Plant Circular RNA Database

Detail information of Os01g0218032_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os01g0218032_circ_g.6
					
						ID in PlantcircBase
						osa_circ_000842
					
						Alias
						Os01circ05808/Os_ciR1077
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 6451427-6452908  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os01g0218032						
					
						Parent gene annotation
						
							Putative DNA demethylase, Endosperm development (Os01t0218032-01
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0218032_circ_g.3 Os01g0218032_circ_g.4 Os01g0218032_circ_g.5 Os01g0218032_circ_g.7 Os01g0218032_circ_g.8 Os01g0218032_circ_g.9 Os01g0218032_circ_g.10 Os01g0218032_circ_g.11 						
					
						Support reads
						3/19/61
					
						Tissues
						leaf and panicle/root/shoot, root, anther, 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  
						
							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
						Os01t0218032-01:6

General Information
CircRNA Name	Os01g0218032_circ_g.6
ID in PlantcircBase	osa_circ_000842
Alias	Os01circ05808/Os_ciR1077
Organism	Oryza sativa
Position	chr1: 6451427-6452908 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os01g0218032
Parent gene annotation	Putative DNA demethylase, Endosperm development (Os01t0218032-01 )
Parent gene strand	+
Alternative splicing	Os01g0218032_circ_g.3 Os01g0218032_circ_g.4 Os01g0218032_circ_g.5 Os01g0218032_circ_g.7 Os01g0218032_circ_g.8 Os01g0218032_circ_g.9 Os01g0218032_circ_g.10 Os01g0218032_circ_g.11
Support reads	3/19/61
Tissues	leaf and panicle/root/shoot, root, anther, 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	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	Os01t0218032-01:6

			
						 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  
						
							GACTCAAGCCGGAACCCGATTGATGTTCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTG
TTTACTTTGGAACTTCAATTCCGACAATATTTAAAGtgcaaggctcgctcttcctggacctgaa
gagaagagtttagttacatctggaaccccaatagctgcagaaaccttccaccagacatatataa
gttctagg

									
								

					

						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: 254
Transcript exons: 6451427-6451615,6452844-6452908
TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT
GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT
CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCTTG
GATATGGAATCTCCCTAGGAGAACTGTTTACTTTGGAACTTCAATTCCGACAATATTTAAAG
Transcript length: 863
Transcript exons: 6451427-6451873,6451978-6452014,6452101-6452158,6452243-
6452382,6452610-6452675,6452794-6452908
TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT
GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT
CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCAGA
ACCTGAACATGAGACAGAAGAGATGAAAGAGTGTGCAATAGAGGATAGTTTTGTCGATGATCCA
GAAGAAATCCCTACTATCAAGCTTAATTTTGAGGAGTTTACACAGAACCTGAAGAGTTATATGC
AAGCAAATAACATTGAGATTGAAGATGCTGATATGTCAAAGGCTTTGGTCGCTATAACTCCTGA
AGTTGCTTCTATCCCAACTCCTAAGCTCAAGAATGTCAGTCGCCTAAGGACAGAGCACCAAGTC
TATGAACTGCCAGATTCACATCCACTTCTTGAAGGATTCAACCAAAGAGAACCAGATGATCCTT
GCCCATACCTACTCTCTATATGGACCCCAGGTGAAACAGCTCAATCAACTGATGCACCTAAGTC
GGTCTGCAATTCACAAGAGAATGGTGAACTATGTGCAAGCAATACATGCTTTAGTTGCAACAGT
ATAAGAGAAGCGCAGGCCCAAAAAGTTCGAGGGACACTGCTGATACCATGCCGAACAGCAATGA
GAGGAAGCTTTCCACTTAATGGGACATATTTTCAAGTCAATGAGGTATTTGCTGATCATGACTC
AAGCCGGAACCCGATTGATGTTCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTGTTTAC
TTTGGAACTTCAATTCCGACAATATTTAAAG
						
					

