GACCATTTGCTTGTATGTGTCTATTACTCCAGTTTCTTTTCACAGATAAGTTAGTTGCTTGTTT
CATATATATGCATATCATAGCTTGCTTATTTTCTATCTGAGAATCTCGTTTGCCTGGCTTAAGT
TTCAATTGTACGTGGGAAGACAGAACTAGGAGCTTTATCTGCTTGACTGTTGTTTGTCTAAACA
GACAACATACTAATTTGTTACCTAGAAATGGTTATAATCTTGATCCAATATCGTCTTCAGGAGA
GAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTC
CCGAGTTCTTCGGTATAAAGTATGAGCAATCCATTATCTCCACTTTTCATATCAAGTGTGGTCT
TATGAAATTATGGCCACATTTTCTTGGTTTGTGTGCTGCTTCATAGAAGATGTTAGAACCTGCT
AATTATCTAATTATTCCATGTTACTTATTCCCAGTTGTCTGATAAGTATTTTTGCATCGACAGC
TATACTATACTCATAAAATTAACAGGAAGTCCATCTTAAATTTTCAATTCAATATCATTGCCCA
ATTCTTTGTGCTATTGAGCTTATCAAGATCACATAGCAAAATTTCAGTGTGTTCTAGTTATTTT
GCCAAAAAAAAAAATGTTGAGACACTGAGAACTATTGGTTGTAATATTGAAAATAAAAAGATAA
CATATACACACCTCAATGTTCTAACTTCCATTCCTTTATTACATAGGTGAATCACGCCTCCTGT
TTGCTTTTAGAGAGGAATCACTTTTGTTGATCCTTCTATTAGCATTATCACTTTCCTTTTTTGT
CCTTATCTACAGTTTTGATTCAATGAATCAATGAGAAAAATCCAAGAAATGCCATTGACAAACA
CCCAAATCCAAGAAATTCCATCAATGAGTGCGAGTTCCATAAAATGCCATCGTACAAACGATTT
TATCTCAGAAATACCATCGCTGTTAGGGTTCCCCCAATCCCGCGCCGTTAAGTGCACTGTTCAT
CCTTAGCACTTAACGGAGGGCTGCTAATGGAACCCTAACGGCAATGGCATTTTTGGGACAAAGT
TGCTTGTATGATGGCATTTCATGGAACTTGTACTTGATGACATTTCTTGAAATTGAGTGCTTGT
CAATGGCATTTCTTGGATTTTCTATTAATGTATTGAATTTGCGCAACTTACTTATGTTTGCATA
TGTGTGCATGCGAATTCTTTCTATCGGAAGGAAAAAAAATGCTGATTCACAATGTTACTTAATA
TATTGACTATCTGTAAGCTGACTCTGTTTGCAACCAGGTTCTTCCACCTCTCTGTGCTGAGTTA
CGCAACATGGTCATGCAGCCAATGATTTTGCCCATGGTTCTAACAATAGCGGAATCTCAGGTCA
TGTTCCTTGTGTTTTACGAATACCTTTTTCTTAAATATTTTATGAATTATATTCTTTGTTCAAT
GATAGTAAGAACTTATCTCACTGATTGTTAACTAATGGGATGATACCATGGTTCTGTAATACCA
CTTTGCATAATGTGAAGTATCATATTTTATTTGACTGTTTTTCATCTGAACTTGCTTTTGACTG
GAGTAAGTCCAATTTAATGTGGTTGTATCATTCTTGCTGCAACACAGAGTCATCCACAGTACTA
ACACTCGAACATTGTTATTTGTTTGTTATGCTTCAATTTCGTGAGTTCATAGAGTTTGTAAAGT
GAAATACATTTAAAGCTATGTTATATGGTAATGTTTCTTTATGATGCAAATGCTATAATTTTTT
TTTCTGAAAATTTGTTCTCTGCTCTCTGGCAGGACAAAGGTGATTTTGAGCTTTCAACACTGCC
GGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTTTTGCTCGTGAAGCATGCG
GATCTTATTATTCACAAG
						
					

			
		