						Genomic sequence
						
							TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT
GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT
CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCAGA
ACCTGAACATGAGACAGAAGAGATGAAAGAGTGTGCAATAGAGGATAGTTTTGTCGATGATCCA
GAAGAAATCCCTACTATCAAGCTTAATTTTGAGGAGTTTACACAGAACCTGAAGAGTTATATGC
AAGCAAATAACATTGAGATTGAAGATGCTGATATGTCAAAGGCTTTGGTCGCTATAACTCCTGA
AGTTGCTTCTATCCCAACTCCTAAGCTCAAGAATGTCAGTCGCCTAAGGACAGAGCACCAAGTG
TATGATCTTGTCCCTCTTGCAAAACCAATCTCATGAATATTTACTATTGACTATCATGTGTTTT
GCTGCATTGCTTACTTCTCTGTTTTCAACATATATGTAGCTATGAACTGCCAGATTCACATCCA
CTTCTTGAAGGAGTAAGTTCATAAAACATTATAGAATTCTGTACTTTCCTTATCACCAACTGAG
AATATATTGATGCTTATTTTCTTACAATACACAGTTCAACCAAAGAGAACCAGATGATCCTTGC
CCATACCTACTCTCTATATGGACCCCAGGTAAGAAGTGCATAAACAGAACACAATATCATGGGA
ACCAAACTTTTTTCAATGGTTACTTATAATTGTTGAAATATGCAACAGGTGAAACAGCTCAATC
AACTGATGCACCTAAGTCGGTCTGCAATTCACAAGAGAATGGTGAACTATGTGCAAGCAATACA
TGCTTTAGTTGCAACAGTATAAGAGAAGCGCAGGCCCAAAAAGTTCGAGGGACACTGCTGGTAA
GTAGTTGTTTCTGTAACATATGCTCAGTTGCCCTTGGTTCAAGATGTGCTATTCAAGTTTATCA
TGTTCACGAATAGTGATAAAGCTGCTATCTGTCCTAGCTATTGTCCAAGCTATAACAGTTCTGA
TTCACTGGTTGGGCACCAGCTAGGGAATAGGATGTAAAAAACTTATCCCGCAGTTTGTTGACAA
TCTGTTTTTCTTTGTTGAAAATTAAAAATAGATACCATGCCGAACAGCAATGAGAGGAAGCTTT
CCACTTAATGGGACATATTTTCAAGTCAATGAGGTGAAAACAGAAAGTTCTTAAAGTTGATCTT
AGTTTAATTATTATAATACCATTAAAATATATGCAAGTTTCTACTTTCTAGTATCTCTTTTATT
AGTGTTCAAATGTTATGCGGCAGGTATTTGCTGATCATGACTCAAGCCGGAACCCGATTGATGT
TCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTGTTTACTTTGGAACTTCAATTCCGACA
ATATTTAAAG
						
					

			
		