Sequences
Splice junction sequence	TGAGCTTTCAACACTGCCGGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTT TTGCTCGTGAAGCATGCGGATCTTATTATTCACAAGtatatgaattccttgacgtatttaacaa gtgaagccttttctaatattcctgctgatttagtggtggatttgcaaaggatgctatcagttga tgtagcat
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: 477 Transcript exons: 24430955-24431081,24431225-24431286,24431527-24431613,24 432592-24432678,24433099-24433212 TATATGAATTCCTTGACGTATTTAACAAGTGAAGCCTTTTCTAATATTCCTGCTGATTTAGTGG TGGATTTGCAAAGGATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGG CTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTTGAG AGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATT CCCGAGTTCTTCGGTATAAAGTTCTTCCACCTCTCTGTGCTGAGTTACGCAACATGGTCATGCA GCCAATGATTTTGCCCATGGTTCTAACAATAGCGGAATCTCAGGACAAAGGTGATTTTGAGCTT TCAACACTGCCGGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTTTTGCTCG TGAAGCATGCGGATCTTATTATTCACAAG
Genomic sequence	TATATGAATTCCTTGACGTATTTAACAAGTGAAGCCTTTTCTAATATTCCTGCTGATTTAGTGG TGGATTTGCAAAGGATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGG TAAATTATCACTTATCATTTCTTTATCTTGGGCATAAGATCTTCCAGAATGGAGTTTTTGGATG TTCTATTTGATTGGAGATCACCAGGTTACCTATACTTACATGAAATTCTTTTGAAATGTTGCAC CTTCTGTCTGATAGGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTT GACCATTTGCTTGTATGTGTCTATTACTCCAGTTTCTTTTCACAGATAAGTTAGTTGCTTGTTT CATATATATGCATATCATAGCTTGCTTATTTTCTATCTGAGAATCTCGTTTGCCTGGCTTAAGT TTCAATTGTACGTGGGAAGACAGAACTAGGAGCTTTATCTGCTTGACTGTTGTTTGTCTAAACA GACAACATACTAATTTGTTACCTAGAAATGGTTATAATCTTGATCCAATATCGTCTTCAGGAGA GAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTC CCGAGTTCTTCGGTATAAAGTATGAGCAATCCATTATCTCCACTTTTCATATCAAGTGTGGTCT TATGAAATTATGGCCACATTTTCTTGGTTTGTGTGCTGCTTCATAGAAGATGTTAGAACCTGCT AATTATCTAATTATTCCATGTTACTTATTCCCAGTTGTCTGATAAGTATTTTTGCATCGACAGC TATACTATACTCATAAAATTAACAGGAAGTCCATCTTAAATTTTCAATTCAATATCATTGCCCA ATTCTTTGTGCTATTGAGCTTATCAAGATCACATAGCAAAATTTCAGTGTGTTCTAGTTATTTT GCCAAAAAAAAAAATGTTGAGACACTGAGAACTATTGGTTGTAATATTGAAAATAAAAAGATAA CATATACACACCTCAATGTTCTAACTTCCATTCCTTTATTACATAGGTGAATCACGCCTCCTGT TTGCTTTTAGAGAGGAATCACTTTTGTTGATCCTTCTATTAGCATTATCACTTTCCTTTTTTGT CCTTATCTACAGTTTTGATTCAATGAATCAATGAGAAAAATCCAAGAAATGCCATTGACAAACA CCCAAATCCAAGAAATTCCATCAATGAGTGCGAGTTCCATAAAATGCCATCGTACAAACGATTT TATCTCAGAAATACCATCGCTGTTAGGGTTCCCCCAATCCCGCGCCGTTAAGTGCACTGTTCAT CCTTAGCACTTAACGGAGGGCTGCTAATGGAACCCTAACGGCAATGGCATTTTTGGGACAAAGT TGCTTGTATGATGGCATTTCATGGAACTTGTACTTGATGACATTTCTTGAAATTGAGTGCTTGT CAATGGCATTTCTTGGATTTTCTATTAATGTATTGAATTTGCGCAACTTACTTATGTTTGCATA TGTGTGCATGCGAATTCTTTCTATCGGAAGGAAAAAAAATGCTGATTCACAATGTTACTTAATA TATTGACTATCTGTAAGCTGACTCTGTTTGCAACCAGGTTCTTCCACCTCTCTGTGCTGAGTTA CGCAACATGGTCATGCAGCCAATGATTTTGCCCATGGTTCTAACAATAGCGGAATCTCAGGTCA TGTTCCTTGTGTTTTACGAATACCTTTTTCTTAAATATTTTATGAATTATATTCTTTGTTCAAT GATAGTAAGAACTTATCTCACTGATTGTTAACTAATGGGATGATACCATGGTTCTGTAATACCA CTTTGCATAATGTGAAGTATCATATTTTATTTGACTGTTTTTCATCTGAACTTGCTTTTGACTG GAGTAAGTCCAATTTAATGTGGTTGTATCATTCTTGCTGCAACACAGAGTCATCCACAGTACTA ACACTCGAACATTGTTATTTGTTTGTTATGCTTCAATTTCGTGAGTTCATAGAGTTTGTAAAGT GAAATACATTTAAAGCTATGTTATATGGTAATGTTTCTTTATGATGCAAATGCTATAATTTTTT TTTCTGAAAATTTGTTCTCTGCTCTCTGGCAGGACAAAGGTGATTTTGAGCTTTCAACACTGCC GGCCCTTGTTCCGGTATTTACTTCAGCGTCAGGTGAAACACTTCTTTTGCTCGTGAAGCATGCG GATCTTATTATTCACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.216912264