Sequences
Splice junction sequence	GACTCAAGCCGGAACCCGATTGATGTTCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTG TTTACTTTGGAACTTCAATTCCGACAATATTTAAAGtgcaaggctcgctcttcctggacctgaa gagaagagtttagttacatctggaaccccaatagctgcagaaaccttccaccagacatatataa gttctagg
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: 254 Transcript exons: 6451427-6451615,6452844-6452908 TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCTTG GATATGGAATCTCCCTAGGAGAACTGTTTACTTTGGAACTTCAATTCCGACAATATTTAAAG Transcript length: 863 Transcript exons: 6451427-6451873,6451978-6452014,6452101-6452158,6452243- 6452382,6452610-6452675,6452794-6452908 TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCAGA ACCTGAACATGAGACAGAAGAGATGAAAGAGTGTGCAATAGAGGATAGTTTTGTCGATGATCCA GAAGAAATCCCTACTATCAAGCTTAATTTTGAGGAGTTTACACAGAACCTGAAGAGTTATATGC AAGCAAATAACATTGAGATTGAAGATGCTGATATGTCAAAGGCTTTGGTCGCTATAACTCCTGA AGTTGCTTCTATCCCAACTCCTAAGCTCAAGAATGTCAGTCGCCTAAGGACAGAGCACCAAGTC TATGAACTGCCAGATTCACATCCACTTCTTGAAGGATTCAACCAAAGAGAACCAGATGATCCTT GCCCATACCTACTCTCTATATGGACCCCAGGTGAAACAGCTCAATCAACTGATGCACCTAAGTC GGTCTGCAATTCACAAGAGAATGGTGAACTATGTGCAAGCAATACATGCTTTAGTTGCAACAGT ATAAGAGAAGCGCAGGCCCAAAAAGTTCGAGGGACACTGCTGATACCATGCCGAACAGCAATGA GAGGAAGCTTTCCACTTAATGGGACATATTTTCAAGTCAATGAGGTATTTGCTGATCATGACTC AAGCCGGAACCCGATTGATGTTCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTGTTTAC TTTGGAACTTCAATTCCGACAATATTTAAAG
Genomic sequence	TGCAAGGCTCGCTCTTCCTGGACCTGAAGAGAAGAGTTTAGTTACATCTGGAACCCCAATAGCT GCAGAAACCTTCCACCAGACATATATAAGTTCTAGGCCTGTAGTAAGTCAGCTTGAGTGGAATT CAAACACCTGTCACCATGGTATGAACAATCGCCAGCCAATCATTGAGGAGCCAGCAAGCCCAGA ACCTGAACATGAGACAGAAGAGATGAAAGAGTGTGCAATAGAGGATAGTTTTGTCGATGATCCA GAAGAAATCCCTACTATCAAGCTTAATTTTGAGGAGTTTACACAGAACCTGAAGAGTTATATGC AAGCAAATAACATTGAGATTGAAGATGCTGATATGTCAAAGGCTTTGGTCGCTATAACTCCTGA AGTTGCTTCTATCCCAACTCCTAAGCTCAAGAATGTCAGTCGCCTAAGGACAGAGCACCAAGTG TATGATCTTGTCCCTCTTGCAAAACCAATCTCATGAATATTTACTATTGACTATCATGTGTTTT GCTGCATTGCTTACTTCTCTGTTTTCAACATATATGTAGCTATGAACTGCCAGATTCACATCCA CTTCTTGAAGGAGTAAGTTCATAAAACATTATAGAATTCTGTACTTTCCTTATCACCAACTGAG AATATATTGATGCTTATTTTCTTACAATACACAGTTCAACCAAAGAGAACCAGATGATCCTTGC CCATACCTACTCTCTATATGGACCCCAGGTAAGAAGTGCATAAACAGAACACAATATCATGGGA ACCAAACTTTTTTCAATGGTTACTTATAATTGTTGAAATATGCAACAGGTGAAACAGCTCAATC AACTGATGCACCTAAGTCGGTCTGCAATTCACAAGAGAATGGTGAACTATGTGCAAGCAATACA TGCTTTAGTTGCAACAGTATAAGAGAAGCGCAGGCCCAAAAAGTTCGAGGGACACTGCTGGTAA GTAGTTGTTTCTGTAACATATGCTCAGTTGCCCTTGGTTCAAGATGTGCTATTCAAGTTTATCA TGTTCACGAATAGTGATAAAGCTGCTATCTGTCCTAGCTATTGTCCAAGCTATAACAGTTCTGA TTCACTGGTTGGGCACCAGCTAGGGAATAGGATGTAAAAAACTTATCCCGCAGTTTGTTGACAA TCTGTTTTTCTTTGTTGAAAATTAAAAATAGATACCATGCCGAACAGCAATGAGAGGAAGCTTT CCACTTAATGGGACATATTTTCAAGTCAATGAGGTGAAAACAGAAAGTTCTTAAAGTTGATCTT AGTTTAATTATTATAATACCATTAAAATATATGCAAGTTTCTACTTTCTAGTATCTCTTTTATT AGTGTTCAAATGTTATGCGGCAGGTATTTGCTGATCATGACTCAAGCCGGAACCCGATTGATGT TCCAAGGAGTTGGATATGGAATCTCCCTAGGAGAACTGTTTACTTTGGAACTTCAATTCCGACA ATATTTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_001897* osi_circ_011387 						
					
						PMCS
						0.381527485

Conservation Information
Conserved circRNAs	osi_circ_001897* osi_circ_011387
PMCS	0.381527485

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6451576-6451464(+)
6452651-6451450(+)
						
						Potential amino acid sequence
						
							MNNRQPIIEEPASPEPEHETEEMKECAIEDSFVDDPEEIPTIKLNFEEFTQNLKSYMQANNIEI
EDADMSKALVAITPEVASIPTPKLKNVSRLRTEHQVYELPDSHPLLEGFNQREPDDPCPYLLSI
WTPGETAQSTDAPKSVCNSQENGELCASNTCFSCNSIREAQAQKVRGTLLIPCRTAMRGSFPLN
GTYFQVNEVFADHDSSRNPIDVPRSWIWNLPRRTVYFGTSIPTIFKVQGSLFLDLKRRV*(+)
MGHIFKSMRYLLIMTQAGTRLMFQGVGYGISLGELFTLELQFRQYLKCKARSSWT*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6451576-6451464(+) 6452651-6451450(+)
Potential amino acid sequence	MNNRQPIIEEPASPEPEHETEEMKECAIEDSFVDDPEEIPTIKLNFEEFTQNLKSYMQANNIEI EDADMSKALVAITPEVASIPTPKLKNVSRLRTEHQVYELPDSHPLLEGFNQREPDDPCPYLLSI WTPGETAQSTDAPKSVCNSQENGELCASNTCFSCNSIREAQAQKVRGTLLIPCRTAMRGSFPLN GTYFQVNEVFADHDSSRNPIDVPRSWIWNLPRRTVYFGTSIPTIFKVQGSLFLDLKRRV(+) MGHIFKSMRYLLIMTQAGTRLMFQGVGYGISLGELFTLELQFRQYLKCKARSSWT(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0218032_circ_g.6

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