Conservation Information
Conserved circRNAs	NA
PMCS	0.216912264

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24430959-24433209(+)
24432655-24433208(-)
						
						Potential amino acid sequence
						
							MNSLTYLTSEAFSNIPADLVVDLQRMLSVDVASRPSAMAFTGSSFFRNDTRLRALRFLDHLLER
DNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAELRNMVMQPMILPMVLTIAESQDKGDFELS
TLPALVPVFTSASGETLLLLVKHADLIIHKYMNSLTYLTSEAFSNIPADLVVDLQRMLSVDVAS
RPSAMAFTGSSFFRNDTRLRALRFLDHLLERDNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLC
AELRNMVMQPMILPMVLTIAESQDKGDFELSTLPALVPVFTSASGETLLLLVKHADLIIHKYMN
SLTYLTSEAFSNIPADLVVDLQRMLSVDVASRPSAMAFTGSSFFRNDTRLRALRFLDHLLERDN
MQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAELRNMVMQPMILPMVLTIAESQDKGDFELSTL
PALVPVFTSASGETLLLLVKHADLIIHKYMNSLTYLTSEAFSNIPADLVVDLQRMLSVDVASRP
SAMAFTGSSFFRNDTRLRALRFLDHLLERDNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAE
LRNMVMQPMILPMVLTIAESQDKGDFELSTLPALVPVFTSASGETLLLLVKHADLIIHK(+)
MGKIIGCMTMLRNSAQRGGRTLYRRTRESKSFHISDNAFRNSVFCILSLSSKWSRKRRARNRVS
FRKKEEPVNAIALGRDATSTDSILCKSTTKSAGILEKASLVKYVKEFIYL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24430959-24433209(+) 24432655-24433208(-)
Potential amino acid sequence	MNSLTYLTSEAFSNIPADLVVDLQRMLSVDVASRPSAMAFTGSSFFRNDTRLRALRFLDHLLER DNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAELRNMVMQPMILPMVLTIAESQDKGDFELS TLPALVPVFTSASGETLLLLVKHADLIIHKYMNSLTYLTSEAFSNIPADLVVDLQRMLSVDVAS RPSAMAFTGSSFFRNDTRLRALRFLDHLLERDNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLC AELRNMVMQPMILPMVLTIAESQDKGDFELSTLPALVPVFTSASGETLLLLVKHADLIIHKYMN SLTYLTSEAFSNIPADLVVDLQRMLSVDVASRPSAMAFTGSSFFRNDTRLRALRFLDHLLERDN MQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAELRNMVMQPMILPMVLTIAESQDKGDFELSTL PALVPVFTSASGETLLLLVKHADLIIHKYMNSLTYLTSEAFSNIPADLVVDLQRMLSVDVASRP SAMAFTGSSFFRNDTRLRALRFLDHLLERDNMQKTEFLKALSDMWKDFDSRVLRYKVLPPLCAE LRNMVMQPMILPMVLTIAESQDKGDFELSTLPALVPVFTSASGETLLLLVKHADLIIHK(+) MGKIIGCMTMLRNSAQRGGRTLYRRTRESKSFHISDNAFRNSVFCILSLSSKWSRKRRARNRVS FRKKEEPVNAIALGRDATSTDSILCKSTTKSAGILEKASLVKYVKEFIYL*(-)
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 Os01g0616100_circ_g.2

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